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Lowis, D. R. "Application of theoretical methods to the study of small molecules in solution." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.240696.
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King, Paul M. "Application of free energy perturbation calculations to molecular biophysics." Thesis, University of Oxford, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.257951.
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James, Richard. "Applications of perturbation theory in high energy electron diffraction." Thesis, University of Bath, 1990. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.235789.
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Jackson, Brendan Marc. "Modelling dark energy." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5763.
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One of the most pressing, modern cosmological mysteries is the cause of the accelerated expansion of the universe. The energy density required to cause this large scale opposition to gravity is known to be both far in excess of the known matter content, and remarkably smooth and unclustered across the universe. While the most commonly accepted answer is that a cosmological constant is responsible, alternatives abound. This thesis is primarily concerned with such alternatives; both their theoretical nature and observational consequences. In this thesis, we will dedicate Chapter 1 to a brief review on the fundamentals of general relativity, leading into the basics of theoretical cosmology. Following this we will recall some of the key observations that has lead to the standard CDM cosmology. The standard model has well known problems, many of which can be answered by the theoretical ideas of inflation. In Chapter 2 we explore these ideas, including a summary of classical field theory in the context of cosmology, upon which inflation is based. This also serves as the groundwork for Chapter 3, where the varied models of dark energy (and their motivations) are discussed - many of which are also reliant on field theory (such as quintessence). These notions are combined in a model described in Chapter 4, where we describe our own addition to a scenario that unifies dark energy and inflation. This addition - involving a coupling of the inflation field to an additional one - alter the way reheating takes place after inflation, removing some of the shortcomings of the original proposal. The analysis is extended in Chapter 5, to include the effect of quantum corrections. There we show that although a cursory analysis indicates a coupling between quintessence and some other field does not necessarily give rise to dangerously large quantum corrections, provided the effects of decoupling are taken into account. We move on in Chapter 6 to examine the basics of cosmological perturbation theory, and derive the general equations of motion for density and velocity perturbations for a system of fluids, allowing for the exchange of energy-momentum. We make use of this in Chapters 7 and 8, were we examine the growth of structure in a universe where energy is exchanged between dark matter and dark energy. In particular, in Chapter 7 we see that a particular form of the interaction can lead to an instability in the early universe, and we derive the condition for this to be the case. In Chapter 8, we discuss how a similar interaction can lead to a mimicry of modified gravity, and relate this directly to cosmological observations. Finally we summarise our conclusions and discuss avenues of future research in Chapter 9.
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Hollenstein, Lukas. "Applications of Cosmological Perturbation Theory to Dynamical Dark Energy and Primordial Magnetogenesis." Thesis, University of Portsmouth, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.508870.
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Masango, Senamile Khethekile Ntombizothando. "Measuring transitional matrix elements using first-order perturbation theory in Coulomb excitation." University of the Western Cape, 2019. http://hdl.handle.net/11394/6704.
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Magister Scientiae - MScThe aim of nuclear structure physics is to study the interplay between singleparticle and collective degrees of freedom in nuclei and to explain how nuclei get excited and decay under di erent external conditions, such as strong electric and magnetic elds. If nuclei absorb a large amount of energy and angular momentum, like in a scattering reaction when you bombard a target that is in the ground state with a projectile at high bombarding energies, the energy from the projectile gets transfered to the target and vice versa, hence both projectile and target may get excited. During the de-excitation process nuclei may release the energy in a form of electromagnetic radiation (gamma rays) which carries angular momentum. The atomic nucleus is a many-body system, whose structure is de ned in terms of interactions between protons and neutrons. In nature there are only around 300 stable isotopes [1]. They are all in their ground states (although some are in a low-energy excited isomeric state with a long lifetime). To study excited states in these nuclei one needs to provide energy to the system. In addition, there are some 3000 unstable nuclei, most of which do not exist in nature. Many have been produced and studied in research laboratories, and there could be more than 3000 other unstable nuclei that can in principle exist in astrophysical environments, but have not yet been synthesized on Earth [1].
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FREIRE, LUCAS. "RENEWABLE ENERGY COMMERCIALIZATION MODEL FOR THE FREE MARKET VIA COOPERATIVE GAMES THEORY." PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO, 2013. http://www.maxwell.vrac.puc-rio.br/Busca_etds.php?strSecao=resultado&nrSeq=22134@1.
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PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIROCONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO
No Brasil, as três principais fontes renováveis de energia elétrica são eólica, pequenas centrais hidrelétricas (PCHs) e biomassa. A comercialização da energia proveniente dessas fontes ocorre majoritariamente no ambiente de contratação regulada (ACR), através de leilões, em detrimento do ambiente de contratação livre (ACL). Isso devido ao fato de seus recursos naturais serem sazonais, estabelecendo o risco de preço-quantidade no ACL, em que o excesso ou déficit de energia gerada em relação à quantidade contratada é liquidado ao preço de liquidação de diferenças (PLD), uma variável sistêmica e altamente volátil. Contudo, a complementaridade dessas fontes permite reduzir esses riscos quando a energia é comercializada de forma conjunta, através de um fundo de energia que gera aumento do valor do portfólio com relação à comercialização individual. Esta dissertação utiliza a teoria de jogos cooperativos para analisar formas de repartir o benefício gerado, através da alocação de quotas financeiras. O conjunto de soluções onde o resultado individual das fontes no fundo é maior do que o resultado individual em qualquer subcoalisão define o núcleo do jogo. Assim, a complexidade de encontrar uma solução dentro do núcleo depende do número de subcoalizões, que cresce exponencialmente com o número de jogadores. Nesse contexto, este trabalho se propôs a apresentar: (i) um modelo de portfólio que incentiva a participação de fontes renováveis no ACL; (ii) um modelo de programação linear que busca o núcleo do jogo; (iii) uma metodologia eficiente baseada em decomposição de Benders, capaz de suprimir a questão da explosão combinatória do problema.
In Brazil, the three main sources of renewable energy are wind, small run-of-river hidros (SH) and biomass. The energy sale of such sources occurs mainly in the Regulated Trading Environment (RTE), through auctions, with shy occurrences in the Free Trading Environment (FTE). This is due to the fact that their natural resources are seasonal, establishing the so-called price-quantity risk in the FTE, as the surplus or deficit of energy generated relative to the contracted amount is settled at the market’s spot price, a systemic and highly volatile variable. However, the complementary nature of these sources allows risk reduction if their energy are trade jointly, through an energy hedge pool that increases the value of the portfolio in comparison to individual strategies. This work makes use of cooperative games theory to analyze ways of sharing the generated benefit, through financial quotas allocation. The set of solutions where the individual sources results in the pool are greater than its results at any possible subcoalition defines the core of the game. Thus, the challenge of finding a solution inside the core depends on the number of subcoalitions, which grows exponentially with the number of players. In this context, this work proposes to present: (i) a model of portfolio that encourages the penetration of renewable sources in the FTE; (ii) a linear programming model that pursuits the game’s core; (iii) an efficient methodology based on Benders decomposition that is capable of suppress the problem of combinatorial explosion, typical of cooperative games with many players.
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Pearson, Jonathan Andrew. "Generalized perturbations in modified gravity and dark energy." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/generalized-perturbations-in-modified-gravity-and-dark-energy(ac520c15-f240-4c63-84af-1110fdfc9815).html.
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When recent observational data and the GR+FRW+CDM model are combined we obtain the result that the Universe is accelerating, where the acceleration is due to some not-yet-understood "dark sector". There has been a considerable number of theoretical models constructed in an attempt to provide a description of the dark sector: dark energy and modified gravity theories. The proliferation of modified gravity and dark energy models has brought to light the need to construct a "generic" way to parameterize perturbations in the dark sector. In this thesis we discuss our new way of approaching this problem. We write down an effective action for linearized perturbations to the gravitational field equations for a given field content and use it to compute generalized gravitational field equations for linearized perturbations. Our approach is inspired by that taken in particle physics, where the most general modifications to the standard model are written down for a given field content that is compatible with some assumed symmetry (which we take to be isotropy of the background spatial sections). After applying the formalism we obtain equations of state for dark sector perturbations, where the number of free parameters for wide classes of theories are identified.
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Keränen, Henrik. "Advances in Ligand Binding Predictions using Molecular Dynamics Simulations." Doctoral thesis, Uppsala universitet, Beräknings- och systembiologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-230777.
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Biochemical processes all involve associations and dissociations of chemical entities. Understanding these is of substantial importance for many modern pharmaceutical applications. In this thesis, longstanding problems with regard to ligand binding are treated with computational methods, applied to proteins of key pharmaceutical importance. Homology modeling, docking, molecular dynamics simulations and free-energy calculations are used here for quantitative characterization of ligand binding to proteins. By combining computational tools, valuable contributions have been made for pharmaceutically relevant areas: a neglected tropical disease, an ion channel anti-drug-target, and GPCR drug-targets. We report three compounds inhibiting cruzain, the main cysteine protease of the protozoa causing Chagas’ disease. The compounds were found through an extensive virtual screening study and validated with experimental enzymatic assays. The compounds inhibit the enzyme in the μM-range and are therefore valuable in further lead optimization studies. A high-resolution crystal structure of the BRICHOS domain is reported, together with molecular dynamics simulations and hydrogen-deuterium exchange mass spectrometry studies. This work revealed a plausible mechanism for how the chaperone activity of the domain may operate. Rationalization of structure-activity relationships for a set of analogous blockers of the hERG potassium channel is given. A homology model of the ion channel was used for docking compounds and molecular dynamics simulations together with the linear interaction energy method employed for calculating the binding free-energies. The three-dimensional coordinates of two GPCRs, 5HT1B and 5HT2B, were derived from homology modeling and evaluated in the GPCR Dock 2013 assessment. Our models were in good correlation with the experimental structures and all of them placed among the top quarter of all models assessed. Finally, a computational method, based on molecular dynamics free-energy calculations, for performing alanine scanning was validated with the A2A adenosine receptor bound to either agonist or antagonist. The calculated binding free-energies were found to be in good agreement with experimental data and the method was subsequently extended to non-alanine mutations. With extensive experimental mutation data, this scheme is a valuable tool for quantitative understanding of ligand binding and can ultimately be used for structure-based drug design.
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Itoh, Kazuhito, and Masaki Sasai. "Multidimensional theory of protein folding." American Institite of Physics, 2009. http://hdl.handle.net/2237/12626.
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Heintze, Olaf. "A Computationally Efficient Free Energy Model for Shape Memory Alloys - Experiments and Theory." NCSU, 2004. http://www.lib.ncsu.edu/theses/available/etd-12172004-221828/.
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Shape memory alloys (SMA) belong to the class of active materials and have recently been considered as novel actuation and damping mechanisms in micro- and macro-scale applications. Combined with their advantageous lightweight and high work output characteristics is a complex, highly non-linear and hysteretic material behavior, which is also thermo-mechanically coupled. Due to this complexity, model development for SMA material behavior is a challenging task, and experimental data in particular about the inner hysteresis loops is necessary to gain further understanding and successfully design applications. In this thesis, a single crystal material model is presented and subsequently extended to the more realistic polycrystalline case considering material inhomogeneities, grain impurities and lattice imperfections. A first implementation, based on a stochastic homogenization procedure, provides a very accurate description of the observed phenomena, but also requires very high computation times. A reformulation of the underlying concept leads to a parameterization method, which preserves the advantages of the original method, but dramatically reduces the computation times. It is shown that the material behavior prediction of both models are identical, and the parameterization method is compared extensively to data from tensile experiments with a pseudoelastic SMA wire. Remarkably, the model is able to capture all facets of the material behavior including rate-dependence and minor loops. The versatility of the model also allows for the simulation of SMA actuator behavior including the electrical resistance. Finally, a MEMS device using polycrystalline SMA thin film actuators is experimentally investigated. As a first step, the material behavior of the SMA thin films is presented using strain-temperature and resistance-temperature measurements. Secondly, the performance of the MEMS device was determined for different driving frequencies.
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Doshi, Urmi R. "One-dimensional free energy surface models of protein folding: connecting theory and experiments." College Park, Md. : University of Maryland, 2007. http://hdl.handle.net/1903/6875.
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Thesis (Ph. D.) -- University of Maryland, College Park, 2007.Thesis research directed by: Biochemistry. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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Sund, Johan. "From Structure to Function with Binding Free Energy Calculations for Codon Reading, Riboswitches and Lectins." Doctoral thesis, Uppsala universitet, Beräknings- och systembiologi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-207140.
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Molecular association is part of many important processes in living cells. Computational methods for calculating binding free energies allows for a quantitative examination of biomolecular structures and hypotheses drawn from biochemical experiments. Here, binding free energy calculations for tRNAs and release factors binding to mRNA codons on the ribosome, sugars binding to lectins and purine analogs binding to the purine riboswitch are presented. The relative affinities between cognate and non-cognate tRNAs for different states involved in codon reading on the ribosome were determined. The calculations show that tRNA discrimination varies between different conformations of the 30S subunit, where the existence of both low and high selectivity states provides an efficient common mechanism for initial selection and proofreading. The simulations reveal a desolvation mechanism for the 30S conformational switch with which the accuracy of peptide bond formation can be amplified. When an mRNA stop codon (UAA, UAG or UGA) is located in the ribosomal A-site release factors bind to the ribosome and the synthesized protein is released. RF1 is specific for UAA and UAG whereas RF2 is specific for UAA and UGA. The free energy calculations and an analysis of the performed simulations show the mechanisms for how RF1 and RF2 are able to read the stop codons with different specificities. Also mitochondrial release factors were investigated. Vertebrate mitochondria have four stop codons, UAA, UAG, AGA and AGG and two release factors mtRF1 and mtRF1a. The calculations show how the specificities of both mtRF1 and mtRF1a agree with RF1 and that none of them are likely to read the non-standard stop codons AGA and AGG. The linear interaction energy method has also been examined for the RSL and PA-IIL lectins and for the purine riboswitch. The standard parameterization of the method works well for RSL, but fails for PA-IIL and the purine riboswitch due to compositions of the active sites in these systems. The development of new parameterizations to overcome these problems leads to a better understanding of both the method and the binding mechanisms in these systems.
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Nelson, Daniel Richard. "Partially Quenched Chiral Perturbation Theory and a Massless Up Quark: A Lattice Calculation of the Light-Quark-Mass Ratio." Connect to this title online, 2002. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1038343149.
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Thesis (Ph. D.)--Ohio State University, 2002.Title from first page of PDF file. Document formatted into pages; contains xxiii, 296 p.; also includes graphics (some col.) Includes bibliographical references (p. 293-296). Available online via OhioLINK's ETD Center
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Stevenson, Paul. "Nuclear structure calculations using many-body perturbation theory with a separable interaction." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312333.
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Tian, Yongzhe. "Applications of Slattery - Lagoudas' theory for the stress deformation behavior." Texas A&M University, 2005. http://hdl.handle.net/1969.1/4252.
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The thermodynamics of three-dimensional, single-component elastic crystalline
solids was developed by Slattery and Lagoudas (2005). Considering the inïnitesimal
deformations, the stress can be expressed as a function of the lattice vectors and
density in the reference configuration and ù(I;mn), which is defined as the derivative of
specific Helmoholtz free energy with respect to the I(mn). Using the Cauchy - Born rule
to connect the interatomic potential energy and the specific Helmholtz free energy, it is
possible to calculate the elastic properties of both nano-scale materials such as carbon
nanotubes and macro-scale materials such as diamond and silicon. In this study, we
used Tersoî (1988a) - Brenner (1990b) Potential, Tersoî (1988b) potential and Finnis
and Sinclair (1984) potential for carbon, silicon, and vanadium systems respectively.
Using the interatomic potentials to describe the specific Helmholtz free energy, the
elastic properties of graphite, diamond, silicon and vanadium were calculated. This
method was also extended to the calculation of Young's modulus of single-walled
carbon nanotubes (SWCNTs), which are composed of a two dimensional array of
carbon atoms. For SWCNT, we get good agreement with the available experimental
data. For diamond and silicon, C11 and C12 were consistent with both the superelastic
model and the experimental data. The difference of C44 between the calculation and
experimental data was due to accuracy of the potential functions.
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Yoffe, Samuel Robert. "Investigation of the transfer and dissipation of energy in isotropic turbulence." Thesis, University of Edinburgh, 2012. http://hdl.handle.net/1842/7541.
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Numerical simulation is becoming increasingly used to support theoretical effort into understanding the turbulence problem. We develop theoretical ideas related to the transfer and dissipation of energy, which clarify long-standing issues with the energy balance in isotropic turbulence. These ideas are supported by results from large scale numerical simulations. Due to the large number of degrees of freedom required to capture all the interacting scales of motion, the increase in computational power available has only recently allowed flows of interest to be realised. A parallel pseudo-spectral code for the direct numerical simulation (DNS) of isotropic turbulence has been developed. Some discussion is given on the challenges and choices involved. The DNS code has been extensively benchmarked by reproducing well established results from literature. The DNS code has been used to conduct a series of runs for freely-decaying turbulence. Decay was performed from a Gaussian random field as well as an evolved velocity field obtained from forced simulation. Since the initial condition does not describe developed turbulence, we are required to determine when the field can be considered to be evolved and measurements are characteristic of decaying turbulence. We explore the use of power-law decay of the total energy and compare with the use of dynamic quantities such as the peak dissipation rate, maximum transport power and velocity derivative skewness. We then show how this choice of evolved time affects the measurement of statistics. In doing so, it is found that the Taylor dissipation surrogate, u^3 / L, is a better surrogate for the maximum inertial flux than dissipation. Stationary turbulence has also been investigated, where we ensure that the energy input rate remains constant for all runs and variation is only introduced by modifying the fluid viscosity (and lattice size). We present results for Reynolds numbers up to Rλ = 335 on a 1024^3 lattice. Using different methods of vortex identification, the persistence of intermittent structure in an ensemble average is considered and shown to be reduced as the ensemble size increases. The longitudinal structure functions are computed for smaller lattices directly from an ensemble of realisations of the real-space velocity field. From these, we consider the generalised structure functions and investigate their scaling exponents using direct analysis and extended self-similarity (ESS), finding results consistent with the literature. An exploitation of the pseudo-spectral technique is used to calculate second- and third-order structure functions from the energy and transfer spectra, with a comparison presented to the real-space calculation. An alternative to ESS is discussed, with the second-order exponent found to approach 2/3. The dissipation anomaly is then considered for both forced and free-decay. Using different choices of the evolved time for a decaying simulation, we show how the behaviour of the dimensionless dissipation coefficient is affected. The Karman-Howarth equation (KHE) is studied and a derivation of a work term presented using a transformation of the Lin equation. The balance of energy represented by the KHE is then investigated using the pseudo-spectral method mentioned above. The consequences of this new input term for the structure functions are discussed. Based on the KHE, we develop a model for the behaviour of the dimensionless dissipation coefficient that predicts Cɛ= Cɛ(∞)+CL/RL. DNS data is used to fit the model. We find Cɛ(∞) = 0.47 and CL = 19.1 for forced turbulence, with excellent agreement to the data. Theoretical methods based on the renormalization group and statistical closures are still being developed to study turbulence. The dynamic RG procedure used by Forster, Nelson and Stephen (FNS) is considered in some detail and a disagreement in the literature over the method and results is resolved here. An additional constraint on the loop momentum is shown to cause a correction to the viscosity increment such that all methods of evaluation lead to the original result found by FNS. The application of statistical closure and renormalized perturbation theory is discussed and a new two-time model probability density functional presented. This has been shown to be self-consistent to second order and to reproduce the two-time covariance equation of the local energy transfer (LET) theory. Future direction of this work is discussed.
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Hara, Takayuki. "A calculation of fermi energy in selected materials using doppler broadened positron annihilation spectroscopy." Thesis, Georgia Institute of Technology, 1986. http://hdl.handle.net/1853/20238.
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Randeniya, Lakshman Kumar. "Low-energy collision phenomena in free jet expansions: Molecular relaxation theory and ion-molecule rate studies." Diss., The University of Arizona, 1990. http://hdl.handle.net/10150/185207.
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Theoretical and experimental development of a new kinetic method to measure the rate coefficients of ion-molecule reactions occurring in free jet expansions below 20K is presented. The method is successfully used to determine the temperature dependences of numerous bimolecular and termolecular ion-molecule reactions over the temperature range of 0.5-20K. A new theoretical method based on the generalized Boltzmann equation is developed to calculate macroscopic flow properties of pure molecular supersonic flows. The variation of the different temperature components, hydrodynamic speed and density of the free jet as a function of distance is presented assuming a Maxwellian anisotropic distribution function. This theory facilitates the kinetic analysis and the assignment of temperatures to the chemical reactions occurring in jets. Using the Boltzmann equation, the flow properties of a mixed atomic free jet expansion are also analyzed. The method is more general than previous treatments which assume a vanishingly small mole fraction for one component of the mixture. The presence of velocity slip arising from the difference in hydrodynamic speeds of the two components complicates this treatment. Expressions for the calculation of flow properties for an atomic mixture with an arbitrary composition are presented. Temperature dependences of the termolecular association rate coefficients for the reactions of, N₂⁺ + 2N₂, O₂⁺ + 2O₂ and NO⁺ + 2NO over the temperature range of 3-15K are presented. The results are discussed in the light of statistical phase space theory. For the reactions of N₂⁺ + 2N₂ and O₂⁺ + 2O₂ excellent agreement between theory and experiment is obtained. The kinetic analysis of NO⁺ + 2NO is complicated due to the competing charge transfer reaction. The observed temperature dependence for this reaction does not agree with the predictions of the statistical theory. The ternary association rate coefficients for the reaction, Ar⁺ + 2Ar, show a strong temperature dependence at very low temperatures (0.5-2.5K). Current statistical formulations cannot predict this temperature dependence and a comprehensive model for this reaction mechanism has yet to be developed. Three distinct temperature dependences are observed for the bimolecular reactions of N₂⁺ with CH₄, O₂ and n-H₂ at temperatures below 15K. Speculations are made regarding the interaction potential energy surfaces that may lead to the observed behaviors.
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Jenkins, Robert David. "Higher order energy transfer : quantum electrodynamical calculations and graphical representation." Thesis, University of East Anglia, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.327601.
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Martínez, Monge Álvaro. "Free energy and information-content measurements in thermodynamic and molecular ensembles." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/667026.
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Single-molecule experiments have emerged as a powerful tool that allow researchers to investigate the physical behavior of individual molecules with unprecedented resolution. The feasibility exerting forces at the piconewton scale (10^-12 N) and measuring nanometric displacements in the sub-millisecond scale, offer a widespread range of exciting possibilities. The major part of this thesis is devoted to address fundamental topics of statistical physics using single-molecule experiments. In particular, in the first part of the thesis, we aimed to study one of the eldest questions in statistical mechanics: the issue of ensemble inequivalence. By performing single- molecule experiments on a well-known molecule (the CD4 DNA hairpin), we have been able of exploring two conjugate ensembles: the fixed-extension and the force-fixed ensemble. Both ensembles are conjugate with respect to energy since the product force times extension equals has energy dimensions. We carried out experiments in the fixed-force ensemble using both optical tweezers and magnetic tweezers, and in the fixed-extension using optical tweezers. We have found that these two conjugate ensembles are not equivalent at the level of thermodynamics nor in kinetics. Moreover, we showed that the often-neglected boundary terms in the definition of the thermodynamic work are essential to the validity of the fluctuation theorem. The second part of this thesis is also merely theoretical. Recent single-molecule assays confirmed the connection between information theory and statistical physics. Single- molecule experiments have turned out to be the perfect playground to explore the thermodynamic implications of having —or lacking— information. It is worthwhile to mention the experimental realization of the Szilard engine and the experimental verification of Landauer’s limit. With the current existing results, the information-to- energy connection is well established. We have been able to experimentally demonstrate, for the first time, the reversed implication. We have been able to quantify the information-content of neutral molecular ensembles by means of thermodynamic measurements. That is, we experimentally demonstrated the energy- to-information conversion. Our works are built on what we call ensemble force spectroscopy, a systematic procedure capable of obtaining a robust characterization of molecular ensembles in the best tradition of statistical physics, by measuring few tens of molecules. In the final part of the thesis we aimed to measure the specific binding energy of a metallic ion to the tertiary structure of a three-way RNA junction belonging
to the central domain of the 16S ribosomal RNA (rRNA). From the physics perspective, to the best of our knowledge, first time we have been able to discern the free energy contribution due to the specific binding of magnesium ions to an RNA substrate by means of single-molecule assays. On the other hand, such molecule is able to form, besides its native conformation, a force-induced misfolded state. Despite this fact was already pointed out in previous single-molecule studies, there was a lack of knowledge regarding the molecular kinetics and the folding pathway. Aiming to fill this gap, we performed a thorough study of the three-helix RNA junction using dynamic force spectroscopy. As a result, we have characterized the full folding pathway of the molecule, including both the native and the misfolded structure. Furthermore, we have experimentally confirmed the fact that the presence of magnesium promotes the stabilization of the native structure and we have measured this contribution. We have found that magnesium is able to rescue the native structure from the misfolded structure via electrostatic interactions due to magnesium binding. This fact is biologically relevant, since we have been able to characterize the conditions in which a misfolded molecule is able to recover its native conformation.En esta tesis hemos abordado cuestiones fundamentales de la física estadística. En particular, hemos estudiado el problema de la equivalencia entre colectivos estadísticos, la conversión de energía a información y el estudio de las energías específicas de unión de iones metálicos a sustratos de RNA. Esta tesis doctoral se ha llevado a cabo empleando dos de los instrumentos de molécula individual más conocidos, las pinzas ópticas y las pinzas magnéticas. Ambas son técnicas que permiten la aplicación controlada de fuerzas mecánicas a los extremos de una molécula individual. El poder aplicar fuerzas a sistemas moleculares permite llevar a cabo una profunda caracterización de las propiedades físicas de los llamados sistemas pequeños. Las dimensiones de estos sistemas abarcan desde unos pocos nanómetros —una millonésima parte del metro— hasta varios cientos de nanómetros. Además, los sistemas pequeños están lejos del llamado límite termodinámico y están dominados por las fluctuaciones térmicas del entorno. Por lo tanto, debido a estas peculiaridades, el estudio de sistemas pequeños mediante los instrumentos de molécula individual permite impulsar y extender los horizontes de la física de no equilibrio.
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Dornbach, Mark [Verfasser], and Hans-Joachim [Akademischer Betreuer] Werner. "Analytical energy gradients for open-shell local second-order Møller-Plesset perturbation theory and applications to large molecules / Mark Dornbach ; Betreuer: Hans-Joachim Werner." Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2018. http://d-nb.info/1166141381/34.
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Shamsudin, Khan Yasmin. "Non-Steroidal Anti-Inflammatory Drugs in Cyclooxygenases 1 and 2 : Binding modes and mechanisms from computational methods and free energy calculations." Doctoral thesis, Uppsala universitet, Beräkningsbiologi och bioinformatik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-328478.
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Non-steroidal anti-inflammatory drugs (NSAIDs) are one of the most commonly used classes of drugs. They target the cyclooxygenases (COX) 1 and 2 to reduce the physiological responses of pain, fever, and inflammation. Due to their role in inducing angiogenesis, COX proteins have also been identified as targets in cancer therapies. In this thesis, I describe computational protocols of molecular docking, molecular dynamics simulations and free energy calculations. These methods were used in this thesis to determine structure-activity relationships of a diverse set of NSAIDs in binding to their target proteins COX-1 and 2. Binding affinities were calculated and used to predict the binding modes. Based on combinations of molecular dynamics simulations and free energy calculations, binding mechanisms of sub-classes of NSAIDs were also proposed. Two stable conformations of COX were probed to understand how they affect inhibitor affinities. Finally, a brief discussion on selectivity towards either COX isoform is discussed. These results will be useful in future de novo design and testing of third-generation NSAIDs.
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Khabir, Mohmed Hassan Mohmed. "Numerical singular perturbation approaches based on spline approximation methods for solving problems in computational finance." Thesis, University of the Western Cape, 2011. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_7416_1320395978.
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Options are a special type of derivative securities because their values are derived from the value of some underlying security. Most options can be grouped into either of the two categories: European options which can be exercised only on the expiration date, and American options which can be exercised on or before the expiration date. American options are much harder to deal with than European ones. The reason being the optimal exercise policy of these options which led to free boundary problems. Ever since the seminal work of Black and Scholes [J. Pol. Econ. 81(3) (1973), 637-659], the differential equation approach in pricing options has attracted many researchers. Recently, numerical singular perturbation techniques have been used extensively for solving many differential equation models of sciences and engineering. In this thesis, we explore some of those methods which are based on spline approximations to solve the option pricing problems. We show a systematic construction and analysis of these methods to solve some European option problems and then extend the approach to solve problems of pricing American options as well as some exotic options. Proposed methods are analyzed for stability and convergence. Thorough numerical results are presented and compared with those seen in the literature.
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Ringer, Ashley L. "From small to big." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/28089.
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Thesis (M. S.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2009.Committee Chair: Sherrill, C. David; Committee Member: Bredas, Jean-Luc; Committee Member: El-Sayed, Mostafa A.; Committee Member: Harvey, Stephen C; Committee Member: Hernandez, Rigoberto.
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Dai, Ping. "Réjection de perturbation sur un système multi-sources - Application à une propulsion hybride." Thesis, Poitiers, 2015. http://www.theses.fr/2015POIT2251/document.
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Ce mémoire porte sur l'étude d'un système de gestion d'énergie électrique dans un système multi-sources soumis à des perturbations exogènes. L'application visée est l'alimentation d'une propulsion hybride diesel/électrique équipée d'un système d'absorption des pulsations de couple. Les perturbations exogènes considérées peuvent être transitoires ou persistantes. Une perturbation transitoire correspond à une variation rapide du couple de charge, due par exemple à une accélération ou une décélération du véhicule. Une perturbation persistante provient du système de compensation des pulsations de couple générées par le moteur thermique. Le premier objectif du contrôle est de maintenir constante la tension du bus continu. Le deuxième objectif est d'absorber dans un système de stockage rapide constitué de super condensateur ces perturbations qui peuvent à terme provoquer une usure prématurée de la batterie. Le troisième objectif est de compenser l'auto-décharge dans le super condensateur en maintenant constante sa tension nominale. Les deux sources (batterie et super condensateur) sont reliées au bus continu par l'intermédiaire de deux convertisseurs boost DC/DC. La commande consiste à piloter les rapports cycliques de chaque convertisseur. C'est un système non linéaire où la commande est multiplicative de l'état. L'approche classique consistant à résoudre les équations Francis-Byrnes-Isidori ne s'applique pas directement dans ce cas où la sortie et la matrice d'interconnection dépendent de la commande. De plus, si cette approche est bien adaptée au rejet de perturbations persistantes, elle montre ces limites pour le rejet de perturbations non persistantes combiné à des objectifs de régulation. Notre approche a consisté à écrire le système sous un formalisme Port-Controlled Hamiltonian et à s'affranchir de la contrainte de la dépendance de la matrice d'interconnection avec la commande en utilisant la théorie des perturbations singulières. La commande du système dégénéré peut ensuite être calculée par une approche passive. Les performances de cette commande ont été testées en simulation et à l'aide d'un banc d'essai expérimental. Les résultats montrent l'efficacité du système d'absorption des différents types de perturbation tout en respectant les deux objectifs de régulationThis thesis presents the research of energy management in a battery/ultracapacitor hybrid energy storage system with exogenous disturbance in hybrid electric vehicular application. Transient and harmonic persistent disturbances are the two kinds of disturbances considered in this thesis. The former is due to the transient load power demand during acceleration and deceleration, and the latter is introduced from the process of the internal combustion engine torque ripples compensation. Our control objective is to absorb the disturbances causing battery wear via the ultracapacitor, and meanwhile, to maintain a constant DC voltage and to compensate the self-discharge in the ultracapacitor to maintain it operating at the nominal state of charge. The object system is nonlinear due to the multiplicative relation between the input and the state. The traditional approach to solve Francis-Byrnes-Isidori equations cannot be directly applied in this case since the interconnect matrix depends on the control input. Besides, even if this approach is well suited to the rejection of persistent disturbances, it shows the limits for the case of non-persistent disturbances which is also our object. Our contributed control method is realized through a cascade control structure based on the singular perturbation theory. The ultracapacitor current with the fastest motion rate is controlled in the inner fast loop through which we impose the desired dynamic to the system. The reduced system controlled in the outer slow loop is a Hamiltonian system and the controller is designed via interconnection and damping assignment. Simulations and experiments have been carried out to evaluate the control performance. A contrast of the system responses with and without the control algorithm shows that, with the control algorithm, the ultracapacitor effectively absorbs the disturbances; and verifies the effectiveness of the control algorithm
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Troha, Anthony Lawrence. "The theory and design of a chirped-pulse inverse free-electron laser : an innovative, compact, high-energy, vacuum-based, electron accelerator /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2003. http://uclibs.org/PID/11984.
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Timrov, Iurii. "Ab initio study of plasmons and electron-phonon coupling in bismuth: from free-carrier absorption towards a new method for electron energy-loss spectroscopy." Palaiseau, Ecole polytechnique, 2013. http://pastel.archives-ouvertes.fr/docs/00/82/37/58/PDF/thesis.pdf.
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Ce travail a été consacré à l'étude théorique du bismuth semi-métallique à l'aide de méthodes basées sur la théorie de la fonctionnelle de la densité (DFT). Les effets de couplage spin-orbite et d'échange et de corrélation dans l'approximation de densité locale (LDA) et de gradient généralisé (GGA) ont été approfondis de façon systématique. J'ai trouvé que les poches d'électrons et de trous au niveau de Fermi sont correctement décrites, ce qui m'a permis d'interpréter avec succés les expériences pompe-sonde dans le bismuth photoexcité menées au laboratoire des Solides Irradiés. Le calcul du couplage électron-phonon a montré la forte dépendance, par rapport au vecteur d'onde électronique, du couplage de la bande de valence la plus haute avec le phonon A1g LO de centre de zone, ce qui explique l'observation de la forte dépendance en k de l'amplitude d'oscillation de l'énergie de liaison de cette même bande en photoémission résolue en temps. J'ai aussi montré que la présence d'extréma dans les bandes de valence et de conduction, où la masse des porteurs peut atteindre 18 m0, favorise une accumulation des porteurs et conduit à une augmentation de leur fréquence plasma au cours du temps aprés photoexcitation, un effet qui n'a pas (encore) été observé dans d'autres matériaux. Enfin, j'ai développé une nouvelle méthode en théorie de perturbation de la fonctionnelle de la densité dépendante du temps (TDDFPT), qui permet de calculer la réponse électronique du matériau pour n'importe quelle valeur du moment transféré. Cette approche basée sur la méthode de récursion de Lanczos m'a permis de calculer les spectres de perte d'énergie électronique de Bi dans la gamme d'énergie 0-100 eV et de combler l'intervalle d'énergie entre les pertes des électrons de valence et celles des électrons de cœur. Cette méthode ouvre des perspectives considérables, comme le calcul des plasmons de surfaceThis work has been devoted to the theoretical study of bulk semimetallic bismuth with methods based on the density functional theory (DFT). Effects of spin-orbit coupling and of the exchange-and-correlation functionals in the local density (LDA) and generalized gradient approximation (GGA) have been systematically investigated. I have found that electron and hole pockets at the Fermi level are accurately reproduced, which has enabled me to successfully interpret the pump-probe experiments in the photoexcited bismuth performed in the Laboratoire des Solides Irradiés. The strong dependence on the electronic wave vector, of the calculated electronic coupling of the upper valence band with the zone-center A1g LO phonon, explains the observation of a strongly k-dependent oscillation amplitude of the upper valence band in time-resolved photoemission experiments upon activation of the coherent A1g phonon under photoexcitation. I have also shown that the presence of local extrema in the conduction and valence bands structure, where the carrier mass can be as large as 18 m0, favours an accumulation of photoexcited carriers in these extrema and contributes to the augmentation of the plasma frequency as a function of time after the photoexcitation, an effect which has no analogy in other materials (as yet). Finally, I have developed a new ab initio approach in the time-dependent density functional perturbation theory (TDDFPT), which allows us to calculate the electronic response of materials for any momentum transfer. This approach based on the Lanczos recursion method has enabled me to calculate for the first time the electron energy-loss spectrum of Bi in the 0-100 eV energy range, bridging the gap between valence and core losses. This method opens the way to the routine calculation of surface plasmons
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Boukharta, Lars. "Computational Modelling of Ligand Complexes with G-Protein Coupled Receptors, Ion Channels and Enzymes." Doctoral thesis, Uppsala universitet, Beräknings- och systembiologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-212103.
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Accurate predictions of binding free energies from computer simulations are an invaluable resource for understanding biochemical processes and drug action. The primary aim of the work described in the thesis was to predict and understand ligand binding to several proteins of major pharmaceutical importance using computational methods. We report a computational strategy to quantitatively predict the effects of alanine scanning and ligand modifications based on molecular dynamics free energy simulations. A smooth stepwise scheme for free energy perturbation calculations is derived and applied to a series of thirteen alanine mutations of the human neuropeptide Y1 G-protein coupled receptor and a series of eight analogous antagonists. The robustness and accuracy of the method enables univocal interpretation of existing mutagenesis and binding data. We show how these calculations can be used to validate structural models and demonstrate their ability to discriminate against suboptimal ones. Site-directed mutagenesis, homology modelling and docking were further used to characterize agonist binding to the human neuropeptide Y2 receptor, which is important in feeding behavior and an obesity drug target. In a separate project, homology modelling was also used for rationalization of mutagenesis data for an integron integrase involved in antibiotic resistance. Blockade of the hERG potassium channel by various drug-like compounds, potentially causing serious cardiac side effects, is a major problem in drug development. We have used a homology model of hERG to conduct molecular docking experiments with a series of channel blockers, followed by molecular dynamics simulations of the complexes and evaluation of binding free energies with the linear interaction energy method. The calculations are in good agreement with experimental binding affinities and allow for a rationalization of three-dimensional structure-activity relationships with implications for design of new compounds. Docking, scoring, molecular dynamics, and the linear interaction energy method were also used to predict binding modes and affinities for a large set of inhibitors to HIV-1 reverse transcriptase. Good agreement with experiment was found and the work provides a validation of the methodology as a powerful tool in structure-based drug design. It is also easily scalable for higher throughput of compounds.
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Le, Bars Solène. "Action-effect prediction in intention-based and stimulus-driven actions : an exploration of the ideomotor theory and of the brain free-energy principle." Thesis, Sorbonne Paris Cité, 2017. http://www.theses.fr/2017USPCB235.
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Les actions motrices humaines peuvent être envisagées comme étant soit volontaires, c'est-à-dire intérieurement déclenchées afin d’atteindre un certain but, soit réactives, c'est-à-dire extérieurement déclenchées par des stimuli environnementaux. Cette dissociation a notamment été proposée au sein de la théorie idéomotrice suggérant que la réalisation d'actions volontaires repose sur notre capacité à prédire les conséquences sensorielles de nos actions, grâce aux associations action-effet qui sont acquises avec l'expérience. Selon les modèles computationnels tels que le principe de minimisation de l’énergie libre, la prédiction sensorielle est également considérée comme un processus majeur de la perception et du contrôle moteur, indépendamment du type d’action. Dès lors, les études visant à explorer la prédiction sensorielle liée au contrôle moteur ont systématiquement minimisé la distinction potentielle entre deux types d'actions plus ou moins indépendantes. Dans la présente thèse, nous nous sommes principalement attelés à tester la théorie idéomotrice originale qui suggère une implication supérieure de la prédiction sensorielle dans les actions intentionnelles par rapport à des actions plus réactives. Nous avons réalisé ce travail selon trois axes : (1) À travers des expériences comportementales, nous avons cherché à préciser à quel(s) stade(s) moteur(s) la prédiction de l'effet de l'action pouvait être associée, dans les actions intentionnelles d’une part et dans les actions davantage réactives d’autre part, afin de pouvoir dissocier la dynamique temporelle de la prédiction sensorielle au sein de ces deux catégories d'actions. (2) En tirant parti des postulats dérivés des approches computationnelles, nous avons utilisé l'EEG pour explorer d'abord le niveau d'erreur de prédiction liée aux effets sensoriels imprévisibles ou mal-prédits afin de dissocier ces deux types d'événements non prédits au niveau neural. Par la suite, nous avons étudié si les marqueurs EEG de la prédiction sensorielle (c'est-à-dire l'erreur de prédiction et l'atténuation sensorielle) étaient modulés par le type d'action déclenchant l'effet sensoriel. (3) Enfin, nous avons examiné si des variations dans le processus de prédiction des effets de l'action pouvaient être associés à certains déficits moteurs dans la maladie de Parkinson et à des tendances impulsives mesurées chez des participants sains, pour éventuellement conférer une dimension clinique au processus de prédiction sensorielle. Nos résultats ont démontré (1) que la dynamique temporelle de la prédiction des effets de l'action semble effectivement dépendre du type d'action, en étant liée aux étapes précoces et tardives de la préparation motrice des actions intentionnelles, mais seulement aux étapes tardives de la préparation motrice des actions réactives. Nous avons également montré que (2) les événements mal prédits généraient une erreur de prédiction plus importante comparativement à des événements imprévisibles. Par ailleurs, les marqueurs EEG de la prédiction sensorielle étaient plus prononcés pour les effets auditifs déclenchés par des actions intentionnelles par rapport aux effets auditifs déclenchés par des actions réactives. Enfin, nos résultats ont permis de démontrer que (3) le processus de prédiction sensorielle semble être altéré lors de la réalisation d’actions intentionnelles chez des patients atteints de la maladie de Parkinson, et que les marqueurs EEG de la prédiction d’effets auditifs déclenchés par des actions intentionnelles sont modulés par les tendances impulsives d’individus sains. Dans l'ensemble, nos résultats soutiennent l’existence d’une dissociation fonctionnelle entre actions intentionnelle et réactive, et sont également cohérents avec la version originale de la théorie idéomotrice étant donné que la prédiction sensorielle semble être impliquée plus tôt et plus fortement dans les actions intentionnelles que dans les actions réactives. (…)Motor actions can be classified as being either intention-based, i.e. internally triggered in order to reach a certain goal, or either stimulus-driven, i.e. externally triggered in order to accommodate to environmental events. This elementary dissociation was notably theorized within the original ideomotor theory stating that performing intention-based actions relies on our capacity to predict the sensory consequences of our actions, due to action-effect associations learnt through experience. In recent neurocomputational models such as the brain free-energy principle, this sensory prediction is considered as a key process of overall sensorium and motor control, regardless the action type. Henceforth, experiments studying sensory prediction related to motor control have systematically minimized the potential distinction between two more or less independent action types. In the current thesis, we mainly attempted to address this issue by testing the original ideomotor viewpoint, suggesting a superior involvement of action-effect prediction in intention-based actions compared to more reactive actions. We achieved this work according to three axes: (1) Through behavioural experiments, we aimed at clarifying which motor stage(s) action-effect prediction is related to, within intention-based actions and within stimulus-driven actions, in order to potentially dissociate the temporal dynamics of action-effect prediction in these two categories of actions. (2) Taking advantage from assumptions derived from neurocomputational approaches, we used EEG to first explore the level of prediction error related to unpredicted vs. mispredicted auditory events in order to dissociate these two types of nonpredicted events at a neural level. Then, we investigated whether EEG markers of sensory prediction (i.e., prediction error and sensory attenuation) were modulated by the kind of action triggering the sensory effect. (3) Finally, we intended to examine whether action-effect prediction variations could be linked to motor deficits in Parkinson's disease on the one hand, and to impulsivity tendencies in healthy participants on the other hand, for possibly yielding a clinical dimension to the sensory prediction process. Our findings demonstrated (1) the temporal dynamics of action-effect prediction seems to depend on the action kind, being linked to both early and late stages of motor preparation of intention-based actions and only to late stages of motor preparation of stimulus-driven actions. We also showed that (2) mispredicted events were linked to enhanced prediction error compared to unpredicted events, and that EEG markers of sensory prediction were more pronounced for auditory effects triggered by intention-based actions compared to auditory effects triggered by stimulus-driven actions. Then, our results sustained that (3) the action-effect prediction process seems to be impaired for intention-based actions in Parkinson's disease, and that EEG markers of sensory prediction for effects triggered by intention-based actions are modulated by impulsiveness tendencies in healthy participants. Altogether, our findings are consistent with the original version of the ideomotor theory given the action-effect prediction appeared to be earlier and stronger involved in intention-based actions compared to stimulus-driven actions. Our EEG data also modernized the ideomotor principle, reconciling it with neurocomputational approaches of sensory prediction. Finally, the clinical exploration of the action-effect prediction process in pathologies affecting motor control appeared promising to understand intermediate neurocognitive processes which are involved in motor symptoms or characteristics
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Cote, Yoann. "Theory and molecular dynamics simulations of the local dynamics and free energy profiles of proteins : application to the interpretation of protein NMR data." Thesis, Dijon, 2012. http://www.theses.fr/2012DIJOS075.
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Comprendre la dynamique locale des protéines dans leur état natif (structure repliée etfonctionnelle) est essentiel pour comprendre leur dynamique globale et leur fonction biologique. Aucours de cette thèse, nous avons étudié la dynamique locale de plusieurs petites protéines enmesurant les fluctuations de sondes locales le long de la séquence d’acide aminé de ces protéines.Nous avons essayé de comprendre la dynamique de ces sondes locales, comment celles-ci serelaxaient entre leurs différentes conformations, comment leurs fluctuations étaient corrélées lesunes aux autres et comment peuvent-elles être reliées à la fonction biologique des protéines.Dans les trois premiers chapitres, nous introduisons les concepts du mouvement Browniende rotation libre, de la spectroscopie par Résonance Magnétique Nucléaire (RMN) et de ladynamique moléculaire (DM). Dans les chapitres 4 et 5, nous avons étudié la dynamique desliaisons amides de la chaine principale (backbone) des protéines sur leurs paysages d’énergie libre.Dans le chapitre 4, nous avons démontré que les fluctuations des liaisons amide dubackbone de la protéine VA3 sont décrites par une diffusion rotationnelle anormale plutôt que parune diffusion rotationnelle libre généralement utilisée pour interpréter les données RMN enrelaxation de spins et en couplage résiduel dipolaire. [...] Dans le chapitre 5, nous avons démontré la diffusion rotationnelle anormale de ces liaisons jusqu’à une échelle de temps de 100 ns en utilisant dix simulations de DM de 1 μs de la protéineUbiquitine. Nous avons aussi étudié la convergence des paramètres RMN extraits des trajectoiresde DM en fonction de leur durée. [...] Dans le chapitre 6, nous avons réalisé une l’étude de la corrélation entre les mouvements du backbone et des chaines latérales des protéines. [...] Dans la première partie du dernier chapitre de cette thèse, nous avons étudié l’évolution de la corrélation dynamique entre les chaines latérales et la chaine principale d’une protéine durant des évènements de dépliement/repliement. Pour cette étude préliminaire, nous avons utilisé unesimulation de DM d’un « ultra-fast folder » nommé Trp-cage réalisée à 380K. Nous avons confirméles résultats précédemment trouvés pour les protéines dans leur état natif. Nous avons observél’augmentation de la corrélation entre les séries temporelles yn(t) and δn(t) pendant un évènementde dépliement caractérisé par la sortie du tryptophane de sa cage. Un paramètre stérique s aégalement été défini afin de quantifier les intéractions des chaines latérales avec leurenvironnement. Dans une seconde partie de ce dernier chapitre, nous présentons une étudepréliminaire du dépliement d’un « downhill folder » nommé gpW sous contrainte d’une force. Pourcaractériser le dépliement de la protéine gpW, nous avons calculé les chemical shifts des atomes Cª et Hⁿ du backbone le long de sa séquence en fonction d’une coordonnée réactionnelle choisie comme étant la distance entre les Cª de résidus C- et N- terminaux. Nous avons démontré qu’il était difficile de discerner un comportement particulier à partir des tous les chemical shifts en fonction de la distance. Cependant, en moyennant la valeur des chemical shifts en sur tous lesrésidus de la protéine nous trouvons que l’évolution de cette valeur moyenne en fonction de ladistance permettait de décrire les évènements du dépliement de la protéine en fonction de lacoordonnée de réaction durant la simulation de DMUnderstand the local dynamics of proteins in their native state, i.e. in their folded functionalstructure, is a prerequisite to understand their global dynamics and their biological function. In thepresent thesis, we investigated the local dynamics of several small proteins by recording thefluctuations of local probes along the amino-acid sequence of those proteins. We tried tounderstand the dynamics of the local probe, i.e. how they relax between their differentconformations, how their fluctuations are correlated to each other, how their fluctuations arerelated to the function of the proteins. In the first three chapters, we introduced the concepts of the free rotational Brownian motion, of the Nuclear Magnetic Resonance spectroscopy and of the Molecular Dynamics (MD)simulations. In chapters 4 and 5, we studied the dynamics of the backbone amide bonds of theproteins on their free-energy landscape. In chapter 4, we demonstrated that the fluctuations of the backbone amide bonds of the protein VA3 are described by a rotational anomalous diffusion rather than by a free rotationaldiffusion, as often assumed in the interpretation of the raw NMR-measured data (Spin relaxation(SR) data and Residual Dipolar Coupling (RDC) data. [...] In chapter 5, we demonstrated the anomalous diffusion of backbone amide bonds up to 100 ns by using ten MD trajectories of 1 μs of duration for the protein ubiquitin. We also studied the convergence of the NMR-derived parameters extracted from the MD trajectories in function of their duration. [...] In chapter 6, we addressed the question of the correlation between the motions of the side chains and main chain of a protein. [...] In the first part of the final chapter of the present thesis, we investigated the evolution of the correlation between the side-chain and the main-chain motions of a protein during unfolding/folding events. In this preliminary work, we used a single MD simulation of the ultrafast folder Trp-cage performed at 380 K. We confirmed the results found for proteins in theirnative state. We observed an increase of the correlation between the two time series yn(t) and δn(t) during an unfolding event characterized, here, by the exit of the TRP residue of its “cage”.A steric parameter s was also defined in order to quantify interactions of the amino-acid side chainwith its environment. In a second part of the last chapter, we present a preliminary study of theunfolding of the downhill folder gpW under a mechanical force. To characterized the unfolding ofgpW, we computed the chemical shift of the Cª and of the Hⁿ atoms along the amino-acidsequence of the protein in function of a reaction coordinate: the distance, rCªCª , between the Cª atoms of the N and C terminal residues. We demonstrated that it is hard to distinguish a typical behavior of all the chemical shift of all the residues along the amino-acid sequence in function of the distance rCªCª . However, by averaging the chemical shift over all the residues of the protein we found that the evolution of the average value of the chemical shift described the unfolding eventsof the protein during the MD simulations
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Piccini, GiovanniMaria. "Ab initio free energies of adsorption from anharmonic vibrations." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät, 2015. http://dx.doi.org/10.18452/17239.
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Die Thermodynamik von Adsorptionsvorgängen wurde mittels quantenchemischer Methoden und der statistischen Thermodynamik untersucht. Eine neue rechentechnische Methode wird vorgestellt, die den Mangel an Genauigkeit vorhandener Methoden zur Untersuchung periodischer Systeme, wie z. B. der Dichte-Funktional-Theorie, behebt, und es ermöglicht thermodynamische Funktionen mit chemischer Genauigkeit zu bestimmen. Das im Rahmen dieser Arbeit entwickelte Protokoll besteht aus verschiedenen rechentechnischen Schritten, als da wären, eine Strukturoptimierung in Normalkoordinaten anstatt in kartesischen Koordinaten, eine numerische Berechnung der harmonischen Frequenzen durch Abtasten der Potentialenergieoberfläche entlang der Normalkoordinaten und anschließender anharmonischer Korrektur. Die Normalkoordinatenoptimierung garantiert eine korrekte Relaxation der Struktur mit ausschließlich reellen harmonischen Frequenzen. Die anharmonischen Korrekturen ermöglichen eine gute Beschreibung der Schwingungsstrukturen von Systemen die durch eine besonders Flache PES gekennzeichnet sind. Gleichzeitig, wird durch die Verwendung eines QM:QM-Hybridverfahrens zur Bestimmung des elektronischen Anteils der Adsorptionsenergie eine höhere Genauigkeit in der Bestimmung der Korrelationsenergie im Vergleich zu DFT garantiert. Der elektronische Anteil der Adsorptionsenergie, sowie der Schwingungsthermische Anteil werden abschließend kombiniert um einen genauen Wert der thermodynamischen Funktionen zu erhalten.The thermodynamic of adsorption is investigated from the vibrational point of view using quantum chemical methods via statistical mechanics. Due to the lack of accuracy of the present available methods for investigating periodic systems, such as plane-wave density functional theory (DFT), a novel computational strategy is presented to overcome these limitations and bring the estimate of the thermodynamic functions within chemical accuracy limits. The protocol presented in this work consists of different computational steps, namely a structure optimization using normal mode coordinates instead of Cartesians, a numerical harmonic frequency calculation via sampling of the potential energy surface along the normal mode coordinates and the inclusion of anharmonic correction to the latter. The normal mode coordinate optimization ensures a proper relaxation of the structure and a reliable set of real harmonic frequencies while the anharmonic corrections account for a proper description of the vibrational structure of a system characterized by a very flat potential energy surface. Parallel to these calculations the electronic part of the adsorption energy is corrected using a hybrid QM:QM scheme to account the electronic correlations effects more accurately than DFT. The hybrid electronic adsorption energy and the vibrational thermal contributions obtained using anharmonic corrections are finally combined to get accurate estimate of the adsorption thermodynamic functions.
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Bhatta, Fanindra P. "Phase Separation in Binary Lipid Monolayers Bilayers: Experiment and Theory." Kent State University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=kent1322501214.
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Kognole, Abhishek A. "UNDERSTANDING CARBOHYDRATE RECOGNITION MECHANISMS IN NON-CATALYTIC PROTEINS THROUGH MOLECULAR SIMULATIONS." UKnowledge, 2018. https://uknowledge.uky.edu/cme_etds/80.
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Non-catalytic protein-carbohydrate interactions are an essential element of various biological events. This dissertation presents the work on understanding carbohydrate recognition mechanisms and their physical significance in two groups of non-catalytic proteins, also called lectins, which play key roles in major applications such as cellulosic biofuel production and drug delivery pathways. A computational approach using molecular modeling, molecular dynamic simulations and free energy calculations was used to study molecular-level protein-carbohydrate and protein-protein interactions. Various microorganisms like bacteria and fungi secret multi-modular enzymes to deconstruct cellulosic biomass into fermentable sugars. The carbohydrate binding modules (CBM) are non-catalytic domains of such enzymes that assist the catalytic domains to recognize the target substrate and keep it in proximity. Understanding the protein-carbohydrate recognition mechanisms by which CBMs selectively bind substrate is critical to development of enhanced biomass conversion technology. We focus on CBMs that target both oligomeric and non-crystalline cellulose while exhibiting various similarities and differences in binding specificity and structural properties; such CBMs are classified as Type B CBMs. We show that all six cellulose-specific Type B CBMs studied in this dissertation can recognize the cello-oligomeric ligands in bi-directional fashion, meaning there was no preference towards reducing or non-reducing end of ligand for the cleft/groove like binding sites. Out of the two sandwich and twisted forms of binding site architectures, twisted platform turned out to facilitate tighter binding also exhibiting longer binding sites. The exterior loops of such binding sites were specifically identified by modeling the CBMs with non-crystalline cellulose showing that high- and low-affinity binding site may arise based on orientation of CBM while interacting with non-crystalline substrate. These findings provide various insights that can be used for further understanding of tandem CBMs and for various CBM based biotechnological applications.
The later part of this dissertation reports the identification of a physiological ligand for a mammalian glycoprotein YKL-40 that has been only known as a biomarker in various inflammatory diseases and cancers. It has been shown to bind to oligomers of chitin, but there is no known function of YKL-40, as chitin production in the human body has never been reported. Possible alternative ligands include proteoglycans, polysaccharides, and fibers such as collagen, all of which make up the mesh comprising the extracellular matrix. It is likely that YKL-40 is interacting with these alternative polysaccharides or proteins within the body, extending its function to cell biological roles such as mediating cellular receptors and cell adhesion and migration. We considered the feasibility of polysaccharides, including cello-oligosaccharides, hyaluronan, heparan sulfate, heparin, and chondroitin sulfate, and collagen-like peptides as physiological ligands for YKL-40. Our simulation results suggest that chitohexaose and hyaluronan preferentially bind to YKL-40 over collagen, and hyaluronan is likely the preferred physiological ligand, as the negatively charged hyaluronan shows enhanced affinity for YKL-40 over neutral chitohexaose. Collagen binds in two locations at the YKL-40 surface, potentially related to a role in fibrillar formation. Finally, heparin non- specifically binds at the YKL-40 surface, as predicted from structural studies. Overall, YKL-40 likely binds many natural ligands in vivo, but its concurrence with physical maladies may be related to the associated increases in hyaluronan.
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Banner, Amy Bennett. "A Comparative Study of the Perceptions of Elementary School Administrators, Teachers, and Students Regarding recess and Free Play in the Public School." Digital Commons @ East Tennessee State University, 2005. https://dc.etsu.edu/etd/1005.
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According to recent studies, the number of schools that have severely limited or eliminated recess and free-play opportunities is on the rise across the nation. School officials cite the increasing levels of state and federal pressure to perform on standardized tests as the primary reason for this shift away from the playground. The threat of lawsuits and safety concerns are also listed as factors in this change of policy.
The purpose of this mixed methods study was to examine the perceptions of directors of schools, supervisors, principals, assistant principals, teachers, and students regarding recess and free play in three East Tennessee school systems. Representative schools were chosen from each system and examined. In addition, results from standardized test scores as provided by the state of Tennessee were examined for the selected schools.
The findings of this study revealed that directors, supervisors, principals, teachers, and students were in favor of recess and stated that offering recess and free-play opportunities provided some benefit to students. Even so, two schools in the study had chosen to limit recess and free-play opportunities to varying degrees whereas the third school maintained a policy of recess breaks. In examining the test data, the two schools that had limited recess were found to have lower test scores than the school that had maintained the integrity of recess. Other factors could attribute to the lower scores. The findings did reveal that limiting recess appeared to offer no significant gain in scores just as providing recess did not appear to cause any decrease in test scores. Stakeholders interviewed expressed the perception that the benefits of having recess outweighed any potential threat of time lost in the classroom. Recommendations for further research include repeating this study in other school settings on a larger scale to see if the same results are realized.
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Lind, Christoffer. "Computational Studies of Protein Synthesis on the Ribosome and Ligand Binding to Riboswitches." Doctoral thesis, Uppsala universitet, Beräkningsbiologi och bioinformatik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-328583.
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The ribosome is a macromolecular machine that produces proteins in all kingdoms of life. The proteins, in turn, control the biochemical processes within the cell. It is thus of extreme importance that the machine that makes the proteins works with high precision. By using three dimensional structures of the ribosome and homology modelling, we have applied molecular dynamics simulations and free-energy calculations to study the codon specificity of protein synthesis in initiation and termination on an atomistic level. In addition, we have examined the binding of small molecules to riboswitches, which can change the expression of an mRNA. The relative affinities on the ribosome between the eukaryotic initiator tRNA to the AUG start codon and six near-cognate codons were determined. The free-energy calculations show that the initiator tRNA has a strong preference for the start codon, but requires assistance from initiation factors 1 and 1A to uphold discrimination against near-cognate codons. When instead a stop codon (UAA, UGA or UAG) is positioned in the ribosomal A-site, a release factor binds and terminates protein synthesis by hydrolyzing the nascent peptide chain. However, vertebrate mitochondria have been thought to have four stop codons, namely AGA and AGG in addition to the standard UAA and UAG codons. Furthermore, two release factors have been identified, mtRF1 and mtRF1a. Free-energy calculations were used to determine if any of these two factors could bind to the two non-standard stop codons, and thereby terminate protein synthesis. Our calculations showed that the mtRF’s have similar stop codon specificity as bacterial RF1 and that it is highly unlikely that the mtRF’s are responsible for terminating at the AGA and AGG stop codons. The eukaryotic release factor 1, eRF1, on the other hand, can read all three stop codons singlehandedly. We show that eRF1 exerts a high discrimination against near-cognate codons, while having little preference for the different cognate stop codons. We also found an energetic mechanism for avoiding misreading of the UGG codon and could identify a conserved cluster of hydrophobic amino acids which prevents excessive solvent molecules to enter the codon binding site. The linear interaction energy method was used to examine binding of small molecules to the purine riboswitch and the FEP method was employed to explicitly calculate the LIE b-parameters. We show that the purine riboswitches have a remarkably high degree of electrostatic preorganization for their cognate ligands which is fundamental for discriminating against different purine analogs.
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Sandberg, Lars. "Solubility Modelling in Condensed Matter. Dielectric Continuum Theory and Nonlinear Response." Doctoral thesis, KTH, Physics, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3351.
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Grassein, Paul. "Simulation of receptor-ligand recognition mechanisms of human Glutahione Transferases by free energy landscape calculation : Applications to the science of taste and cancer." Thesis, Bourgogne Franche-Comté, 2019. http://www.theses.fr/2019UBFCK013.
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Les protéines hGSTs (Glutathions Transférases humaines) sont des enzymes qui jouent un rôle majeur dans la détoxification de notre organisme et qui sont impliquées dans le développement du cancer. Le mécanisme moléculaire par lesquel les hGSTs sélectionnent une grande diversité de ligands (médicaments, pesticides...) est incompris jusqu’à ce jour. Comprendre les mécanismes de reconnaissance ligand‐récepteur des hGSTs est un enjeu fondamental majeur aux implications sociétales et économiques fortes pour la recherche sur le cancer et pour les industries agroalimentaire et pharmaceutique (cf. projet détaillé). Dans cette thèse nous utiliserons des moyens de calcul à haute performance pour réaliser des simulations de dynamique moléculaire tout atome en solvant explicite des hGSTs (système de plusieurs centaines de milliers d’atomes). L’équipe a une grande expérience de ce type de défis numériques acquise avec la simulation des protéines chaperones HSP. L’approche novatrice de l’analyse des paysages d’énergie libre des HSP développé récemment dans l’équipe sera adaptée à l’étude des GSTs et une nouvelle modélisation du paysage d’énergie libre (couplage de l’approche de Landau et de la dynamique moléculaire) sera développée dans la thèse pour élucider les mécanismes ligand‐récepteur des GSTs. Des ligands odorants et issus de la chimiothérapie seront utilisés comme modèles et les résultats théoriques seront comparés aux données expérimentales obtenues par différentes techniques (calorimétrie, fluorescence, interférométrie de bio‐couches , nanosondes) à l’Université de BourgogneThe hGSTs (Human Glutathione Transferases) proteins are enzymes which play a major role in the detoxification of our organism and which are involved in the development of cancer. The molecular mechanism by which the hGSTs select a wide variety of ligands (drugs, pesticides, etc.) is not understood to this day. Understanding the mechanisms of ligand-receptor recognition of hGSTs is an issue with a major societal and economic implication for the research on cancer and for the agro-food and pharmaceutical industries (see detailed project). In this thesis we will use high performance computing means to carry out simulations of molecular dynamics any atom in explicit hGSTs solver (system of several hundred thousand atoms). The team has extensive experience with this type of digital challenge acquired with the simulation of the HSP chaperone proteins. The approach of the free energy landscape analysis of developed HSPs recently in the team will be adapted to the study of GSTs and a new modeling of the free energy landscape (coupling of the Landau approach and of the molecular dynamics) will be developed in the thesis to elucidate the ligand-receptor mechanisms of GSTs. Odorous ligands derived from chemotherapy will be used as models and the theoretical results will be compared to experimental data obtained by different techniques (calorimetry, fluorescence, bio-layer interferometry, nanosondes) at the University of Burgundy
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Al, Roumi Fosca. "Théorie Lagrangienne Relativiste de la Formation des Grandes Structures : description Intrinsèque des Perturbations et Gravitoélectromagnétisme." Thesis, Lyon 1, 2015. http://www.theses.fr/2015LYO10136/document.
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La dynamique de formation des structures de l'Univers est habituellement décrite dans le cadre du modèle standard de Cosmologie. Cependant, pour que les observations cosmologiques soient cohérentes avec le modèle standard, il est nécessaire de supposer l'existence d'une grande proportion d'éléments de nature inconnue dans le contenu de l'Univers. Pour tenter de résoudre cette énigme, nous ne considèrerons pas d'autres sources dans le contenu de l'Univers que celles ordinaires et resterons dans le cadre de la Relativité Générale. Nous développerons néanmoins une description plus réaliste de la formation de structures dans le cadre de la théorie d'Einstein. Ainsi, contrairement au modèle standard de Cosmologie, nous ne supposerons pas que l'Univers moyenné est une solution homogène et isotrope des équations d'Einstein. Lors de mon travail sous la direction de Thomas Buchert, j'ai participé au développement d'un formalisme perturbatif permettant une description plus réaliste de la dynamique de l'espace-temps. J'ai également contribué à l'obtention de solutions relativistes à la partie gravitoélectrique des équations d'Einstein en généralisant les solutions perturbatives newtoniennes. Ces travaux ont été réalisés dans le cadre d'une approche lagrangienne intrinsèque, évitant ainsi de définir les grandeurs physiques sur un fond plat. L'approche gravitoélectromagnétique que j'ai adoptée m'a permis une interprétation nouvelle et performante des solutions des équations d'Einstein. Enfin, j'ai étudié l'impact de la topologie sur la dynamique des ondes gravitationelles à l'aide d'une description globale de l'hypersurface spatiale, permise par des théorèmes mathématiques puissantsThe dynamics of structure formation in the Universe is usually described by Newtonian numerical simulations and analytical models in the frame of the Standard Model of Cosmology. The structures are then defined on a homogeneous and isotropic background. Such a description has major drawbacks since, to be self-consistent, it entails a large amount of dark components in the content of the Universe. To address the problem of dark matter and dark energy, we will neither suppose that exotic sources contribute to the content of the Universe, nor that General Relativity is obsolete. We will develop a more realistic description of structure formation in the frame of General Relativity and thus no longer assume that the average model is a homogeneous-isotropic solution of the Einstein equations, as claimed by the Standard Model of Cosmology. During my work under the supervision of Thomas Buchert, I contributed to the development of the perturbative formalism that enables a more realistic description of spacetime dynamics. In the framework of the intrinsic Lagrangian approach, which avoids defining physical quantities on a flat background, I contributed to the building of relativistic solutions to the gravitoelectric part of the Einstein equations from the generalization of the Newtonian perturbative solutions. Moreover, the gravitoelectromagnetic approach I worked with has provided a new understanding of the dynamics of the analytical solutions to the field equations. Finally, treating globally the spatial manifold, I used powerful mathematical tools and theorems to describe the impact of topology on the dynamics of gravitational waves
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JAYASINGHE, MANORI I. "HEAVY-METAL-ION TRANSPORT IN NANOPOROUS SELECTIVE-MEMBRANES: THEORY AND EXPERIMENT." University of Cincinnati / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1186764159.
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Schweinefuß, Maria E., Sergej Springer, Igor A. Baburin, Todor Hikov, Klaus Huber, Stefano Leoni, and Michael Wiebcke. "Zeolitic imidazolate framework-71 nanocrystals and a novel SOD-type polymorph: solution mediated phase transformations, phase selection via coordination modulation and a density functional theory derived energy landscape." Royal Society of Chemistry, 2014. https://tud.qucosa.de/id/qucosa%3A36102.
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We report a rapid additive-free synthesis of nanocrystals (NCs) of RHO-type ZIF-71 (1) of composition [Zn(dcim)₂] (dcim = 4,5-dichloroimidazolate) in 1-propanol as solvent at room temperature. NC-1 has a size of 30–60 nm and exhibits permanent microporosity with a surface area (SBET = 970 m² g−¹) comparable to that of microcrystalline material. When kept under the mother solution NC-1 undergoes transformation into a novel SOD-type polymorph (2), which in turn converts into known ZIF-72 (3) with lcs topology. It is shown that microcrystals (MCs) of 2 can be favourably synthesised using 1-methylimidazole as a coordination modulator. NC-2 with size <200 nm was prepared using NC-ZIF-8 as a template with SOD topology in a solvent assisted ligand exchange-related process. DFT-assisted Rietveld analysis of powder XRD data revealed that novel polymorph 2 possesses an unusual SOD framework conformation. 2 was further characterised with regard to microporosity (SBET = 597 m² g−¹) and thermal as well as chemical stability. DFT calculations were performed to search for further potentially existing but not-yet synthesised polymorphs in the [Zn(dcim)₂] system.
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Luukkonen, Sohvi. "Hydration of drug-like molecules with molecular density functional theory and the hybrid-4th-dimension Monte Carlo approach." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASF030.
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Le développement d’un médicament prend en moyenne plus de 10 ans pour un coût de 1 Mrd de dollars. Pour accélérer le processus et diminuer le coût, on utilise des méthodes in-silico lors de l’étape de découverte qui consiste à cribler ~10⁵ molécules de type médicament pour proposer quelques candidats à l’étape préclinique. Le critère majeur est l’affinité entre la molécule potentielle et la cible biologique. L’interaction se passant dans notre corps: cette affinité doit être prédite dans l’eau et le médicament doit être soluble dans l’eau pour avoir accès à la cible. Globalement, les effets de solvatation ont un rôle important dans la conception de médicaments. Numériquement, pour un champ de force donné, la solvatation peut être étudiée par des méthodes de simulation exactes mais coûteuses, par des modèles de continuum rapides mais qui ignorent la nature moléculaire du solvant, enfin par des théories des liquides approximatives mais capables de garder l’information moléculaire du solvant tout en diminuant le temps de calcul. L’objectif de cette thèse étant la prédiction des énergies libres d’hydratation (ELH) de molécules de type médicament par des méthodes qui soient les plus précises et plus rapides possibles, elle se concentre sur deux approches originales: Le Monte-Carlo hybride à 4ème dimension, une nouvelle méthode pour calculer les ELH selon le principe de Jarzynski à partir simulations courtes hors-équilibre pendant lesquelles on introduit ou retire le soluté doucement depuis le solvant avec un paramètre de couplage dépendant du temps. Nous montrons que cette approche est capable de prédire les ELH de molécules de type pharmaceutique 4-6 fois plus rapidement que l’approche classique de perturbation de l’énergie libre. La théorie de la fonctionnelle de densité moléculaire, une approche de théorie des liquides qui permet l’étude des propriétés de solvatation de n’importe quelle soluté rigide. Dans son état actuel, dans l’approximation hyper-netted-chain couplée à une correction de pression, nous montrons qu’elle est capable de prédire les ELH des mêmes molécules avec une précision de respectivement 0.5 ou 1.0 kcal/mol par rapport aux simulations ou aux données expérimentales, avec une accélération de calcul de l’ordre de 10³-10⁴ par rapport aux simulations. H4D-MC est considéré ici comme une source de références pour développer plus avant la MDFT, elle-même une méthode suffisamment rapide pour être envisagée dans un processus de criblage haut-débitThe development of a drug takes on average over 10 yr. for a cost of 1B dollars. To speed up the process, and reduce its cost, in-silico methods are used at the drug discovery stage. It consists of screening ~10⁵ drug-like molecules to propose few candidates to the pre-clinical stages. The main criterion is the affinity between the potential drug molecule and biological target. As the interaction happens the body, these affinities need to be predicted in water and the molecule needs to be water-soluble to access the receptor. Overall, solvation properties play an important role in drug design. Numerically, for a given force-field, solvation can be studied either with exact but time-consuming simulation methods, fast continuum models that lose the molecular nature of the solvent, or approximate liquid state theories that keep the solvent molecular information while speeding-up the computation. In this thesis, we focus on the prediction of the hydration free energies (HFE) of drug-like molecules with methods that are as fast and precise as possible, and we concentrate on two original approaches: Hybrid-4th-dimension Monte Carlo, a novel method that computes the HFEs according to the Jarzynski principle from short non-equilibrium simulations in which the solute is inserted or removed from the solvent with a time-depending coupling parameter. This approach is shown to predict the HFEs of drug-like molecules 4-6 times faster than the classical free energy perturbation approach. Molecular density functional theory, a liquid-state-theory approach that allows the study of the equilibrium solvation properties of any rigid solute. In its current level, the hyper netted-chain approximation coupled with a pressure correction, it is shown to predict the HFEs of drug-like molecules within 0.5 and 1.0 kcal/mol of simulations and experimental data, respectively, for an average computational speed-up 10³-10⁴ with respect to simulations. H4D-MC is considered here as a source of reference data for MDFT developments. MDFT is itself fast enough to be foreseen in a high-throughput screening pipeline
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Salehi, Kasmaei Babak. "NONEQUILIBRIUM PROBES OF THE QUARK-GLUON PLASMA." Kent State University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=kent1627035862984205.
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Kerman, Solmaz Saime. "Scalar Meson Effects In Radiative Decays Of Vector Mesons." Phd thesis, METU, 2003. http://etd.lib.metu.edu.tr/upload/57968-0/index.pdf.
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The role of scalar mesons in radiative vector meson decays is
investigated. The effects of scalar-isoscalar f_{0}(980) and
scalar-isovector a_{0}(980) mesons are studied in the mechanism of the radiative Phi->pi{+}pi{-}gamma and phi->
pi{0}eta gamma decays, respectively. A phenomenological approach is used to study the radiative phi->
pi{+}p{-}gamma decay by considering the contributions of sigma-meson, rho-meson and f_{0}-meson. The interference effects between different contributions are analyzed and the branching ratio for this decay is calculated. The radiative phi->
pi{0}eta gamma decay is studied within the framework of a phenomenological approach in which the contributions of rho-meson, chiral loop and a_{0}-meson are considered. The interference effects between different contributions are examined and the coupling constants g_{phi a_{0} gamma} and g_{a_{0}K{+}K{-}} are estimated using the experimental branching ratio for the phi->
pi{0}eta gamma decay. Furthermore, the radiative rho{0}pi{+}pi{-}gamma$ and rho{0}->
pi{0}pi{0}gamma decays are studied to investigate the role of scalar-isoscalar sigma-meson. The branching ratios of the rho{0}->
pi{+}pi{-}gamma and rho{0}->
pi{0}pi{0}gamma decays are calculated using a phenomenological approach by adding to the amplitude calculated within the framework of chiral perturbation theory and vector meson dominance the amplitude of sigma-meson intermediate state. In all the decays studied the scalar meson intermediate states make important contributions to the overall amplitude.
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Adamovic, Ivana. "Solvation!" Washington, D.C. : Oak Ridge, Tenn. : United States. Dept. of Energy. Office of Science ; distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy, 2004. http://www.osti.gov/servlets/purl/835373-NLtQXD/webviewable/.
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19 Dec 2004.Published through the Information Bridge: DOE Scientific and Technical Information. "IS-T 2009" Ivana Adamovic. 12/19/2004. Report is also available in paper and microfiche from NTIS.
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Chaput, Ludovic. "Compréhension de l'énantiosélectivité de la lipase B de Candida antarctica : étude par modélisation moléculaire et expérimentation." Phd thesis, Université de La Rochelle, 2012. http://tel.archives-ouvertes.fr/tel-00825876.
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La lipase B de Candida antarctica (CALB) est un enzyme présentant des propriétés énantiosélectives très intéressantes pour l'obtention de molécules énantio pures par dédoublement cinétique de mélanges racémiques,molécules utilisées comme synthons dans l'industrie pharmaceutique. En effet, le principe actif de nombreux médicaments est efficace sous une forme énantio pure, l'autre forme chirale pouvant se révéler délétère pour l'organisme.Les travaux de la thèse s'intéressent à mieux comprendre l'origine de l'énantiosélectivité de la lipase B de Candida antarctica, en particulier pour la résolution d'alcools secondaires par des réactions de transestérification.Nous utilisons pour la première fois la méthode de la perturbation de l'énergie libre pour estimer la différence d'énergie libre entre les intermédiaires tétraédriques obtenus avec les formes R et S d'alcools énantiomères pour une série d'alcools secondaires, dans le but de prédire in silico l'énantiosélectivité de la CALB. Les paramètres cinétiques apparents d'une réaction avec deux alcools substrats énantiopurs sont expérimentalement déterminés et permettent de définir la contribution respective du Km et du kcat de chaque énantiomère pour la définition de l'énantiosélectivité. L'étude expérimentale de l'effet d'empreinte par des molécules co-substrats est réalisée,ainsi qu'une étude par modélisation moléculaire de l'effet d'empreinte par le premier ester substrat de la réaction qui pourrait modifier la conformation du site actif de la CALB. La troisième partie porte sur l'étude de la CALB et de trois variants (T42V, S47A et T42V/S47A) chez lesquels les acides aminés dans la poche stéréospécifiques ont mutés. T42V et S47A permettent d'obtenir une augmentation de l'énantiosélectivité. L'étude propose une étude détaillée de la conformation du site actif à partir de simulations de trajectoires de dynamique moléculaire
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Hartmann, R. (Robert). "Flotation using cellulose-based chemicals." Doctoral thesis, Oulun yliopisto, 2018. http://urn.fi/urn:isbn:9789526219806.
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Abstract Flotation is a well-known and widely used technique for the separation of particles smaller than 250 µm, but efficient performance requires the use of various synthetic chemicals which can potentially damage the health of humans and animals and pollute the environment. Consequently, their replacement through a more environment-friendly and sustainable alternative has been demanded. One promising candidate is cellulose, which is an abundant natural polymer that is environment-friendly and can be treated chemically and physically to yield tailored properties and thus a potential for use in processes such as flotation. This work focuses on the use of cellulose-based reagents in flotation processes to replace the often harmful conventional reagents derived from mineral oil, plant oils or animal fats. The physico-chemical properties of cellulose differ from those of conventional reagents, leading to differences in performance during flotation. In particular, the chemical and morphological heterogeneity of cellulose affects its properties and thus its interaction with minerals and water. Consequently, its use requires the study of the fundamentals of flotation and their application including the physico-chemical heterogeneity of cellulose to determine the optimum conditions and enable efficient performance. This work focuses on the determination of the thermodynamic surface energetics of solid particles and changes in this after reagent adsorption, using the inverse gas chromatography technique in a dry atmosphere. Furthermore, interactions between cellulose and minerals immersed in water are investigated using the DLVO theory, the interaction forces between cellulose and the minerals being derived and correlated with flotability. The importance of free surface charges is then considered by investigating the electric surface potential of cellulose-coated minerals in connection with particle-bubble attachment efficiency. At the same time, conventional amphiphilic reagents are used and its performances are related to cellulose-based reagentsTiivistelmä Vaahdotus on kaivannaisteollisuudessa laajasti käytössä oleva prosessi, jonka avulla saadaan erotettua tehokkaasti pieniä, alle 250 µm kokoisia partikkeleita. Vaahdotuksen apuaineena käytetään erilaisia synteettisiä kemikaaleja, jotka voivat aiheuttaa harmia ympäristölle. Siksi niiden korvaaminen ympäristöystävällisemmillä vaihtoehdoilla on tärkeää. Yksi lupaava vaihtoehto korvaavaksi materiaaliksi on selluloosa. Selluloosa on uusiutuva ja ympäristöystävällinen luonnonpolymeeri, josta voidaan valmistaa kemiallisesti ja fysikaalisesti käsittelemällä erilaisia biokemikaaleja. Näitä voidaan soveltaa erilaisissa prosesseissa, myös vaahdotuksessa. Tässä työssä keskitytään selluloosapohjaisten kemikaalien käyttöön vaahdotuksessa tavanomaisten, usein haitallisten synteettisten kemikaalien korvaamiseksi. Selluloosan fysikaaliskemialliset ominaisuudet eroavat synteettisten vaahdotuskemikaalien ominaisuuksista, mikä vaikuttaa niiden vuorovaikutukseen mineraalien ja veden kanssa. Erityisesti selluloosan kemiallinen ja morfologinen heterogeenisuus on keskeinen tekijä. Selluloosan hyödyntäminen tulevaisuuden vaahdotuskemikaalina edellyttää selluloosan ja mineraalien vuorovaikutuksen syvällistä ymmärtämistä. Tässä työssä tutkitaan selluloosan ja mineraalien vuorovaikutusta sekä IGC-menetelmän avulla, että DLVO-teorian että pintavarausmittausten avulla. Lisäksi tutkitaan selluloosan ja mineraalien vuorovaikutusvoimien yhteyttä vaahdotusprosessin onnistumiseen ja saavutettuja tuloksia verrataan kaupallisten reagenssien toimintaan
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Senanayake, Nishan M. "Exploring Heusler Alloys as Catalysts for Ammonia Dissociation." Bowling Green State University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1467314800.
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Drechsel, Nils Jan Daniel 1980. "Development of a multiscale protocol for the study of energetics of protein dymanics." Doctoral thesis, Universitat Pompeu Fabra, 2013. http://hdl.handle.net/10803/125071.
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Multiscale Molecular Dynamics is a popular trend in the field of computational chemistry and physics. Coarse-grained force-fields have been around for years, and used independently, but used cooperatively with all-atom force-fields combines their advantages and cancels their disadvantages. This seems to be the case, however, only when they are both compatible. In this thesis, a Multiscale Molecular Dynamics Protocol is introduced, based on earlier work by Benjamin Messer, Z. Fan, Arieh Warshel, and in other parts by Christopher Fennel and Ken Dill. The protocol consists of the following tool-set:
• A parametrization machinery that created a new coarse-grained force-field named AmberCG.
• A multiscale thermodynamic cycle utilized within a free energy perturbation context to cooperatively use the best of coarse-grained and all-atom force-fields.
• A collective variable that performs a linearization of the phase space to improve separation of product and reactant states.
• A new algorithm to calculate functional quantities on spheres bounded by complicated solvent accessible surface areas - which as a special case calculates the amount of solvent accessible surface area.
• A novel algorithm based on simple one dimensional Depth-Buffers, to identify atoms which actively form the boundary of the solvent accessible surface areas.
Executing the protocol involves the following steps:
1. Construction of a coarse-grained force-field, based on an all-atom force-field. This involves setting up coarse-grained potentials and optimization of their parameters against selected reference structures and conformations.
2. Parametrization of a solvation model which is compatible to the force-field.
3. Usage of the coarse-grained force-field to sample the conformational space of a reaction.
4. Correction of the coarse-grained results with an all-atom force-field.
5. Analysis of the results using appropriate collective coordinates.
6. Reiteration until accuracies are met.
Alternatively, instead of using the methods in the protocol, they
can be utilized stand-alone. They simplify calculations, thus provid-
ing speed-ups, while at the same time aiming to maintain or improve
accuracy. Of course, there is no free lunch, and often the methods will
include inaccuracies that exceed an acceptable threshold. However, the
multiscale protocol is meant to be seen as an iterative technique, in
which deficiency can be detected, and the protocol adjusted to restore
balance.Las simulaciones de dinámica molecular multiescala (Multiscale Molecular Dynamics) son una tendencia al alza en el sector de la Química y la Física computacionales. Los coarse-grained force-fields o campos de fuerza de grano grueso han existido desde hace años, utilizados de forma independiente, y también en cooperación con all-atom force-fields o campos de fuerza de todos los átomos dónde se combinan sus ventajas y cancelan sus desventajas. En este último caso sólo es cierto cuando los dos force-fields son compatibles. En esta tesis, introduzco un protocolo de Multiscale Molecular Dynamics basado en parte a trabajos anteriores de Benjamin Messer, Z. Fan, Arieh Warshel, y también en los de Christopher Fennell y Ken Dill. El protocolo consiste el siguiente conjunto de herramientas: 1. Un método de parametrización con cuál creé un nuevo coarse-grained force-field llamado AmberCG. 2. Un ciclo termodinámico multiescala utilizado en un contexto de perturbación de energía libre para usar cooperativamente el mejor de los coarse-grained force-fields y el de los all-atom force-fields. 3. Una variable colectiva que realiza una liberalización del espacio de fases para mejorar la separación de los estados de productos y reactivo. 4. Un nuevo algoritmo para calcular las cantidades funcionales en esferas limitadas por complicadas superficies accesibles al solvente - que como un caso especial calcula la cantidad de superficie accesible a solvente. 5. Un nuevo algoritmo basado en un buffer de profundidad, para identificar los átomos que forman activamente el límite de las superficies accesibles al solvente. La ejecución del protocolo implica los siguientes pasos: 1. Construcción de un coarse-grained force-field, basado en un all-atom force-field. Esto implica la creación de potenciales coarse-grained y la optimización de sus parámetros contra las estructuras de referencia seleccionados y sus conformaciones. 2. Parametrización de un modelo de solvatación compatible con el force-field. 3. Uso del coarse-grained force-field para muestrear el espacio con formacional de una reacción. 4. La corrección de los resultados coarse-grained con un all-atom force-field. 5. Análisis de los resultados utilizando coordenadas colectivas adecuadas. 6. Repetición hasta alcanzar las precisiones deseadas. Alternativamente, los métodos del protocolo pueden ser utilizados de forma independiente. Esto simplifica los cálculos y procura mantener, si no mejorar, la precisión. Sin embargo, todo tiene un coste y con frecuencia, los métodos incluirán inexactitudes que superarán el umbral aceptable. Aun y así, el protocolo multiescala es una técnica iterativa, en la que la deficiencia puede ser detectada, y el protocolo ajustado para restablecer el equilibrio.
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Seitenfuss, Alan Bourscheidt. "On the behavior of a linear elastic peridynamic material." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/18/18134/tde-22062017-100938/.
Full textAbstract:
The peridynamic theory is a generalization of classical continuum mechanics and takes into account the interaction between material points separated by a finite distance within a peridynamic horizon δ. The parameter δ corresponds to a length scale and is treated as a material property related to the microstructure of the body. Since the balance of linear momentum is written in terms of an integral equation that remains valid in the presence of discontinuities, the peridynamic theory is suitable for studying the material behavior in regions with singularities. The first part of this work concerns the evaluation of the properties of a linear elastic peridynamic material in the context of a three-dimensional state-based peridynamic theory, which uses the difference displacement quotient field in the neighborhood of a material point and considers both length and relative angle changes. This material model is based upon a free energy function that contains four material constants, being, therefore, different from other peridynamic models found in the literature, which contain only two material constants. Using convergence results of the peridynamic theory to the classical linear elasticity theory in the limit of small horizons and a correspondence argument between the free energy function and the strain energy density function from the classical theory, expressions were obtained previously relating three peridynamic constants to the classical elastic constants of an isotropic linear elastic material. To calculate the fourth peridynamic material constant, which couples both bond length and relative angle changes, the correspondence argument is used once again together with the strain field of a linearly elastic beam subjected to pure bending. The expression for the fourth constant is obtained in terms of the Poisson\'s ratio and the shear elastic modulus of the classical theory. The validity of this expression is confirmed through the consideration of other experiments in mechanics, such as bending of a beam by terminal loads and anti-plane shear of a circular cylinder. In particular, numerical results indicate that the expressions for the constants are independent of the experiment chosen. The second part of this work concerns an investigation of the behavior of a one-dimensional linearly elastic bar of length L in the context of the peridynamic theory; especially, near the ends of the bar, where it is expected that the behavior of the peridynamic bar may be very different from the behavior of a classical linear elastic bar. The bar is in equilibrium without body force, is fixed at one end, and is subjected to an imposed displacement at the other end. The bar has micromodulus C, which is related to the Young\'s modulus E in the classical theory through different expressions found in the literature. Depending on the expression for C, the displacement field may be singular near the ends, which is in contrast to the linear behavior of the displacement field observed in classical linear elasticity. In spite of the above, it is also shown that the peridynamic displacement field converges to its classical counterpart as the peridynamic horizon tends to zero.A teoria peridinâmica é uma generalização da teoria clássica da mecânica do contínuo e considera a interação de pontos materiais devido a forças que agem a uma distância finita entre si, além da qual considera-se nula a força de interação. Por ter o balanço de momento linear formulado como uma equação integral que permanece válida na presença de descontinuidades, a teoria peridinâmica é adequada para o estudo do comportamento de materiais em regiões com singularidades. A primeira parte deste trabalho consiste no cálculo das propriedades de um material peridinâmico elástico linear no contexto de uma teoria peridinâmica de estado, linearmente elástica e tridimensional, que utiliza o campo quociente de deslocamento relativo na vizinhança de um ponto material e leva em conta mudanças relativas angulares e de comprimento. Esse modelo utiliza uma função energia livre que apresenta quatro constantes materiais, sendo, portanto, diferente de outros modelos peridinâmicos investigados na literatura, os quais contêm somente duas constantes materiais. Utilizando resultados de convergência da teoria peridinâmica para a teoria de elasticidade linear clássica no limite de pequenos horizontes e um argumento de correspondência entre as funções energia livre proposta e densidade de energia de deformação da teoria clássica, expressões para três constantes peridinâmicas foram obtidas em função das constantes de um material elástico e isotrópico da teoria clássica. O argumento de correspondêmcia, em conjunto com o campo de deformações de uma viga submetida à flexão pura, é utilizado para calcular a quarta constante peridinâmica do material, que relaciona mudanças angulares relativas e de comprimentos das ligações entre as partículas. Obtem-se uma expressão para a quarta constante em termos do coeficiente de Poisson e do módulo de elasticidade ao cisalhamento da teoria clássica. A validade dessa expressão é confirmada por meio da consideração de outros experimentos da mecânica, tais como flexão de um viga por cargas terminais e cisalhamento anti-plano de um eixo cilíndrico. Em particular, os resultados numéricos indicam que as expressões para as constantes são independentes do experimento escolhido. A segunda parte deste trabalho consiste em uma investigação do comportamento de uma barra unidimensional linearmente elástica de comprimento L no contexto da teoria peridinâmica; especialmente, próximo às extremidades da barra, onde espera-se que o comportamento da barra peridinâmica possa ser muito diferente do comportamento de uma barra elástica linear clássica. A barra está em equilíbrio e sem força de corpo, fixa em uma extremidade, e sujeita a deslocamento imposto na outra extremidade. A barra possui micromódulo C, o qual está relacionado ao módulo de Young E da teoria clássica por meio de diferentes expressões encontradas na literatura. Dependendo da expressão para C, o campo de deslocamento pode ser singular próximo às extremidades, o que contrasta com o comportamento linear do campo de deslocamento observado na elasticidade linear clássica. Apesar disso, é mostrado também que o campo de deslocamento peridinâmico converge para o campo de deslocamento da teoria clássica quando o horizonte peridinâmico tende a zero.