Дисертації з теми "Energy of binding"
Оформте джерело за APA, MLA, Chicago, Harvard та іншими стилями
Ознайомтеся з топ-50 дисертацій для дослідження на тему "Energy of binding".
Біля кожної праці в переліку літератури доступна кнопка «Додати до бібліографії». Скористайтеся нею – і ми автоматично оформимо бібліографічне посилання на обрану працю в потрібному вам стилі цитування: APA, MLA, «Гарвард», «Чикаго», «Ванкувер» тощо.
Також ви можете завантажити повний текст наукової публікації у форматі «.pdf» та прочитати онлайн анотацію до роботи, якщо відповідні параметри наявні в метаданих.
Переглядайте дисертації для різних дисциплін та оформлюйте правильно вашу бібліографію.
Ranganathan, Anirudh. "Protein – Ligand Binding: Estimation of Binding Free Energies." Thesis, KTH, Skolan för kemivetenskap (CHE), 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-147527.
Повний текст джерелаTaylor, Paul Andrew. "Nuclear Binding Energy in Terms of a Redefined (A)symmetry Energy." Thesis, Boston College, 2004. http://hdl.handle.net/2345/460.
Повний текст джерелаWe investigate the structure of the equation of state of finite nuclear matter by examining the nature of isospin dependence in the (a)symmetry energy term. In particular, we include in the description of the binding energy fourth-order dependence with respect to the asymmetry factor, (N-Z)/A, and the regime of the l=0 Landau parameter, F0´ , is required to be less than –1. This modified equation predicts a minimum binding energy where N≠Z, in addition to the standard symmetric minimum when N=Z. Results with the new asymmetry energy term are compared with experimental binding and symmetry energies from standard semi-empirical mass formulas. Importantly, this method reveals one possible mechanism for producing the phenomenon of neutron excess which is seen in physical nuclei
Thesis (BS) — Boston College, 2004
Submitted to: Boston College. College of Arts and Sciences
Discipline: Physics
Discipline: College Honors Program
Cuthbert, A. "Positronium binding to metal surfaces." Thesis, University of Sussex, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.382489.
Повний текст джерелаMercer, James Lee Jr. "New binding models for elemental semiconductors." Diss., Georgia Institute of Technology, 1992. http://hdl.handle.net/1853/27909.
Повний текст джерелаHermansson, Anders. "Calculating Ligand-Protein Binding Energies from Molecular Dynamics Simulations." Thesis, KTH, Skolan för kemivetenskap (CHE), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-170722.
Повний текст джерелаYildirim, Ozlem. "Energy Bands Of Tlse And Tlinse2 In Tight Binding Model." Master's thesis, METU, 2005. http://etd.lib.metu.edu.tr/upload/12606440/index.pdf.
Повний текст джерелаRocklin, Gabriel Jacob. "Predicting charged protein-ligand binding affinities using free energy calculations." Thesis, University of California, San Francisco, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3587895.
Повний текст джерелаPredicting protein-ligand binding free energy from physical principles is a grand challenge in biophysics, with particular importance for drug discovery. Free energy calculations compute binding affinities by using classical mechanics to model the protein and ligand at atomic resolution, and using statistical mechanics to analyze simulations of these models. The binding affinities computed from these simulations are fully rigorous and thermodynamically correct for the model (with adequate sampling), and will agree with experimentally measured binding affinities if the model is accurate. Because free energy calculations capture the full statistical complexity of binding for flexible molecules at ambient temperature, they offer the greatest potential for quantitative accuracy of any physical method for predicting binding.
Here, I (& coauthors) present several studies relating to using free energy calculations to predict protein-ligand binding affinities for charged compounds. First, we introduce the Separated Topologies method, an approach for using free energy calculations to predict relative binding affinities of unrelated ligands. This method is useful for studying charged compounds because charged compounds are very difficult to study using absolute binding calculations, increasing the importance of relative binding calculations. Second, we use free energy calculations to predict absolute binding affinities for charged molecules to a simplified protein binding site, which is specially designed for studying charged interactions. These predictions are compared to new experimental affinity measurements and new high-resolution structures of the protein-ligand complexes. We find that all affinities are predicted to be too strong, and that this error is directly correlated with the polarity of each ligand. By uniformly weakening the strength of electrostatic interactions, we are more successful at predicting binding affinity. Third, we design and validate an analytical correction scheme to correct binding free energy calculations of ions for artifacts caused by the periodic boundary conditions employed in simulations. Fourth, we examine the sensitivity of binding affinities from free energy calculations to the force field parameters used in the simulations. This provides insight into the strength of electrostatic interactions in protein simulations, complementing our previous work comparing simulation results to experiments. Finally, we discuss potential future directions of this work.
Carlsson, Jens. "Challenges in Computational Biochemistry: Solvation and Ligand Binding." Doctoral thesis, Uppsala University, Department of Cell and Molecular Biology, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8738.
Повний текст джерелаAccurate calculations of free energies for molecular association and solvation are important for the understanding of biochemical processes, and are useful in many pharmaceutical applications. In this thesis, molecular dynamics (MD) simulations are used to calculate thermodynamic properties for solvation and ligand binding.
The thermodynamic integration technique is used to calculate pKa values for three aspartic acid residues in two different proteins. MD simulations are carried out in explicit and Generalized-Born continuum solvent. The calculated pKa values are in qualitative agreement with experiment in both cases. A combination of MD simulations and a continuum electrostatics method is applied to examine pKa shifts in wild-type and mutant epoxide hydrolase. The calculated pKa values support a model that can explain some of the pH dependent properties of this enzyme.
Development of the linear interaction energy (LIE) method for calculating solvation and binding free energies is presented. A new model for estimating the electrostatic term in the LIE method is derived and is shown to reproduce experimental free energies of hydration. An LIE method based on a continuum solvent representation is also developed and it is shown to reproduce binding free energies for inhibitors of a malaria enzyme. The possibility of using a combination of docking, MD and the LIE method to predict binding affinities for large datasets of ligands is also investigated. Good agreement with experiment is found for a set of non-nucleoside inhibitors of HIV-1 reverse transcriptase.
Approaches for decomposing solvation and binding free energies into enthalpic and entropic components are also examined. Methods for calculating the translational and rotational binding entropies for a ligand are presented. The possibility to calculate ion hydration free energies and entropies for alkali metal ions by using rigorous free energy techniques is also investigated and the results agree well with experimental data.
Green, David Francis 1975. "Optimization of electrostatic binding free energy : applications to the analysis and design of ligand binding in protein complexes." Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/16888.
Повний текст джерелаVita.
Includes bibliographical references (p. 279-298).
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Electrostatic interactions play an important role in determining the energetics of association in biomolecular complexes. Previous work has shown that, within a continuum electrostatic model, for any given complex there exists a ligand charge distribution which optimizes the electrostatic binding free energy - the electrostatic complement of the target receptor. This electrostatic affinity optimization procedure was applied to several systems both in order to understand the role of electrostatic interactions in natural systems and as a tool in the design of ligands with improved affinity. Comparison of the natural and optimal charges of several ligands of glutaminyl-tRNA synthetase from E. coli, an enzyme with a strong natural requirement for specificity, shows remarkable similarity in many areas, suggesting that the optimization of electrostatic interactions played a role in the evolution of this system. The optimization procedure was also applied to the design of improvements to two inhibitors of HIV-1 viral-cell membrane fusion. Two tryptophan residues that are part of a D-peptide inhibitor were identified as contributing most significantly to binding, and a novel computational screening procedure based on the optimization methodology was developed to screen a library of tryptophan derivatives at both positions. Additionally, the optimization methodology was used to predict four mutations to standard amino acids at three positions on 5-Helix, a protein inhibitor of membrane fusion. All mutations were computed to improve the affinity of the inhibitor, with a five hundred-fold improvement calculated for one triple mutant.
(cont.) In the complex of b-lactamase inhibitor protein with TEM1 b-lactamase, a novel type of electrostatic interaction was identified, with surface exposed charged groups on the periphery of the binding interface projecting significant energetic effects through as much as 10 A of solvent. Finally, a large number of ab initio methods for determining partial atomic charges on small molecules were evaluated in terms of their ability to reproduce experimental values in continuum electrostatic calculations, with several preferred methods identified.
by David Francis Green.
Ph.D.
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.
Повний текст джерелаNandigrami, Prithviraj. "Cooperative allosteric ligand binding in calmodulin." Kent State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=kent1507302866723977.
Повний текст джерелаBruzzi, Eleonora. "Binding energies in large ionic clusters from kinetic energy release measurements." Thesis, University of Nottingham, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.717020.
Повний текст джерелаVoukelatos, Dimitrios. "Binding energy and geometry for the adsorption of NO on Cu." Thesis, University of Birmingham, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.421710.
Повний текст джерелаCabedo, Martinez Ana. "Computing free energy, binding and competition within Fragment Based Drug Discovery." Thesis, University of Southampton, 2016. https://eprints.soton.ac.uk/403850/.
Повний текст джерелаLee, Lee-Peng 1969. "Optimization of electrostatic binding free energy : application to barnase and barstar." Thesis, Massachusetts Institute of Technology, 1999. http://hdl.handle.net/1721.1/85331.
Повний текст джерелаMiao, Yi. "Shape-Dependent Molecular Recognition of Specific Sequences of DNA by Heterocyclic Cations." Digital Archive @ GSU, 2006. http://digitalarchive.gsu.edu/chemistry_diss/4.
Повний текст джерелаWall, Ian. "New simulation methods for the prediction of binding free energies." Thesis, University of Southampton, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313217.
Повний текст джерелаCho, Samuel Sung-Il. "Energy landscapes for protein folding, binding, and aggregation simple funnels and beyond /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2007. http://wwwlib.umi.com/cr/ucsd/fullcit?p3244327.
Повний текст джерелаTitle from first page of PDF file (viewed February 23, 2007). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 99-106).
Durmaz, Vedat [Verfasser]. "Atomistic Binding Free Energy Estimations for Biological Host–Guest Systems / Vedat Durmaz." Berlin : Freie Universität Berlin, 2016. http://d-nb.info/1122111215/34.
Повний текст джерелаQin, Ting. "Binding-energy relations and equations of state for non-magnetic transition metals." Thesis, University of Oxford, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.497079.
Повний текст джерелаKim, Jeongnim. "Total energy calculations of large scale systems in a tight- binding representation /." The Ohio State University, 1996. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487936356157839.
Повний текст джерелаHe, Peng. "FREE ENERGY SIMULATIONS AND STRUCTURAL STUDIES OF PROTEIN-LIGAND BINDING AND ALLOSTERY." Diss., Temple University Libraries, 2018. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/531465.
Повний текст джерелаPh.D.
Protein-ligand binding and protein allostery play a crucial role in cell signaling, cell regulation, and modern drug discovery. In recent years, experimental studies of protein structures including crystallography, NMR, and Cryo-EM are widely used to investigate the functional and inhibitory properties of a protein. On the one hand, structural classification and feature identification of the structures of protein kinases, HIV proteins, and other extensively studied proteins would have an increasingly important role in depicting the general figures of the conformational landscape of those proteins. On the other hand, free energy calculations which include the conformational and binding free energy calculation, which provides the thermodynamics basis of protein allostery and inhibitor binding, have proven its ability to guide new inhibitor discovery and protein functional studies. In this dissertation, I have used multiple different analysis and free energy methods to understand the significance of the conformational and binding free energy landscapes of protein kinases and other disease-related proteins and developed a novel alchemical-based free energy method, restrain free energy release (R-FEP-R) to overcome the difficulties in choosing appropriate collective variables and pathways in conformational free energy methods like umbrella sampling and metadynamics.
Temple University--Theses
Bertazzo, Martina <1990>. "Dynamic Docking, Path Analysis and Free Energy Computation in Protein-Ligand Binding." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2020. http://amsdottorato.unibo.it/9290/1/TESI.pdf.
Повний текст джерелаBushell, Karen Lynne. "The coordination chemistry of polypyridyl ligands with secondary macrocyclic binding sites." Thesis, University of Bristol, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301986.
Повний текст джерелаChen, Zhihong. "Modeling Ion Binding in the Chloride Transporter." University of Cincinnati / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439310689.
Повний текст джерелаMartin, Sarah Friede. "Fluorescence resonance energy transfer studies of protein interactions." Thesis, St Andrews, 2008. http://hdl.handle.net/10023/537.
Повний текст джерелаNervall, Martin. "Binding Free Energy Calculations on Ligand-Receptor Complexes Applied to Malarial Protease Inhibitors." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8338.
Повний текст джерелаMohamed, Noor Asidah Binti. "The evaluation of protein-ligand binding free energies using advanced potential energy function." Thesis, University of Southampton, 2018. https://eprints.soton.ac.uk/428049/.
Повний текст джерелаIkeda, Atsushi. "Development of New Resonance Theory and Theoretical Evaluation of Metal-Ligand Binding Energy." 京都大学 (Kyoto University), 2008. http://hdl.handle.net/2433/57275.
Повний текст джерелаGobbo, Dorothea <1989>. "Free energy and kinetics in protein-ligand binding: experimental measurements and computational estimates." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2019. http://amsdottorato.unibo.it/8982/1/Gobbo_Dorothea_tesi.pdf.
Повний текст джерелаQawasmeh, Yasmeen Jamal [Verfasser]. "Two-Dimensional Potential Energy Surfaces of Binding CO/NO with Coinage Metals / Yasmeen Qawasmeh." Berlin : Freie Universität Berlin, 2020. http://d-nb.info/1212435400/34.
Повний текст джерелаQawasmeh, Yasmeen [Verfasser]. "Two-Dimensional Potential Energy Surfaces of Binding CO/NO with Coinage Metals / Yasmeen Qawasmeh." Berlin : Freie Universität Berlin, 2020. http://d-nb.info/1212435400/34.
Повний текст джерелаOrro, Graña Adolfo. "Examination of the role of binding site water molecules in molecular recognition." Thesis, SciLifeLab Stockholm, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-200164.
Повний текст джерелаSund, 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.
Повний текст джерелаAbdul, Rahim Nur Aida. "Investigating the mechanotransduction by two-photon fluorescence microscopy measurement of intracellular free energy of binding." Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/44746.
Повний текст джерелаIncludes bibliographical references (p. 99-108).
Force, due either to haemodynamic shear stress or relayed directly to the cell through adhesion complexes, is transmitted and translated into biological signals. This process is known as mechanotransduction. Extensive studies have been carried out on the signaling pathways involved in mechanotransduction. However, the mechanism(s) of mechanotransduction has yet to be fully understood. This thesis focuses on the measurement of the intracellular binding constant between focal adhesion proteins of interest, GFP-Paxillin and FAT-mCherry, using two-photon excitation fluorescence microscopy and the utility of it as a measure of protein conformational change. The hypothesis tested is that force-induced changes in protein conformation alter inter-protein binding affinity. A comprehensive toolkit that utilizes fluorescence microscopy techniques, Forster Resonance Energy Transfer (FRET) and its corollary, Fluorescence Lifetime Imaging (FLIM), as well as Fluorescence Correlation Spectroscopy (FCS), was developed. A procedure by which low photon counts cell data from FLIM could be included in global analysis fits and be corrected for was developed. This results in the recovery of maximum information from cellular data. Successful intracellular FCS measurements were combined with FLIM global analysis data to calculate the free energy of binding between GFP-Paxillin and FAT-mCherry. Results demonstrate that inter-cell heterogeneity exists and likely gives rise to differences in measured AIG. The application of these measurement techniques to cells experiencing 10% step strain shows that inter-protein binding is tighter upon stretch application. The source of this change is not clear, though Tyr phosphorylation has been ruled out by biochemical disruption of kinase activity.
by Nur Aida Abdul Rahim.
Ph.D.
Gregor, Craig Robert. "Epitopes, aggregation and membrane binding : investigating the protein structure-function relationship." Thesis, University of Edinburgh, 2012. http://hdl.handle.net/1842/5833.
Повний текст джерелаAlmlöf, Martin. "Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes." Doctoral thesis, Uppsala University, Department of Cell and Molecular Biology, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7421.
Повний текст джерелаThe ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented.
For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions.
A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands.
A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding.
The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.
Ziemann, Dirk. "Theory of Excitation Energy Transfer in Nanohybrid Systems." Doctoral thesis, Humboldt-Universität zu Berlin, 2020. http://dx.doi.org/10.18452/22142.
Повний текст джерелаIn the following, transfer phenomena in nanohybrid systems are investigated theoretically. Such hybrid systems are promising candidates for novel optoelectronic devices and have attracted considerable interest. Despite a vast amount of experimental studies, only a small number of theoretical investigations exist so far. Furthermore, most of the theoretical work shows substantial limitations by either neglecting the atomistic details of the structure or drastically reducing the system size far below the typical device extension. The present thesis shows how existing theories can be improved. This thesis also expands previous theoretical investigations by developing models for four new and highly relevant nanohybrid systems. The first system is a spherical nanostructure consisting of an Au core and a CdS shell. By contrast, the second system resembles a finite nanointerface built up by a ZnO nanocrystal and a para-sexiphenyl aggregate. For the last two systems, a CdSe nanocrystal couples either to a pheophorbide-a molecule or to a tubular dye aggregate. In all of these systems, excitation energy transfer is an essential transfer mechanism and is, therefore, in the focus of this work. The considered hybrid systems consist of tens of thousands of atoms and, consequently, require an individual modeling of the constituents and their mutual coupling. For each material class, suitable methods are applied. The modeling of semiconductor nanocrystals is done by the tight-binding method, combined with a configuration interaction scheme. For the simulation of the molecular systems, the density functional theory is applied. T. Plehn performed the corresponding calculations. For the metal nanoparticle, a model based on quantized plasmon modes is utilized. As a consequence of these theories, excitation energy transfer calculations in hybrid systems are possible with unprecedented system size and complexity.
Han, Ji Hoon. "Fluorescent Nucleobases for Studying DNA Structure, Protein Interaction and Metal Binding." Kyoto University, 2019. http://hdl.handle.net/2433/242637.
Повний текст джерелаSpode, Lennart. "Mapping the binding energy of H inside amorphous and crystalline transition metals using the effective medium theory." Thesis, Uppsala universitet, Materialfysik, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-413982.
Повний текст джерелаEdwards, Angela Celeste. "Probing the Hydrogen Bonding Interaction at the Gas-Surface Interface using Dispersion Corrected Density Functional Theory." Thesis, Virginia Tech, 2015. http://hdl.handle.net/10919/71784.
Повний текст джерелаMaster of Science
Lima, Francisco das Chagas Alves. "Estudo teórico de propriedades químicas de sistemas hetero-macrocíclos que complexam metais de transição divalentes da primeira e segunda filas." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/75/75131/tde-23062008-155103/.
Повний текст джерелаA detailed theoretical study of structures and energies of the 1,7,1l,17-tetraoxa-2,6,12,16-tetraaza-cycloeicosane ligand ([20]AneN4O4) coordinated to Fe2+, Co2+, Ni2+, Ru2+, Rh2+ and Pd2+ transition metals ions was carried out with the B3LYP/Lanl2DZ method. The geometries of the complexes were fully optimized in Cs symmetry with the metal ions coordinated either to four atoms nitrogen (complexes 1a e 1b) or to the four atoms oxygen (complexes 1aq e 1bq). The octahedral and square planar arrangements were considered in this work. The theoretical structure is in excellent agreement with the experimental X-ray diffraction structure determination for the [20]AneN4O4 octahedral Ni2+ complex. The M2+ cations bind preferentially to the nitrogen atoms with binding energies that increase in the order Fe2+ < Ru2+ < Co2+ < Ni2+ < Rh2+ < Pd2+. For the first-row transition metals, the highspin complexes are more stable than the low-spin complexes. In contrast, for the second-row of transition metals, the low-spin states were found more stable than the high spin states. The metal-ligand bonds in the complexes were analyzed in terms of the covalent and ionic interactions and helped to understand why complexes (1a e 1aq) are more stable than complexes (1b e 1bq). The polyamines [20]aneN4 and polyethers [20]aneO4 complexes were obtained substituting the atoms N or O of the alfa position of the macrocycles [20]aneN4O4 and [20]aneO4N4, respectively. The macrocycle [20]aneO4 prefers to complex first-row transition metals; however, the macrocycle [20]aneN4 prefers to complex second-row transition metals.
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.
Повний текст джерелаSong, Young-Ho, Rimantas Lazauskas, and Kolck U. van. "Triton binding energy and neutron-deuteron scattering up to next-to-leading order in chiral effective field theory." AMER PHYSICAL SOC, 2017. http://hdl.handle.net/10150/625299.
Повний текст джерелаHuxtable, Barton Duane Simon Barry. "Absence of a Scott correction for the total binding energy of noninteracting fermions in a smooth potential well /." Diss., Pasadena, Calif. : California Institute of Technology, 1988. http://resolver.caltech.edu/CaltechETD:etd-09062005-101909.
Повний текст джерелаBuch, Mundó Ignasi 1984. "Investigation of protein-ligand interactions using high-throughput all-atom molecular dynamics simulations." Doctoral thesis, Universitat Pompeu Fabra, 2012. http://hdl.handle.net/10803/101407.
Повний текст джерелаMontalvo, Acosta Joel José. "Computational approaches to molecular recognition : from host-guest to protein-ligand binding." Thesis, Strasbourg, 2018. http://www.theses.fr/2018STRAF051/document.
Повний текст джерелаMolecular recognition is a very interesting problem, and foremost, a current challenge for biophysical chemistry. Having reliable predictions on the specific recognition between molecules is highly priority as it will provide an insight of fundamental problems and will raise relevant technological applications. The dissertation presented here is centered on a quantitative analysis of molecular recognition in solution for host-guest, protein-ligand binding and catalysis. The statistical mechanics framework used to describe the state-of-the-art for receptor-ligand binding is an inflection point for the developing of new improved and methods. In fact, a highly performanced and accurate model was obtained for the analysis of host-guest binding. Finally, the presented models were used as a reliable predictive tools for discovering new chemical entities for enhance catalysis in solution
Berg, Emily Katherine. "Thermodynamics of λ-PCR Primer Design and Effective Ribosome Binding Sites". Thesis, Virginia Tech, 2019. http://hdl.handle.net/10919/89900.
Повний текст джерелаMaster of Science
Recombinant DNA technology has been used to genetically enhance organisms to produce greater amounts of a product already made by the organism or to make an organism synthesize a new product. Genes are commonly modified in organisms using cloning practices which typically involves inserting a target gene into a plasmid and transforming the plasmid into the organism of interest. A new cloning process developed in the Senger lab, λ-PCR, improves the cloning process compared to other methods due to its use of relatively inexpensive materials and high efficiency. A primary goal of this study was to develop a procedure for λ-PCR primer design that allows for accurate use of the cloning method. Additionally, this study investigated the use of synthetic ribosome binding sites to control and improve expression of proteins cloned into an organism. Ribosome binding sites are sequences located upstream of the gene that increase the molecule’s affinity for the rRNA sequence on the ribosome, bind to the ribosome just upstream of the beginning of the gene, and initiate expression of the gene. Tools have been developed that create synthetic ribosome binding sites designed to produce specific amounts of protein. For example, the tools can increase or decrease expression of a gene depending on the application. These tools, the Salis Lab RBS Calculator and NUPACK, were used to design and evaluate the effects of the synthetic ribosome binding sites. Additionally, a new method was created to design synthetic ribosome binding sites since the methods used during the design process yielded inaccuracies. Each strain of E. coli contained the same gene, a cyan fluorescent protein (CFP), but had different RBS sequences located upstream of the gene. Expression of CFP was controlled via induction, meaning the addition of a particular molecule, IPTG in this system, triggered expression of CFP. Each of the CFP strains were tested with a variety of v conditions in order to find the conditions most suitable for protein expression; the variables tested include: induction time, IPTG (inducer) concentration, and temperature. Media was also tested for the cell-free systems, meaning the strains were grown overnight for 18 hours and lysed, a process where the cell membrane is broken in order to utilize the cell’s components for protein expression; the cell lysate was resuspended in new media for the experiments. ANOVA and multiple linear regression revealed IPTG concentration, induction time, and media to be significant factors impacting protein expression. This analysis also showed each CFP strain did not perform as the RBS Calculator predicted. Modeling each strain’s CFP expression using the RBS-rRNA binding strengths and secondary structures present in the RBS allowed for the creation of a new model for predicting and designing RBS sequences.
Ferreira, Robson. "Efeitos de tunelamento na energia de ligação de impurezas doadoras rasas em super-redes." Universidade de São Paulo, 1987. http://www.teses.usp.br/teses/disponiveis/54/54131/tde-15042014-114554/.
Повний текст джерелаA variational procedure which takes into account the mixing of a continuum of subband states has been used to investigate the binding energies of shallow donors in superlattices. The calculations where performed for a wide range of superlattices parameters and impurity positions. It is shown that the dependence of the binding energy upon the various superlattice parameters can be completely explained in terms of a simple onedimensional tight-binding model where the bandwidth of the respective conduction subband and the binding energy in the isolated quantum well are the only relevant parameters. The quantitative overall agreement between the binding energies derived from this model and those found variationally is excellent and emphasizes the fundamental role played by the bandwidth as the only relevant parameter accounting for the tunneling effects.
Furuhashi, Toyohisa. "STUDY OF PROPANE ADSORPTION ISOTHERM ON PURIFIED HIPCO SINGLE-WALLED CARBON NANOTUBES." Available to subscribers only, 2009. http://proquest.umi.com/pqdweb?did=1967978731&sid=2&Fmt=2&clientId=1509&RQT=309&VName=PQD.
Повний текст джерела