Relevant bibliographies by topics / MOLECULAR DYNAMCS

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'MOLECULAR DYNAMCS'

Author: Grafiati
Published: 9 March 2023
Last updated: 10 March 2023

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Journal articles on the topic "MOLECULAR DYNAMCS"

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Mori, K., Y. Seki, and K. Soda. "Volume Fluctuation Dynamcs of Lysozyme by Molecular Dynamics Simulation." Seibutsu Butsuri 43, supplement (2003): S54. http://dx.doi.org/10.2142/biophys.43.s54_3.

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WANG, Yu. "A STEERED MOLECULAR DYNAMCS STUDY OF ADSORBED POLYMER CHAIN." Acta Polymerica Sinica 008, no. 3 (September 15, 2008): 216–20. http://dx.doi.org/10.3724/sp.j.1105.2008.00216.

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Tse, John. "Structure, bonding and dynamcs under extreme conditions." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1534. http://dx.doi.org/10.1107/s2053273314084654.

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Knowledge on the composition and structure of a material are essential to the understanding of the properties. Recent advances in structural prediction techniques from first-principles calculations have greatly enhanced the perspective on the large variety of new crystal types, particularly, under extreme conditions at high pressure and high temperature. The structural information helps to develop a new understanding on the change in chemical bonding in highly compressed solids. I will present the results and experience in the use of several structural prediction methods with examples drawn from recent studies on the outstanding problems in pressure-induced amorphization of SnI4, structural transformations, atomic dynamics and structural chemistry of simple elemental and molecular solids at high pressure and high temperature. Our results will highlight the successes, challenges and future development on the practical applications of these methods.
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Okumura, Hisashi, Satoru G. Itoh, and Yuko Okamoto. "1P585 Explicit Symplectic Molecular Dynamics Simulation for Rigid-Body Molecules in the Canonical Ensemble(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S293. http://dx.doi.org/10.2142/biophys.46.s293_1.

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Gough, Craig A., Takashi Gojobori, and Tadashi Imanishi. "1P563 Consistent dynamic phenomena in amyloidogenic forms of transthyretin : a molecular dynamics study(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S287. http://dx.doi.org/10.2142/biophys.46.s287_3.

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Biyani, Manish, T. Aoyama, and K. Nishigaki. "1M1330 Solution structure dynamics of single-stranded oligonucleotides : Experiments and molecular dynamics." Seibutsu Butsuri 42, supplement2 (2002): S76. http://dx.doi.org/10.2142/biophys.42.s76_2.

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Tilokani, Lisa, Shun Nagashima, Vincent Paupe, and Julien Prudent. "Mitochondrial dynamics: overview of molecular mechanisms." Essays in Biochemistry 62, no. 3 (July 20, 2018): 341–60. http://dx.doi.org/10.1042/ebc20170104.

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Mitochondria are highly dynamic organelles undergoing coordinated cycles of fission and fusion, referred as ‘mitochondrial dynamics’, in order to maintain their shape, distribution and size. Their transient and rapid morphological adaptations are crucial for many cellular processes such as cell cycle, immunity, apoptosis and mitochondrial quality control. Mutations in the core machinery components and defects in mitochondrial dynamics have been associated with numerous human diseases. These dynamic transitions are mainly ensured by large GTPases belonging to the Dynamin family. Mitochondrial fission is a multi-step process allowing the division of one mitochondrion in two daughter mitochondria. It is regulated by the recruitment of the GTPase Dynamin-related protein 1 (Drp1) by adaptors at actin- and endoplasmic reticulum-mediated mitochondrial constriction sites. Drp1 oligomerization followed by mitochondrial constriction leads to the recruitment of Dynamin 2 to terminate membrane scission. Inner mitochondrial membrane constriction has been proposed to be an independent process regulated by calcium influx. Mitochondrial fusion is driven by a two-step process with the outer mitochondrial membrane fusion mediated by mitofusins 1 and 2 followed by inner membrane fusion, mediated by optic atrophy 1. In addition to the role of membrane lipid composition, several members of the machinery can undergo post-translational modifications modulating these processes. Understanding the molecular mechanisms controlling mitochondrial dynamics is crucial to decipher how mitochondrial shape meets the function and to increase the knowledge on the molecular basis of diseases associated with morphology defects. This article will describe an overview of the molecular mechanisms that govern mitochondrial fission and fusion in mammals.
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Slavgorodska, Maria, and Alexander Kyrychenko. "Structure and Dynamics of Pyrene-Labeled Poly(acrylic acid): Molecular Dynamics Simulation Study." Chemistry & Chemical Technology 14, no. 1 (February 20, 2020): 76–80. http://dx.doi.org/10.23939/chcht14.01.076.

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Srinivasan, S. G., I. Ashok, Hannes Jônsson, Gretchen Kalonji, and John Zahorjan. "Dynamic-domain-decomposition parallel molecular dynamics." Computer Physics Communications 102, no. 1-3 (May 1997): 44–58. http://dx.doi.org/10.1016/s0010-4655(97)00016-7.

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Paolini, Gaia V. "Dynamic approach to nonequilibrium molecular dynamics." Nuclear Physics B - Proceedings Supplements 5, no. 1 (September 1988): 272–77. http://dx.doi.org/10.1016/0920-5632(88)90054-0.

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Dissertations / Theses on the topic "MOLECULAR DYNAMCS"

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GABAS, FABIO. "IMPLEMENTATION OF SEMICLASSICAL THEORIES FOR SPECTROSCOPY." Doctoral thesis, Università degli Studi di Milano, 2019. http://hdl.handle.net/2434/612132.

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Vibrational spectroscopy is a fundamental tool for detecting and understanding the structure of molecular systems. Alongside the experimental measures, theoretical methods have been always employed to interpret and understand vibrational spectra. The semiclassical approach has demonstrated its reliability in the field, especially by means of the recent “Multiple Coherent” and “Divide and Conquer” formulations. In this PhD thesis the implementation and application of these modern techniques to a variety of molecular systems are presented, ranging from isolated medium size molecules to complex supramolecular systems, up to more than one hundred degrees of freedom. In particular the vibrational features of glycine, deoxyguanosine, a small dipeptide and glycine-based supramolecular systems are illustrated and discussed. A final Section is dedicated to the possibility to employ the Amber94 classical molecular force field, for computationally cheaper semiclassical calculations. This work demonstrates and highlights the validity and accuracy of semiclassical methods as theoretical spectroscopicy tools by successfully detecting quantum effects in medium size systems, whereas other formulations fail.
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Sargant, Robert John. "Molecular dynamics simulations of elongated molecules." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/molecular-dynamics-simulations-of-elongated-molecules(35c31c02-aa1f-4c87-bab9-db81d813974b).html.

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The existence of a thermotropic biaxial nematic liquid crystal phase has been a topic of great interest for almost half a century. Of the various mesogenic shapes suggested as being able to form this phase, theory has suggested that the V-shaped or "bent-core" molecule is one of the most promising candidates. In this thesis we use a simple mesogenic model of a bent-core molecule, constructed from a number of repulsive Weeks-Chandler-Andersen potentials that are assembled into a rigid V shape. Using this model we explore the spontaneous phase behaviour that occurs in a wide array of different systems of mesogens, using molecular dynamics simulations and isotropic initial conditions. We study the relationship between molecular bend angle and phase behavior for molecules constructed from 11 potentials. We find that the phase behaviour splits into two regions, above and below a critical bend angle. Molecules wider than this angle exhibit isotropic, uniaxial nematic and smectic A phases. Narrower molecules show no uniaxially aligned phases, and instead have a clustered phase with short-range ordering and no global alignment director. Increasing system size improves the smectic layering in the wider molecules, but does not affect the global alignment of the narrower molecules. Our model is extended to include the effect of the arm length of the molecule by changing the number of potentials from which the mesogens are constructed. As the molecule is reduced in size, the critical bend angle is seen to move slowly towards more linear molecules, reducing the size of the parameter space in which uniaxial nematic alignment is possible. At 5 beads, all mesophases are seen to disappear and systems remain isotropic. We also study the behaviour of binary mixtures of bent-core molecules, both of differing arm lengths and of differing bend angles. For arm length mixtures, molecules are seen to remain mixed in the isotropic and nematic phases, and phase separate on transition to a smectic phase. In addition, uniaxial nematic phases are induced in systems that have no nematic phase of their own in isolation. For mixtures of different bend angles, systems remain fully mixed in the smectic phases for differences of up to 10 degrees, and beyond this the two components begin to separate at the nematic–smectic transition.
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Doig, Michael. "Molecular dynamics simulations of surface-active molecules under dynamic conditions found in engines." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/17968.

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Lubricants oils play an important role in a wide range of industrial and mechanical processes, where they are used to reduce both the friction and wear between interacting moving surfaces. The current understanding of lubrication is mainly based on empirical evidence, obtained from experiment. In this work, computer simulations are used to gain insight into the microscopic processes that lead to the modification of friction and wear by additive molecules adsorbed on sheared surfaces lubricated by thin liquid films. The specific area of application under consideration is the lubrication of automotive engine parts. The interactions between additive molecules are first determined using density-functional theory calculations. The interactions are then validated against available experimental data, and incorporated in to large-scale molecular-dynamics (MD) simulations, which are used to explore the structure and frictional properties of lubricated surfaces. The surfaces considered are alumina and iron oxide. The lubricating oils are squalane and hexadecane, which are representative of automotive lubricants, and the additive molecules are stearic acid, oleic acid and various oleamides. MD simulations are performed over wide ranges of the relevant physical conditions, namely pressure, temperature, and shear rate. The additives adsorb on to the surfaces and provide a physical connection between the surfaces and the lubricating liquid. The structures of adsorbed films are analysed in microscopic detail using functions of atomic positions and molecular geometry. Several important trends are identified, linking molecular isomerism and architecture with the structure and stability of the adsorbed film. In addition, the simulation results are used to gain insight on recent experimental measurements of film structure. The friction coefficients in various situations are computed and analysed with reference to the structures of the adsorbed films. The synthesis of these data and observed trends yields new insights on the intimate link between the molecular properties of lubricants, and the macroscopic frictional properties of macroscopic lubricated engine parts.
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Baker, Joseph Lee. "Steered Molecular Dynamics Simulations of Biological Molecules." Diss., The University of Arizona, 2011. http://hdl.handle.net/10150/205416.

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Molecular dynamics (MD) simulation, which employs an empirical potential energy function to describe the interactions between the atoms in a system, is used to investigate atomistic motions of proteins. However, the timescale of many biological processes exceeds the reach of standard MD due to computational limitations. To circumvent these limitations, steered molecular dynamics (SMD), which applies external forces to the simulated system, can be used.Dynamical properties of the gonococcal type IV pilus (GC-T4P) from the bacteria Neisseria gonorrhoeae are first considered. T4 pili are long, filamentous proteins constructed from a subunit (pilin) found to emanate from the surface of pathogenic bacteria. They can withstand large forces (~100 pN), and are implicated in infection. SMD simulations are performed to study the response of the filament to an applied force. Our simulations reveal that stability of the pilus likely results from hydrophobic contacts between pilin domains buried within the filament core. Along the filament surface, gaps are formed between pilin globular head domains. These gaps reveal an amino acid sequence that was also observed to become exposed in the experimentally stretched filament. We propose two other regions initially hidden in the native filament that might become exposed upon stretching.The multidrug resistance transporter EmrD, found in the inner membrane of Escherichia coli is also the target of our studies. EmrD removes harmful drugs from the bacterial cell. We use MD to explore equilibrium dynamics of the protein, and MD/SMD to study drug interactions and transport along its central cavity. Motions supporting a previously proposed lateral diffusion pathway for substrate from the cytoplasmic membrane leaflet into the central cavity were observed. Additionally, interactions of a few specific residues with CCCP have been identified.Finally, we describe network analysis as an approach for analyzing conformational sampling by MD simulations. We demonstrate for several model systems that networks can be used to visualize both the dominant conformational substates of a trajectory and the connectivity between them. Specifically, we compare the results of various clustering algorithms to the network layouts and show how information from both methods can be combined.
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Wildman, Jack. "Molecular dynamics simulations of conjugated semiconducting molecules." Thesis, Heriot-Watt University, 2017. http://hdl.handle.net/10399/3261.

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In this thesis, we present a study of conformational disorder in conjugated molecules focussed primarily on molecular dynamics (MD) simulation methods. Along with quantum chemical approaches, we develop and utilise MD simulation methods to study the conformational dynamics of polyfluorenes and polythiophenes and the role of conformational disorder on the optical absorption behaviour observed in these molecules. We first report a classical force-field parameterisation scheme for conjugated molecules which defines a density functional theory method of accuracy comparable to high-order ab-initio calculations. In doing so, we illustrate the role of increasing conjugated backbone and alkyl side-chain length on inter-monomer dihedral angle potentials and atomic partial charge distributions. The scheme we develop forms a minimal route to conjugated force-field parameterisation without substantial loss of accuracy. We then present a validation of our force-field parameterisation scheme based on self-consistent measures, such as dihedral angle distributions, and experimental measures, such as persistence lengths, obtained from MD simulations. We have subsequently utilised MD simulations to investigate the interplay of solvent and increasing side-chain lengths, the emergence of conjugation breaks, and the wormlike chain nature of conjugated oligomers. By utilising MD simulation geometries as input for quantum chemical calculations, we have investigated the role of conformational disorder on absorption spectral broadening and the formation of localised excitations. We conclude that conformational broadening is effectively independent of backbone length due to a reduction in the effect of individual dihedral angles with increasing length and also show that excitation localisation occurs as a result of large dihedral angles and molecular asymmetry.
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Panesar, Kuldeep Singh. "Quantum molecular dynamics of guest molecules in supramolecular complexes." Thesis, University of Nottingham, 2009. http://eprints.nottingham.ac.uk/10741/.

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The quantum motion of guest molecules has been studied in a variety of calixarene host-guest complexes, and in a endohedral fullerene complex. The guest molecules of the calixarene complexes studied each comprise weakly hindered methyl groups, which undergo rotation via quantum tunnelling, even at cryogenic temperatures. The rotational motion of the guest methyl-groups has been studied by making temperature and frequency-dependent measurements of proton T1, using field-cycling NMR, thus revealing the spectral density functions of the magnetic dipole-dipole interaction. Crystallographically inequivalent methyl-group environments have been identified and characterised in p-tert-butylcalix[4]arene(1:1)toluene, p-tert-butylcalix[4]arene(1:1)gamma-picoline and p-isopropylcalix[4]arene(2:1)p-xylene. In many of the calixarene complexes the proton spin-lattice relaxation has been observed to be strongly dependent on the thermal history of the sample. Temperature-dependent measurements of proton T1 in samples of p-tert-butylcalix[4]arene(1:1)toluene with partially deuterated guest molecules reveal a systematic reduction in T1 at low temperatures with increased degree of deuteration. Calixarene and fullerene host-guest complexes have been identified as having a potential application in cryogenic MAS-NMR as cryorelaxor complexes, capable of being attached to a large biomolecule and encouraging proton spin-lattice relaxation. The suitability of the calixarene complexes for use in this capacity has been investigated by measuring the temperature-dependence of proton T1 at low temperatures. The quantised rotational and translational motion of dihydrogen confined within an open-cage fullerene—namely, aza-thio-open-cage-fullerene (ATOCF)—has been revealed by inelastic neutron scattering (INS) measurements. The splitting of excited rotational and translational states, due to the low symmetry of the ellipsoidal fullerene cavity, has been directly measured. Assignment of the peaks observed in the INS spectrum has been aided by analysis of the Q-dependence of excitation bands. The thermodynamics of ortho- and parahydryogen have been investigated via temperature dependence measurements. INS measurements have allowed the anistropic rotational potential experienced by the H2 rotor to be determined.
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Seo, Youngmi. "Structure and Dynamic Properties of Interfacially Modified Block Copolymers from Molecular Dynamics Simulations." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1492628195548591.

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Chen, Jen Hui. "Molecular Dynamics and Interactions in Liquids." Thesis, North Texas State University, 1985. https://digital.library.unt.edu/ark:/67531/metadc331452/.

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Various modern spectroscopies have been utilized with considerable success in recent years to probe the dynamics of vibrational and reorientational relaxation of molecules in condensed phases. We have studied the temperature dependence of the polarized and depolarized Raman spectra of various modes in the following dihalomethanes: dibromomethane, dichloromethane, dichloromethane-d2, and bromochloromethane. Among other observed trends, we have found the following: Vibrational dephasing times calculated from the bend) and (C-Br stretch) lineshapes are of the same magnitude in CI^B^. The vibrational dephasing time of [C-D(H) stretch] is twice as long in CD2Cl2 as in CH-^C^, and the relaxation time of (C-Cl stretch) is greater in CI^C^ than in CD2CI2. Isotropic relaxation times for all three stretching vibrations are significantly shorter in C^BrCl than in CI^C^ or CI^B^. Application of the Kubo model revealed that derived modulation times are close to equal for equivalent vibrations in the various dihalomethanes. Thus, the more efficient relaxation of the A^ modes in CE^BrCl can be attributed almost entirely to the broader mean squared frequency perturbation of the vibrations in this molecule.
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Vaitheeswaran, Subramanian. "Computer Simulations of Partially Confined Water." Fogler Library, University of Maine, 2004. http://www.library.umaine.edu/theses/pdf/VaitheeswaranS2004.pdf.

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Palaiokostas-Avramidis, Michail. "Molecular dynamics simulations of small molecule permeation through lipid membranes." Thesis, Queen Mary, University of London, 2017. http://qmro.qmul.ac.uk/xmlui/handle/123456789/31859.

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Passive permeation through biological membranes is an important mechanism for transporting molecules and regulating the cellular content. Studying and understanding passive permeation is also extremely relevant to many industrial applications, including drug design and nanotechnology. In vivo membranes typically consist of mixtures of lamellar and nonlamellar lipids. Lamellar lipids are characterised by their tendency to form lamellar bilayer phases, which are predominant in biology. Nonlamellar lipids, when isolated, instead form non-bilayer structures such as inverse hexagonal phases. While mixed lamellar/nonlamellar lipid membranes tend to adopt the ubiquitous bilayer structure, the presence of nonlamellar lipids is known to have profound effects on key membrane properties, such as internal distributions of stress and elastic properties. This dissertation examines permeation through lamellar and nonlamellar lipid membranes by utilising atomistic molecular dynamics simulations in conjunction with two di erent methods, the z-constraint and the z-restraint, in order to obtain transfer free energy profiles, diffusion profiles and permeation coefficients. An assessment of these methods is performed in search for the optimal, with the goal to create an automated, accurate and robust permeation study framework. Part of the dissertation involves the creation of the corresponding software. Furthermore, this work examines the effect of changing the lamellar vs. nonlamellar lipid composition on the passive permeation mechanism of a series of 13 small molecules and drugs. These nonlamellar lipids are known to affect the lateral pressure distribution inside the membranes. This work investigates the hypothesis that the differences in lateral pressure should increase the resistance to permeation. The results indicate that, upon addition of nonlamellar lipids, permeation is hindered for small molecules but is facilitated for the largest. All results are in agreement with previous experimental and computational studies. This work represents an advancement towards the development of more realistic in silico permeability assays, which may have a substantial future impact in the area of rational drug design.
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Books on the topic "MOLECULAR DYNAMCS"

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Raymond, Daudel, ed. Structure and dynamics of molecular systems. Dordrecht, Holland: D. Reidel, 1985.

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Toshio, Yanagida, and Ishii Yoshiharu, eds. Single molecule dynamics in life science. Weinheim: Wiley-VCH, 2009.

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Molecular dynamics. Berlin: Springer-Verlag, 1986.

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Leimkuhler, Ben, and Charles Matthews. Molecular Dynamics. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-16375-8.

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Goodfellow, Julia M., ed. Molecular Dynamics. London: Macmillan Education UK, 1991. http://dx.doi.org/10.1007/978-1-349-11044-5.

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EPS Southern European School of Physics (1st 1991 Avila, Spain). Dynamical processes in molecular physics: First EPS Southern European School of Physics, Avila, Spain, 1-14 September 1991. Edited by Delgado-Barrio G and European Physical Society. Bristol, England: Institute of Physics Pub., 1993.

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Toshio, Yanagida, and Ishii Yoshiharu, eds. Single molecule dynamics in life science. Weinheim: Wiley-VCH, 2009.

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S, Child M., and Royal Society (Great Britain), eds. Molecular Rydberg dynamics. London: Imperial College Press, 1999.

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Vrakking, Marc J. J., and Franck Lepine, eds. Attosecond Molecular Dynamics. Cambridge: Royal Society of Chemistry, 2018. http://dx.doi.org/10.1039/9781788012669.

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Yonezawa, Fumiko, ed. Molecular Dynamics Simulations. Berlin, Heidelberg: Springer Berlin Heidelberg, 1992. http://dx.doi.org/10.1007/978-3-642-84713-4.

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Book chapters on the topic "MOLECULAR DYNAMCS"

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Jones, R. O. "Molecules and Molecular Dynamics." In NATO ASI Series, 273–97. Boston, MA: Springer US, 1995. http://dx.doi.org/10.1007/978-1-4757-9975-0_12.

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Clarke, Julian H. R. "Molecular Dynamics of Chain Molecules." In Computer Modelling of Fluids Polymers and Solids, 203–17. Dordrecht: Springer Netherlands, 1990. http://dx.doi.org/10.1007/978-94-009-2484-0_8.

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Moss, D. S., and T. P. Flores. "Molecular Dynamics of Protein Molecules." In Supercomputational Science, 251–68. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4684-5820-6_20.

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Wang, Pengyu, and Zhong Chen. "Vapor Condensation Under Electric Field: A Study Using Molecular Dynamics Simulation." In Supercomputing Frontiers, 20–30. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-10419-0_2.

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AbstractThe condensation of water vapor on the substrate surface under electric field is studied by molecular dynamics simulation, and a series of behaviors of water molecules during condensation were studied, such as nucleation, growth and coalescence. In the process of condensation, there will be some small clusters, whose size increases with the increase of time, and under the action of the movement of water molecules in vapor, the clusters move irregularly on the substrate surface and coalesced into larger clusters. And the droplets will be stretched along the direction of the electric field. Interestingly, the condensation will decrease with the increase of the electric field strength under the electric field perpendicular to the surface. The results also show that the orientations of water molecule dipole are closely related to the direction of electric field, indicating that the electric field causes the realignment of water molecules. The research shows that the electric intensity will have great impact on vapor condensation, which provides guidance for reversible adjustment of vapor condensation and the design of intelligent surface.
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Koch, Christiane P. "Quantum Effects in Cold and Controlled Molecular Dynamics." In Molecular Beams in Physics and Chemistry, 477–90. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-63963-1_21.

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AbstractThis chapter discusses three examples of quantum effects that can be observed in state-of-the-art experiments with molecular beams—scattering resonances as a probe of interparticle interactions in cold collisions, the protection of Fano-Feshbach resonances against decay despite resonant coupling to a scattering continuum, and a circular dichroism in photoelectron angular distributions arising in the photoionization of randomly oriented chiral molecules. The molecular beam setup provides molecules in well-defined quantum states. This, together with a theoretical description based on first principles, allows for excellent agreement between theoretical prediction and experimental observation and thus a rigorous understanding of the observed quantum effects.
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Braun, Christina, Robert Knüppel, Jorge Perez-Fernandez, and Sébastien Ferreira-Cerca. "Non-radioactive In Vivo Labeling of RNA with 4-Thiouracil." In Ribosome Biogenesis, 199–213. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2501-9_12.

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AbstractRNA molecules and their expression dynamics play essential roles in the establishment of complex cellular phenotypes and/or in the rapid cellular adaption to environmental changes. Accordingly, analyzing RNA expression remains an important step to understand the molecular basis controlling the formation of cellular phenotypes, cellular homeostasis or disease progression. Steady-state RNA levels in the cells are controlled by the sum of highly dynamic molecular processes contributing to RNA expression and can be classified in transcription, maturation and degradation. The main goal of analyzing RNA dynamics is to disentangle the individual contribution of these molecular processes to the life cycle of a given RNA under different physiological conditions. In the recent years, the use of nonradioactive nucleotide/nucleoside analogs and improved chemistry, in combination with time-dependent and high-throughput analysis, have greatly expanded our understanding of RNA metabolism across various cell types, organisms, and growth conditions.In this chapter, we describe a step-by-step protocol allowing pulse labeling of RNA with the nonradioactive nucleotide analog, 4-thiouracil, in the eukaryotic model organism Saccharomyces cerevisiae and the model archaeon Haloferax volcanii.
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Bruder, Lukas, Markus Koch, Marcel Mudrich, and Frank Stienkemeier. "Ultrafast Dynamics in Helium Droplets." In Topics in Applied Physics, 447–511. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-94896-2_10.

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Abstract Helium nanodroplets are peculiar systems, as condensed superfluid entities on the nanoscale, and as vessels for studies of molecules and molecular aggregates and their quantum properties at very low temperature. For both aspects, the dynamics upon the interaction with light is fundamental for understanding the properties of the systems. In this chapter we focus on time-resolved experiments in order to study ultrafast dynamics in neat as well as doped helium nanodroplets. Recent experimental approaches are reviewed, ranging from time-correlated photon detection to femtosecond pump-probe photoelectron and photoion spectroscopy, coherent multidimensional spectroscopy as well as applications of strong laser fields and novel, extreme ultraviolet light sources. The experiments examined in more detail investigate the dynamics of atomic and molecular dopants, including coherent wave packet dynamics and long-lived vibrational coherences of molecules attached to and immersed inside helium droplets. Furthermore, the dynamics of highly-excited helium droplets including interatomic Coulombic decay and nanoplasma states are discussed. Finally, an outlook concludes on the perspectives of time-resolved experiments with helium droplets, including recent options provided by new radiation sources of femto- or even attosecond laser pulses up to the soft X-ray range.
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Fang, Fengzhou, and Pengzhe Zhu. "Molecular Dynamics." In CIRP Encyclopedia of Production Engineering, 1–5. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-35950-7_16729-1.

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Ladd, Anthony J. C. "Molecular Dynamics." In Computer Modelling of Fluids Polymers and Solids, 55–82. Dordrecht: Springer Netherlands, 1990. http://dx.doi.org/10.1007/978-94-009-2484-0_3.

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Shimono, Masato. "Molecular Dynamics." In Springer Handbook of Metrology and Testing, 975–1012. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-16641-9_17.

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Conference papers on the topic "MOLECULAR DYNAMCS"

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Tagaya, Yoichi, Yasunaga Mitsuya, Susumu Ogata, Hedong Zhang, and Kenji Fukuzawa. "A Simulation Method for Spreading Dynamics of Molecularly Thin Lubricant Films on Magnetic Disks Using Bead-Spring Model." In World Tribology Congress III. ASMEDC, 2005. http://dx.doi.org/10.1115/wtc2005-64393.

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An effective simulation technique for describing the spreading properties of molecularly thin lubricant films on magnetic disks has been developed. We propose a molecular precipitation method that can simulate initial molecule arrangement of the films dip-coated onto the disks. Reptation and Rouse models as the model of the molecular motion, and molecular insertion and molecular precipitation methods as the method for putting molecules in initial positions were compared. From the results of the spreading profiles and diffusion coefficients, it has been revealed that the molecular precipitation method combined with the Rouse model is effective in simulating the spreading of the lubricant films.
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Xie, Jian-Fei, and Bing-Yang Cao. "Molecular Dynamics Study on Fluid Flow in Nanochannels With Permeable Walls." In ASME 2016 5th International Conference on Micro/Nanoscale Heat and Mass Transfer. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/mnhmt2016-6421.

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This paper presents the fluid flow in nanochannels with permeable walls using the molecular dynamics (MD) simulations. A three-dimensional Couette flow has been carried out to investigate the effect of the permeable surface on the fluid density distributions and the slip velocity. The ordering layer of molecules is constructed near the smooth surface but it was destroyed by the permeable ones resulting in the density drop in porous wall. The fluid density in porous wall is large under strong fluid-structure interaction (FSI) and it is decreased under weak FSI. The negative slip is observed for fluid flow past solid walls under strong FSI, no-slip under medium FSI and positive slip under weak FSI whatever it is smooth or porous. Moreover, the largest slip velocity and slip length occur on the smooth surface of solid wall. As predicted by Maxwell theory, the molecule is bounced back when it impinges on the smooth surface. The molecules, however, can reside in porous wall by replacing the molecules that are trapped in the pores. Moreover, the molecule can escape from the pore and enter the channel becoming a free molecule. After travelling for a period time in the channel, the molecule can enter the pore again. During the molecular movement, the momentum exchange has been implemented not only between fluid molecules and wall but also between the fluid molecules themselves in the pore, and the multi-collision between fluid molecules takes place. The reduced slip velocity at the porous wall results in the larger friction coefficient compared to the smooth surface wall. The molecular boundary condition predicted by Maxwell theory on the smooth surface is no longer valid for flow past the permeable surface, and a novel boundary condition should be introduced.
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Sauer, M., K. H. Drexhage, K. T. Han, S. Nord, and C. Zander. "Following the Dynamics of Single Oligonucleotide Molecules in Water." In Laser Applications to Chemical and Environmental Analysis. Washington, D.C.: Optica Publishing Group, 1998. http://dx.doi.org/10.1364/lacea.1998.lmc.14.

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The dynamic fluorescence characteristics of individual dye molecules in specific local environment are of particular interest for many biological applications.1,2 Furthermore, dye molecules that are influenced by the environment can act as molecular probes, i. e. they exhibit information about neighbouring groups and changes in the microenvironment. They also allow the direct observation of individual dynamic events such as conformational changes of a biological macromolecule if they are monitored on the single-molecule level. In addition, measurements on individual molecules are well suited for the study of complex systems in which it is not known whether all molecules exhibit the same characteristics or each molecule contributes with its individual characteristics to the observed behaviour.
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Darbandi, Masoud, Hossein Reza Abbasi, Moslem Sabouri, and Rasool Khaledi-Alidusti. "Simulation of Heat Transfer in Nanoscale Flow Using Molecular Dynamics." In ASME 2010 8th International Conference on Nanochannels, Microchannels, and Minichannels collocated with 3rd Joint US-European Fluids Engineering Summer Meeting. ASMEDC, 2010. http://dx.doi.org/10.1115/fedsm-icnmm2010-31065.

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We investigate heat transfer between parallel plates separated by liquid argon using two-dimensional molecular dynamics (MD) simulations incorporating with 6–12 Lennard-Jones potential between molecule pairs. In molecular dynamics simulation of nanoscale flows through nanochannels, it is customary to fix the wall molecules. However, this approach cannot suitably model the heat transfer between the fluid molecules and wall molecules. Alternatively, we use thermal walls constructed from the oscillating molecules, which are connected to their original positions using linear spring forces. This approach is much more effective than the one which uses a fixed lattice wall modeling to simulate the heat transfer between wall and fluid. We implement this idea in analyzing the heat transfer in a few cases, including the shear driven and poiseuille flow with specified heat flux boundary conditions. In this method, the work done by the viscous stress (in case of shear driven flow) and the force applied to the fluid molecules (in case of poiseuille flow) produce heat in the fluid, which is dissipated from the nanochannel walls. We present the velocity profiles and temperature distributions for the both chosen test cases. As a result of interaction between the fluid molecules and their adjacent wall molecules, we can clearly observe the velocity slip in the velocity profiles and the temperature jump in the cross-sectional temperature distributions.
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Gullapalli, Ramachandra, Melik Demirel, and Peter J. Butler. "Molecular Dynamics Simulations of Dialkyl Carbocyanine Dyes in a DPPC Bilayer: Atomistic Insights Into Single Molecule Fluorescence." In ASME 2007 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2007. http://dx.doi.org/10.1115/sbc2007-176614.

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Our group uses di-alkyl carbocyanine dyes to detect force-induced membrane perturbation in mechanotransduction studies (Butler et al 2000). These dyes are also used extensively in single molecule spectroscopic techniques to infer dynamics of native membrane lipids. However, the precise distribution and orientation of the dye in a bilayer and how well the dye dynamics mimic native lipid dynamics are not known. Thus we present the results of a 40 nanosecond molecular dynamics simulation of a fully hydrated bilayer containing 0, 2, or 4 molecules of 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate (DiI-C18) and 128 molecules of dipalmitoylphosphatidyl choline (DPPC).
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Darbandi, Masoud, Rasoul Khaledi-Alidusti, Majid Abbaspour, Hossein Reza Abbasi, and Gerry Schneider. "Study of Cut-Off Radius and Temperature Effects on Water Molecular Behavior Using Molecular Dynamics Method." In ASME 2011 9th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2011. http://dx.doi.org/10.1115/icnmm2011-58216.

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Water molecules are one of the important molecules in nanofluidics. Its structure and its behavior can change with Temperature and cut-off distance parameters. In this study temperature and cut-off distance effects on the nano-scale water molecules behavior are investigated by molecular dynamics simulations. Many water molecular models have been developed in order to help discover the structure of water molecules. In this study, the flexible three centered (TIP3P-C) water potential is used to model the inter- and intramolecular interactions of the water molecules. In this simulation, we have been studied 512 water molecules with periodic boundary conditions and in a simulation box with 25 angstrom dimensions, which gives water density about 0.99 g/cm3. To examine of accuracy of TIP3P-C model, Radial distribution function of remarkable water model has been compared with experimental data. In this paper, to study temperature effect on water behavior, mentioned system with 300, 450 and 600 K have been considered and compared. The results have showed that with decreasing temperature, the tetrahedrality of the distribution of the water molecules around the central water molecule is enhanced, and the hydrogen bonds become more linear. It is found that as the temperature rises, kinetic energy rises too, and it makes that the average number of hydrogen bonds per water molecule decrease. In addition to temperature effects, cut-off radius parameter effects have been considered too, and four different cut-off radiuses 7.5, 9.0, 10.5, and 12.0 angstrom have been studied.
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Xu, Dongyan, Deyu Li, and Yongsheng Leng. "Molecular Dynamics Simulations of Water and Ion Structures Near Charged Surfaces." In ASME 2007 International Mechanical Engineering Congress and Exposition. ASMEDC, 2007. http://dx.doi.org/10.1115/imece2007-42536.

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Extensive research has been devoted to nanofluidics in the past decade because of its potential applications in single molecule sensing and manipulations. Fundamental studies have attracted significant attention in this research field since the success of nanofluidic devices depends on a thorough understanding of the fluidic, ionic, and molecular behavior in highly confined nano-environments. In this paper, we report on molecular dynamics simulations of the effect of surface charge densities on the ion distribution and the water density profile close to a charged surface. We demonstrate that surface charges not only interact with mobile ions in the electrolyte, but also interact with water molecules due to their polarizability, and hence influence the orientation of water molecules in the near wall region. For the first time, we show that as the surface charge density increases, the water molecules within ∼ 5 Å of the {100} silicon surface will evolve from one layer into two layers. Meanwhile, the orientation of the water molecules is more aligned instead of randomly distributed. This layering effect may have important implications on electroosmotic flow through nanochannels and heat transfer across the solid-liquid interface.
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Tokmakoff, A., D. Zimdars, and M. D. Fayer. "Vibrational Dynamics in Liquids and Glasses Probed with Infrared Photon Echoes Using a Free Electron Laser." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1994. http://dx.doi.org/10.1364/up.1994.fa.1.

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Molecular vibrations are involved in a vast number of physical, chemical, and biological processes. Coupling between molecular vibrations and external mechanical degrees of freedom (heat bath) is responsible for the flow of energy into and out of molecules and for thermally activated processes. Fluctuations of vibrational energy levels of a molecule caused by interactions with a dynamic environment are important in fundamental chemical and biological processes, such as electron transfer and chemical reactions. In spite of the importance of the coupling of molecular vibrations to a heat bath, relatively little is known about the temperature dependent dynamics of molecular vibrations in liquids and glasses. Here we give an account of the first ps infrared (IR) vibrational photon echo experiments performed on molecular vibrations in liquids and glasses [1,2]. The photon echo experiment is an optical line narrowing experiment that has been applied extensively to the study of electronic excitation dynamics in condensed matter systems [3-6]. However, the study of vibrations in condensed phases using photon echoes has been limited because of the need to work with ps IR pulses. Very recently the first vibrational Raman echoes were performed [7] and a vibrational photon echo study of a group attached to a surface in high vacuum was conducted [8].
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Chong, W. W. F., and M. Teodorescu. "Fast Converging Model for Load and Shear of Molecularly Thin Surface Films." In ASME 2012 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/imece2012-87852.

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Predicting the contact load and the shear losses in a narrow conjunction separated by a molecularly thin fluid layer must account for a significant number of factors: the chemical composition of the fluid and solid boundaries, the length of molecular chains, the intermolecular forces, the concentration of different species of molecules in the mixture, molecule-to-surface adsorption and surface topography. The most commonly used solutions to this problem either neglect a significant part of the participating phenomena or are computationally expensive (e.g. molecular dynamics simulations). The current paper proposes a statistical mechanics model, which predicts the behavior of a molecularly thin film confined within a nano-scale conjunction. The advantage of this approach is that it is fast converging (semi-analytic) and all the aforementioned phenomena could be accounted for, within a single frame-work. The model is tested for an idealized bimolecular fluid and it was found that it can predict the influence of the packing fraction and the concentration ratio over the discontinuous discharge of fluid out of the a nano-scale conjunction. The main application is accurate prediction of the shear stress-induced losses in a nano-scale contact (e.g. between asperities on opposite sides of a tribological conjunction) and modern drug delivery techniques (e.g. transdermal drug delivery patches).
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Baumert, T., C. Röttgermann, R. Thalweiser, V. Weiß, and G. Gerber. "Femtosecond Time-Resolved Photochemistry of Molecules and Metal-Clusters." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/up.1992.fd4.

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We report experimental studies of femtosecond time-resolved multiphoton ionization and - fragmentation of molecules and metal-clusters in molecular beam experiments. In particular we studied the real time dynamics of ionization and fragmentation of the diatomic Na2 molecule, of the triatomic Na3 cluster and of larger sodium metal-clusters Nan.
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Reports on the topic "MOLECULAR DYNAMCS"

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Grest, Gary Stephen, Mark Jackson Stevens, Steven James Plimpton, Thomas B. Woolf, Richard B. Lehoucq, Paul Stewart Crozier, Ahmed E. Ismail, Rudranarayan M. Mukherjee, and Andrei I. Draganescu. Substructured multibody molecular dynamics. Office of Scientific and Technical Information (OSTI), November 2006. http://dx.doi.org/10.2172/902881.

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Perez, Danny. Accelerated molecular dynamics methods. Office of Scientific and Technical Information (OSTI), January 2011. http://dx.doi.org/10.2172/1045413.

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Chu, P. M. Y. Collision dynamics of methyl radicals and highly vibrationally excited molecules using crossed molecular beams. Office of Scientific and Technical Information (OSTI), October 1991. http://dx.doi.org/10.2172/6947829.

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Chu, Pamela Mei-Ying. Collision dynamics of methyl radicals and highly vibrationally excited molecules using crossed molecular beams. Office of Scientific and Technical Information (OSTI), October 1991. http://dx.doi.org/10.2172/10184972.

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Dayal, Kaushik. Dynamics of Structural Phase Transformations Using Molecular Dynamics. Fort Belvoir, VA: Defense Technical Information Center, December 2013. http://dx.doi.org/10.21236/ada606824.

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Woolf, Thomas B., Paul Stewart Crozier, and Mark Jackson Stevens. Molecular dynamics of membrane proteins. Office of Scientific and Technical Information (OSTI), October 2004. http://dx.doi.org/10.2172/919637.

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Nagumo, Mark. Molecular Dynamics of Lipid Bilayers. Fort Belvoir, VA: Defense Technical Information Center, August 1989. http://dx.doi.org/10.21236/ada211492.

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Mountain, R. D. Transport coefficients and molecular dynamics:. Gaithersburg, MD: National Institute of Standards and Technology, 2004. http://dx.doi.org/10.6028/nist.ir.7170.

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Skeel, R. D. Numerical methods for molecular dynamics. Office of Scientific and Technical Information (OSTI), January 1991. http://dx.doi.org/10.2172/5436878.

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Rinderspacher, Berend C., Jaydeep P. Bardhan, and Ahmed E. Ismail. Wavelet Analysis for Molecular Dynamics. Fort Belvoir, VA: Defense Technical Information Center, June 2015. http://dx.doi.org/10.21236/ada619816.

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