Relevant bibliographies by topics / Molecular Dynamics Simulation Molecular dynamics

Academic literature on the topic 'Molecular Dynamics Simulation Molecular dynamics'

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Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "Molecular Dynamics Simulation Molecular dynamics"

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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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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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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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SHINTO, Hiroyuki. "Molecular Dynamics Simulation." Journal of the Japan Society of Colour Material 86, no. 10 (2013): 380–85. http://dx.doi.org/10.4011/shikizai.86.380.

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Krienke, Hartmut. "Molecular dynamics simulation." Journal of Molecular Liquids 75, no. 3 (March 1998): 271–72. http://dx.doi.org/10.1016/s0167-7322(97)00106-2.

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Rapaport, D. C. "Molecular dynamics simulation." Computing in Science & Engineering 1, no. 1 (1999): 70–71. http://dx.doi.org/10.1109/5992.743625.

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Sugiyama, Ayumu, Tetsunori Yamamoto, Hidemi Nagao, Keigo Nishikawa, Nobutaka Numoto, Kunio Miki, and Yoshihiro Fukumori. "1P567 Molecular dynamics study of dynamical structure stability of giant hemoglobin from Oligobrachia mashikoi(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S288. http://dx.doi.org/10.2142/biophys.46.s288_3.

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Terada, Tohru, and Kentaro Shimizu. "1P581 Improving efficiency of conformation sampling in multicanonical molecular dynamics simulation(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S292. http://dx.doi.org/10.2142/biophys.46.s292_1.

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Anam, Muhammad Syaekhul, and S. Suwardi. "Hydration Structures and Dynamics of Ga3+ Ion Based on Molecular Mechanics Molecular Dynamics Simulation (Classical DM)." Indonesian Journal of Chemistry and Environment 4, no. 2 (March 10, 2022): 49–56. http://dx.doi.org/10.21831/ijoce.v4i2.48401.

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The structure and hydration dynamics of Ga3+ ion have been studied using classical Molecular Dynamics (MD) simulations. The data collection procedure includes determining the best base set, constructing 2-body and 3-body potential equations, classical molecular dynamics simulations based on 2-body potentials, classical molecular dynamics simulations based on 2-body + 3 potential-body. The trajectory file data analysis was done to obtain structural properties parameters such as RDF, CND, ADF, and dynamic properties, namely the movement of H2O ligands between hydrations shells. The results of the research indicated that the hydration complex structure of Ga(H2O)83+ and Ga(H2O)63+ was observed in molecular dynamics simulations (MM-2 body) and (MM-2 body + 3-body), respectively. The movement of H2O ligands occurs between the first and second shell or vice versa in the MD simulation of MM-2 bodies but does not occur in MD simulations of (MM-2 bodies + MM-3 bodies). Therefore, the water ligands in the first hydrated shell are stable.
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YONEDA, Tomoyuki, Moritaka HIDA, and Akira SAKAKIBARA. "Molecular Dynamics Simulations. Molecular Dynamics Simulation of Ni Crystals under Uniaxial Deformation." Journal of the Society of Materials Science, Japan 46, no. 3 (1997): 228–31. http://dx.doi.org/10.2472/jsms.46.228.

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Dissertations / Theses on the topic "Molecular Dynamics Simulation Molecular dynamics"

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Cai, Qiong. "Hybrid molecular dynamics simulation." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/10849.

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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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Bekker, Hendrik. "Molecular dynamics simulation methods revised." [Groningen] : [Groningen] : Rijksuniversiteit Groningen ; [University Library Groningen] [Host], 1996. http://irs.ub.rug.nl/ppn/14860532X.

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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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Tarmyshov, Konstantin B. "Molecular dynamics simulations." Phd thesis, [S.l.] : [s.n.], 2007. https://tuprints.ulb.tu-darmstadt.de/787/1/000_pdfsam_PhD_thesis_-_All_-_LinuxPS2PDF.ps.pdf.

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Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble via its development in time and space. Chapter 1 gives a short overview of techniques used today in molecular simulations field, their limitations, and their development. Chapter 2 concentrates on the description of methods used in this work to perform molecular dynamics simulations of cucurbit[6]uril in aqueous and salt solutions as well as metal-isopropanol interface. This is followed by Chapter 3 that outlines main areas in our life where these systems can be used. The development of instruments is as important as the scientific part of molecular simulations like methods and algorithms. Parallelization procedure of the atomistic molecular dynamics program YASP for shared-memory computer architectures is described in Chapter 4. Parallelization was restricted to the most CPU-time consuming parts: neighbour-list construction, calculation of non-bonded, angle and dihedral forces, and constraints. Most of the sequential FORTRAN code was kept; parallel constructs were inserted as compiler directives using the OpenMP standard. Only in the case of the neighbour list the data structure had to be changed. The parallel code achieves a useful speed-up over the sequential version for systems of several thousand atoms and above. On an IBM Regatta p690+, the throughput increases with the number of processors up to a maximum of 12-16 processors depending on characteristics of the simulated systems. On dual-processor Xeon systems, the speed-up is about 1.7. Certainly, these results will be of interest to other scientific groups in academia and industry that would like to improve their own simulation codes. In order to develop a molecular receptor or choose from already existing ones that fits certain needs one must have quite good knowledge of non-covalent host-guest interactions. One also wants to have control over the capture/release process via environment of the receptor (pH, salt concentration, etc.). Chapter 5 is devoted to molecular dynamics simulations preformed to study the microscopic structure and dynamics of cations bound to cucurbit[6]uril (CB[6]) in water and in aqueous solutions of sodium, potassium, and calcium chloride. The molarities are 0.183M for the salts, and 0.0184M for CB[6]. The cations bind only to CB[6] carbonyl oxygens. They are never found inside the CB[6] cavity. Complexes with Na+ and K+ mostly involve one cation, whereas with Ca2+ single- and double-cation complexes are formed in similar proportions. The binding dynamics strongly depends on the type of cation. A smaller size or higher charge increases the residence time of a cation at a given carbonyl oxygen. The diffusion dynamics also corresponds to the binding strength of cations: the stronger binding the slower diffusion and reorientation dynamics. When bound to CB[6], sodium and potassium cations jump mainly between nearest or second-nearest neighbours. Calcium shows no hopping dynamics. It is coordinated predominantly by one CB[6] oxygen. A few water molecules (zero to four) can occupy the CB[6] cavity, which is delimited by the CB[6] oxygen faces. Their residence time is hardly influenced by sodium and potassium ions. In the case of calcium the residence time of the inner water increases notably. A simple structural model for the cations acting as “lids” over the CB[6] portal cannot, however, be confirmed. The slowing of the water exchange by the ions is a consequence of the generally slower dynamics in their presence and of their stable solvation shells. The study of binding behaviour of simple hydrophobic (Lennard-Jones) particles by CB[6] showed that these particles do not bind. A simple test showed that the size of hydrophobic particles in this case is important for a stable encapsulation. Another challenging field of research is the metal-organic interfaces. Particularly, transition metals are more difficult as they form chemical bonds, though sometimes very weak, with a large number of organic compounds. In Chapter 6 a molecular dynamics model and its parameterization procedure are devised and used to study adsorption of isopropanol on platinum(111) (Pt(111)) surface in unsaturated and oversaturated coverages regimes. Static and dynamic properties of the interface between Pt(111) and liquid isopropanol are also investigated. The magnitude of the adsorption energy at unsaturated level increases at higher coverages. At the oversaturated coverage (multilayer adsorption) the adsorption energy reduces, which coincides with findings by Panja et al. in their temperature-programmed desorption experiment (ref. 25). The density analysis showed a strong packing of molecules at the interface followed by a depletion layer and then by an oscillating density profile up to 3 nm. The distribution of individual atom types showed that the first adsorbed layer forms a hydrophobic methyl “brush”. This “brush” then determines the distributions further from the surface. In the second layer methyl and methine groups are closer to the surface and are followed by the hydroxyl groups; the third layer has exactly the inverted distribution. The alternating pattern extends up to about 2 nm from the surface. The orientational structure of molecules as a function of distance of molecules is determined by the atoms distribution and surprisingly does not depend on the electrostatic or chemical interactions of isopropanol with the metal surface. However, possible formation of hydrogen bonds in the first layer is notably influenced by these interactions. The surface-adsorbate interactions influence mobility of isopropanol molecules only in the first layer. Mobility in the higher layers is independent of these interactions. Finally, Chapter 7 summarizes main conclusions of the studies presented in this thesis and outlines perspectives of the future research.
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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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Ernst, Matthew Brian. "Molecular dynamics simulation of DNA lesions." Online access for everyone, 2005. http://www.dissertations.wsu.edu/Thesis/Fall2005/m%5Fernst%5F121305.pdf.

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Naser, Md Abu. "Molecular dynamics simulation of protein adsorption." Thesis, Heriot-Watt University, 2008. http://hdl.handle.net/10399/2187.

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Lu, Lanyuan Berkowitz Max L. "Molecular dynamics simulation of amphiphilic aggregates." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2007. http://dc.lib.unc.edu/u?/etd,787.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2007.
Title from electronic title page (viewed Dec. 18, 2007). " ... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Chemistry." Discipline: Chemistry; Department/School: Chemistry.
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Books on the topic "Molecular Dynamics Simulation Molecular dynamics"

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Haile, J. M. Molecular dynamics simulation: Elementary methods. New York: Wiley, 1992.

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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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The art of molecular dynamics simulation. 2nd ed. Cambridge, UK: Cambridge University Press, 2004.

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The art of molecular dynamics simulation. Cambridge: Cambridge University Press, 1995.

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Satō, Akira. Introduction to practice of molecular simulation: Molecular dynamics, Monte Carlo, Brownian dynamics, Lattice Boltzmann, dissipative particle dynamics. Amsterdam: Elsevier, 2011.

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Heinecke, Alexander, Wolfgang Eckhardt, Martin Horsch, and Hans-Joachim Bungartz. Supercomputing for Molecular Dynamics Simulations. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-17148-7.

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Massobrio, Carlo, Jincheng Du, Marco Bernasconi, and Philip S. Salmon, eds. Molecular Dynamics Simulations of Disordered Materials. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-15675-0.

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Kholmurodov, Kholmirzo. Molecular simulation in material and biological research. Hauppauge, NY: Nova Science Publishers, 2009.

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Bird, G. A. Molecular gas dynamics and the direct simulation of gas flows. Oxford: Clarendon Press, 1998.

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Molecular gas dynamics and the direct simulation of gas flows. Oxford: Clarendon Press, 1994.

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Book chapters on the topic "Molecular Dynamics Simulation Molecular dynamics"

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Heinecke, Alexander, Wolfgang Eckhardt, Martin Horsch, and Hans-Joachim Bungartz. "Molecular Dynamics Simulation." In Supercomputing for Molecular Dynamics Simulations, 11–29. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-17148-7_2.

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Li, Zhigang. "Molecular dynamics simulation." In Nanofluidics, 45–78. Boca Raton : Taylor & Francis, a CRC title, part of the Taylor &: CRC Press, 2018. http://dx.doi.org/10.1201/b22007-3.

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Raabe, Gabriele. "Molecular Dynamics Simulations." In Molecular Simulation Studies on Thermophysical Properties, 83–113. Singapore: Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-3545-6_4.

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Frenkel, D. "Simulation of Sub-molecular and Supra-molecular Fluids." In Molecular Dynamics Simulations, 111–29. Berlin, Heidelberg: Springer Berlin Heidelberg, 1992. http://dx.doi.org/10.1007/978-3-642-84713-4_10.

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Straatsma, T. P. "NWChem Molecular Dynamics Simulation." In High Performance Computing Systems and Applications, 231–39. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4615-5611-4_21.

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Xu, Dongyan, and Deyu Li. "Molecular Dynamics Simulation Method." In Encyclopedia of Microfluidics and Nanofluidics, 2290–97. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4614-5491-5_1052.

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Xu, Dongyan, and Deyu Li. "Molecular Dynamics Simulation Method." In Encyclopedia of Microfluidics and Nanofluidics, 1–10. Boston, MA: Springer US, 2014. http://dx.doi.org/10.1007/978-3-642-27758-0_1052-2.

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Tildesley, D. J. "The Molecular Dynamics Method." In Computer Simulation in Chemical Physics, 23–47. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1679-4_2.

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Galli, G., and A. Pasquarello. "First-principles Molecular Dynamics." In Computer Simulation in Chemical Physics, 261–313. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1679-4_8.

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Turner, James, Paul K. Weiner, Barry Robson, Ravi Venugopal, Harry Schubele, and Ramen Singh. "Reduced variable molecular dynamics." In Computer Simulation of Biomolecular Systems, 122–49. Dordrecht: Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-017-1120-3_4.

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Conference papers on the topic "Molecular Dynamics Simulation Molecular dynamics"

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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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Takagi, Shu, Gota Kikugawa, and Yoichiro Matsumoto. "Molecular Dynamics Simulation of Nanobubbles." In ASME/JSME 2003 4th Joint Fluids Summer Engineering Conference. ASMEDC, 2003. http://dx.doi.org/10.1115/fedsm2003-45675.

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Some results have been reported recently related to the bubble formation with Molecular Dynamics (MD) simulation method. Some of them conduct the MD simulations of the bubble nucleation including impurity molecules with L-J potential [1,2]. In the present study, we investigate the stability of the nanometer size bubble in water, using molecular dynamics (MD) simulation method. MD simulation of an aqueous surfactant system: water liquid and alcohols below the liquid saturation density is carried out to investigate the stability of “nanobubbles” and the structure of the gas-liquid interface. To analyze the effect of surfactant structure, volume, and polarization on the stability of bubble nuclei, we use water by SPC/E model as the solvent molecules and 1-propanol, 1-pentanol, 1-heptanol as the surfactant molecules. Fig.1 shows the numerical result of instantaneous behavior of nanobubbles under the presence of surfactant in water. The calculation system is the cubic cell which has a side length of 25.057[Å], and a three-dimensional periodic boundary condition is applied. To include the intramolecular motion, AMBER force field [3] is adopted as a potential function. The momentum equations are integrated by velocity-Verlet argorithm [4]. Further, the time integration is extended to the Multi Time Scale algorithm by r-RESPA method [5]. As the surfactant molecules, to evaluate the influence of the hydrophobic effect of surfactants on the stability of bubble nuclei, we adopt 1-propanol (C3H7OH), 1-pentanol (C5H11OH), and 1-heptanol (C7H15OH), and to investigate the influence of the polarization of hydrophilic groups (-OH), “pseudo” 1-pentanol of which charge is cancelled away is also calculated. As a result, it was found that from the MD simulation at the condition that the bubble nuclei could not exist stably in pure water, a stable bubble is formed in aqueous surfactant system and hydroxyl groups of surfactants tend to point to the liquid phase at the gas-liquid interface. It is also shown that the longer hydrophobic chains the surfactants have, the more stably the bubble nuclei can exist.
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Matsumoto, D. "Quantum Molecular Dynamics Simulation of Guest Molecules in Gas Hydrate." In SLOW DYNAMICS IN COMPLEX SYSTEMS: 3rd International Symposium on Slow Dynamics in Complex Systems. AIP, 2004. http://dx.doi.org/10.1063/1.1764312.

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Koda, Tomonori. "Molecular dynamics simulation of mixtures of hard rod-like molecules." In SLOW DYNAMICS IN COMPLEX SYSTEMS: 3rd International Symposium on Slow Dynamics in Complex Systems. AIP, 2004. http://dx.doi.org/10.1063/1.1764099.

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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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Takeuchi, Hideki, Kyoji Yamamoto, Toru Hyakutake, and Takashi Abe. "Molecular Dynamics Simulation of Reflected Gas Molecules on Water Adsorbed Surface." In RARIFIED GAS DYNAMICS: Proceedings of the 26th International Symposium on Rarified Gas Dynamics. AIP, 2008. http://dx.doi.org/10.1063/1.3076560.

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Mareschal, Michel, Andrei Popruga, Joaquín Marro, Pedro L. Garrido, and Pablo I. Hurtado. "Molecular ordering at an interface by molecular dynamics." In MODELING AND SIMULATION OF NEW MATERIALS: Proceedings of Modeling and Simulation of New Materials: Tenth Granada Lectures. AIP, 2009. http://dx.doi.org/10.1063/1.3082272.

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Aksenova, O. A., and I. A. Khalidov. "Molecular Dynamics Simulation of Gas Molecules Reflected from Rough Surface." In 27TH INTERNATIONAL SYMPOSIUM ON RAREFIED GAS DYNAMICS. AIP, 2011. http://dx.doi.org/10.1063/1.3562687.

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Terrell, Elon J., Eric Landry, Alan McGaughey, and C. Fred Higgs. "Molecular Dynamics Simulation of Nanoindentation." In STLE/ASME 2008 International Joint Tribology Conference. ASMEDC, 2008. http://dx.doi.org/10.1115/ijtc2008-71287.

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A molecular dynamics model of a nanoindentation experiment was simulated in order to calculate the elastic modulus of several different Lennard-Jones (LJ) solids. It was found that the elastic modulus increased significantly as the depth of the potential well that describes the interactions between the atoms in the sample was increased.
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Kharlamov, Georgy V., Andrey A. Onischuk, Piotr A. Purtov, Sergey V. Vosel, and Alexey V. Bolesta. "Molecular dynamics simulation of nanodrops." In 2009 International Conference and Seminar on Micro/Nanotechnologies and Electron Devices (EDM). IEEE, 2009. http://dx.doi.org/10.1109/edm.2009.5173932.

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Reports on the topic "Molecular Dynamics Simulation Molecular dynamics"

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THOMPSON, AIDAN P. Molecular Dynamics Simulation of Polymer Dissolution. Office of Scientific and Technical Information (OSTI), February 2003. http://dx.doi.org/10.2172/808631.

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Mountain, Raymond D., and Joseph Hubbard. Molecular dynamics simulation of tethered chains. Gaithersburg, MD: National Institute of Standards and Technology, 1998. http://dx.doi.org/10.6028/nist.ir.6150.

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Micci, Michael M. Molecular Dynamics Simulation of Supercritical Spray Phenomena. Fort Belvoir, VA: Defense Technical Information Center, September 2008. http://dx.doi.org/10.21236/ada492151.

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Gu, Wei, and B. P. Schoenborn. Molecular dynamics simulation of hydration in myoglobin. Office of Scientific and Technical Information (OSTI), September 1995. http://dx.doi.org/10.2172/104441.

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Moyers, Aidan, Derek Davies, Michael Becker, and Desiderio Kovar. Molecular dynamics simulation of yttria (Y2O3) nanoparticle impacts. Office of Scientific and Technical Information (OSTI), February 2022. http://dx.doi.org/10.2172/1846111.

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Kress, Joel D., Lee A. Collins, Leonid Burakovsky, Stuart D. Herring, Christopher Ticknor, and Scott Crockett. Simulations as Data: Quantum Molecular Dynamics. Office of Scientific and Technical Information (OSTI), October 2012. http://dx.doi.org/10.2172/1052783.

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Barros, Kipton Marcos. Advances in machine learned potentials for molecular dynamics simulation. Office of Scientific and Technical Information (OSTI), October 2018. http://dx.doi.org/10.2172/1477636.

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Hammerberg, J. E., B. L. Holian, M. S. Murillo, and D. Winske. Molecular dynamics simulations of dipolar dusty plasmas. Office of Scientific and Technical Information (OSTI), December 1998. http://dx.doi.org/10.2172/307953.

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Wong, C. C., A. R. Lopez, M. J. Stevens, and S. J. Plimpton. Molecular dynamics simulations of microscale fluid transport. Office of Scientific and Technical Information (OSTI), February 1998. http://dx.doi.org/10.2172/574190.

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Wirth, B. D., M. J. Caturla, and Diaz de la Rubia, T. Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo. Office of Scientific and Technical Information (OSTI), October 2000. http://dx.doi.org/10.2172/792741.

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