Relevant bibliographies by topics / Molecular dynamics

Contents

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

Academic literature on the topic 'Molecular dynamics'

Author: Grafiati
Published: 4 June 2021
Last updated: 2 November 2024

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Journal articles on the topic "Molecular dynamics"

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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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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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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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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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Davies, Matt. "Molecular dynamics." Biochemist 26, no. 4 (August 1, 2004): 53–54. http://dx.doi.org/10.1042/bio02604053.

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Bergstra, J. A., and I. Bethke. "Molecular dynamics." Journal of Logic and Algebraic Programming 51, no. 2 (June 2002): 193–214. http://dx.doi.org/10.1016/s1567-8326(02)00021-8.

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Goodfellow, Julia M., and Mark A. Williams. "Molecular dynamics." Current Biology 2, no. 5 (May 1992): 257–58. http://dx.doi.org/10.1016/0960-9822(92)90373-i.

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Goodfellow, Julia M., and Mark A. Williams. "Molecular dynamics." Current Opinion in Structural Biology 2, no. 2 (April 1992): 211–16. http://dx.doi.org/10.1016/0959-440x(92)90148-z.

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Alder, Berni J. "Slow dynamics by molecular dynamics." Physica A: Statistical Mechanics and its Applications 315, no. 1-2 (November 2002): 1–4. http://dx.doi.org/10.1016/s0378-4371(02)01220-7.

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Dissertations / Theses on the topic "Molecular dynamics"

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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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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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Batchelor, Colin. "Molecular Rydberg dynamics." Thesis, University of Oxford, 2003. http://ora.ox.ac.uk/objects/uuid:46b5699b-1dcf-4860-8d76-09fc487a09d4.

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A simple theory relating the dynamics of electrons to the long-range properties of the molecular ionic core is developed for asymmetric top molecules in general and water in particular. It is combined with the molecular version of multichannel quantum defect theory developed by Fano and Jungen and applied to the resonance-enhanced multiphoton ionization spectra of Child and Glab (M. S. Child and W. G. Glab, J. Chem. Phys., 2001, 112, 3754-3765), the mass-analysed threshold ionization spectra of Dickinson et al. (H. Dickinson, S. R. Mackenzie and T. P. Softley, Phys. Chem. Chem. Phys., 2000, 2, 4669-4675) and the as-yet unpublished work of Glab on the photoelectron branching ratios of the nd and nf Rydberg lines of the water molecule. The effect of resonances between electronic and rotational motion in Rydberg molecules is investigated using multichannel quantum defect theory with special reference to the time-resolved wave packet experiments of Smith et al. (R. A. L. Smith, J. R. R. Verlet, E. D. Boleat, V. G. Stavros and H. H. Fielding, Faraday Discuss., 2000, 115, 63-70).
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O'Mahony, John. "Molecular photodissociation dynamics." Thesis, University of Nottingham, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.277879.

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Docker, M. P. "Molecular photodissociation dynamics." Thesis, University of Nottingham, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.378987.

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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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Lin, Jr-Hung. "Nonatomistic molecular dynamics /." Aachen : Shaker, 2008. http://d-nb.info/991265556/04.

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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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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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Books on the topic "Molecular dynamics"

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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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Santamaria, Ruben. Molecular Dynamics. Cham: Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-37042-7.

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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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Gatti, Fabien, ed. Molecular Quantum Dynamics. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-45290-1.

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Sone, Yoshio, ed. Molecular Gas Dynamics. Boston, MA: Birkhäuser Boston, 2007. http://dx.doi.org/10.1007/978-0-8176-4573-1.

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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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Levine, Raphael D. Molecular reaction dynamics. Cambridge, UK: Cambridge University Press, 2005.

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Shuichi, Nosé, ed. Molecular dynamics simulations. Kyoto: Progress of theoretical physics, 1991.

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Book chapters on the topic "Molecular dynamics"

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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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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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Shimono, Masato. "Molecular Dynamics." In Springer Handbook of Materials Measurement Methods, 915–52. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/978-3-540-30300-8_17.

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Bungartz, Hans-Joachim, Stefan Zimmer, Martin Buchholz, and Dirk Pflüger. "Molecular Dynamics." In Springer Undergraduate Texts in Mathematics and Technology, 317–35. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-39524-6_13.

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Lanig, Harald. "Molecular Dynamics." In Chemoinformatics, 301–19. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2018. http://dx.doi.org/10.1002/9783527816880.ch8_03.

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Wang, Sun-Chong. "Molecular Dynamics." In Interdisciplinary Computing in Java Programming, 133–45. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4615-0377-4_8.

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Fang, Fengzhou, and Pengzhe Zhu. "Molecular Dynamics." In CIRP Encyclopedia of Production Engineering, 1236–39. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-53120-4_16729.

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Stickler, Benjamin A., and Ewald Schachinger. "Molecular Dynamics." In Basic Concepts in Computational Physics, 97–109. Cham: Springer International Publishing, 2013. http://dx.doi.org/10.1007/978-3-319-02435-6_7.

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Conference papers on the topic "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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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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Miles, R., and W. Lempert. "Three-dimensional diagnostics in air and water by molecular tagging and molecular scattering." In Fluid Dynamics Conference. Reston, Virigina: American Institute of Aeronautics and Astronautics, 1996. http://dx.doi.org/10.2514/6.1996-1963.

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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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Cacciatore, M., and M. Rutigliano. "Molecular Dynamics Studies on Fundamental Molecular Surface Processes." In 27TH INTERNATIONAL SYMPOSIUM ON RAREFIED GAS DYNAMICS. AIP, 2011. http://dx.doi.org/10.1063/1.3562686.

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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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Hernández, E. R., Luis Manuel Montaño Zetina, Gabino Torres Vega, Miguel Garcia Rocha, Luis F. Rojas Ochoa, and Ricardo Lopez Fernandez. "Molecular Dynamics: from basic techniques to applications (A Molecular Dynamics Primer)." In FRONTIERS IN CONTEMPORARY PHYSICS. AIP, 2008. http://dx.doi.org/10.1063/1.3040265.

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Bowers, Kevin J., Federico D. Sacerdoti, John K. Salmon, Yibing Shan, David E. Shaw, Edmond Chow, Huafeng Xu, et al. "Molecular dynamics---Scalable algorithms for molecular dynamics simulations on commodity clusters." In the 2006 ACM/IEEE conference. New York, New York, USA: ACM Press, 2006. http://dx.doi.org/10.1145/1188455.1188544.

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Kasai, Toshio. "Stereospecific Control by Molecular Orientation." In RAREFIED GAS DYNAMICS: 24th International Symposium on Rarefied Gas Dynamics. AIP, 2005. http://dx.doi.org/10.1063/1.1941641.

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Reports on the topic "Molecular dynamics"

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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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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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Debenedetti, P. G. Molecular interactions in dilute supercritical mixtures: Molecular dynamics investigation. Office of Scientific and Technical Information (OSTI), January 1991. http://dx.doi.org/10.2172/5093976.

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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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