Academic literature on the topic 'Approach-to-equilibrium molecular dynamics (AEMD)'
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Journal articles on the topic "Approach-to-equilibrium molecular dynamics (AEMD)"
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Dong, Dengpan, Weiwei Zhang, Adam Barnett, Jibao Lu, Adri van Duin, Valeria Molinero, and Dmitry Bedrov. "Multiscale Modeling of Structure, Transport and Reactivity in Alkaline Fuel Cell Membranes: Combined Coarse-Grained, Atomistic and Reactive Molecular Dynamics Simulations." Polymers 10, no. 11 (November 20, 2018): 1289. http://dx.doi.org/10.3390/polym10111289.
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In this study, molecular dynamics (MD) simulations of hydrated anion-exchange membranes (AEMs), comprised of poly(p-phenylene oxide) (PPO) polymers functionalized with quaternary ammonium cationic groups, were conducted using multiscale coupling between three different models: a high-resolution coarse-grained (CG) model; Atomistic Polarizable Potential for Liquids, Electrolytes and Polymers (APPLE&P); and ReaxFF. The advantages and disadvantages of each model are summarized and compared. The proposed multiscale coupling utilizes the strength of each model and allows sampling of a broad spectrum of properties, which is not possible to sample using any of the single modeling techniques. Within the proposed combined approach, the equilibrium morphology of hydrated AEM was prepared using the CG model. Then, the morphology was mapped to the APPLE&P model from equilibrated CG configuration of the AEM. Simulations using atomistic non-reactive force field allowed sampling of local hydration structure of ionic groups, vehicular transport mechanism of anion and water, and structure equilibration of water channels in the membrane. Subsequently, atomistic AEM configuration was mapped to ReaxFF reactive model to investigate the Grotthuss mechanism in the hydroxide transport, as well as the AEM chemical stability and degradation mechanisms. The proposed multiscale and multiphysics modeling approach provides valuable input for the materials-by-design of novel polymeric structures for AEMs.
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Lampin, E., P. L. Palla, P. A. Francioso, and F. Cleri. "Thermal conductivity from approach-to-equilibrium molecular dynamics." Journal of Applied Physics 114, no. 3 (July 21, 2013): 033525. http://dx.doi.org/10.1063/1.4815945.
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SUMI, R., and Z. NÉDA. "MOLECULAR DYNAMICS APPROACH TO CORRELATION CLUSTERING." International Journal of Modern Physics C 19, no. 09 (September 2008): 1349–58. http://dx.doi.org/10.1142/s0129183108012984.
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A many-body system with co-existing attractive and repulsive interactions is considered on a ring. The competing interactions lead to a frustration similar with the one existing in Correlation Clustering (CC). The optimal mechanical equilibrium of the system is searched by molecular dynamics simulations. As a function of the disorder quenched in the interactions, the system exhibits the phase-transition recently reported in CC. The simulated system can be considered as a continuous and efficient approach to the otherwise discrete, NP hard CC problem.
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Reilly, A. M., D. A. Wann, C. A. Morrison, and D. W. H. Rankin. "A molecular dynamics approach to equilibrium structures in crystals." Acta Crystallographica Section A Foundations of Crystallography 64, a1 (August 23, 2008): C221. http://dx.doi.org/10.1107/s0108767308092908.
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Stock, Gerhard, and Peter Hamm. "A non-equilibrium approach to allosteric communication." Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1749 (May 7, 2018): 20170187. http://dx.doi.org/10.1098/rstb.2017.0187.
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While the theory of protein folding is well developed, including concepts such as rugged energy landscape, folding funnel, etc., the same degree of understanding has not been reached for the description of the dynamics of allosteric transitions in proteins. This is not only due to the small size of the structural change upon ligand binding to an allosteric site, but also due to challenges in designing experiments that directly observe such an allosteric transition. On the basis of recent pump-probe-type experiments (Buchli et al. 2013 Proc. Natl Acad. Sci. USA 110 , 11 725–11 730. ( doi:10.1073/pnas.1306323110 )) and non-equilibrium molecular dynamics simulations (Buchenberg et al. 2017 Proc. Natl Acad. Sci. USA 114 , E6804–E6811. ( doi:10.1073/pnas.1707694114 )) studying an photoswitchable PDZ2 domain as model for an allosteric transition, we outline in this perspective how such a description of allosteric communication might look. That is, calculating the dynamical content of both experiment and simulation (which agree remarkably well with each other), we find that allosteric communication shares some properties with downhill folding, except that it is an ‘order–order’ transition. Discussing the multiscale and hierarchical features of the dynamics, the validity of linear response theory as well as the meaning of ‘allosteric pathways’, we conclude that non-equilibrium experiments and simulations are a promising way to study dynamical aspects of allostery. This article is part of a discussion meeting issue ‘Allostery and molecular machines’.
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Likić, Vladimir A., Paul R. Gooley, Terence P. Speed, and Emanuel E. Strehler. "A statistical approach to the interpretation of molecular dynamics simulations of calmodulin equilibrium dynamics." Protein Science 14, no. 12 (December 2005): 2955–63. http://dx.doi.org/10.1110/ps.051681605.
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Borgis, D., and M. Moreau. "On the equilibrium approach to isomerization dynamics in liquids." Molecular Physics 57, no. 1 (January 1986): 33–53. http://dx.doi.org/10.1080/00268978600100031.
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de Oliveira Cardozo, Giovano, and José Pedro Rino. "Molecular Dynamics Calculations of InSb Thermal Conductivity." Defect and Diffusion Forum 297-301 (April 2010): 1400–1407. http://dx.doi.org/10.4028/www.scientific.net/ddf.297-301.1400.
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Equilibrium and non-equilibrium molecular dynamics calculations of thermal conductivity coefficient are presented for bulk systems of InSb, using an effective two- and three-body inter atomic potential which demonstrated to be very transferable. In the calculations, the obtained coefficients were comparable to the experimental data. In the case of equilibrium simulations a Green-Kubo approach was used and the thermal conductivity was calculated for five temperatures between 300 K and 900 K. For the non equilibrium, or direct method, which is based on the Fourier’s law, the thermal conductivity coefficient was determined at a mean temperature of 300K. In this case it was used a pair of reservoirs, placed at a distance L from each other, and with internal temperatures fixed in 250 K, for the cold reservoir, and 350 K for the hot one. In order to obtain an approach to an infinite system coefficient, four different values of L were used, and the data was extrapolated to L→∞.
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Ilčin, Michal, Martin Michalík, Klára Kováčiková, Lenka Káziková, and Vladimír Lukeš. "Water liquid-vapor equilibrium by molecular dynamics: Alternative equilibrium pressure estimation." Acta Chimica Slovaca 9, no. 1 (April 1, 2016): 36–43. http://dx.doi.org/10.1515/acs-2016-0007.
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Abstract The molecular dynamics simulations of the liquid-vapor equilibrium of water including both water phases — liquid and vapor — in one simulation are presented. Such approach is preferred if equilibrium curve data are to be collected instead of the two distinct simulations for each phase separately. Then the liquid phase is not restricted, e.g. by insufficient volume resulting in too high pressures, and can spread into its natural volume ruled by chosen force field and by the contact with vapor phase as vaporized molecules are colliding with phase interface. Averaged strongly fluctuating virial pressure values gave untrustworthy or even unreal results, so need for an alternative method arisen. The idea was inspired with the presence of vapor phase and by previous experiences in gaseous phase simulations with small fluctuations of pressure, almost matching the ideal gas value. In presented simulations, the first idea how to calculate pressure only from the vapor phase part of simulation box were applied. This resulted into very simple method based only on averaging molecules count in the vapor phase subspace of known volume. Such simple approach provided more reliable pressure estimation than statistical output of the simulation program. Contrary, also drawbacks are present in longer initial thermostatization time or more laborious estimation of the vaporization heat. What more, such heat of vaporization suffers with border effect inaccuracy slowly decreasing with the thickness of liquid phase. For more efficient and more accurate vaporization heat estimation the two distinct simulations for each phase separately should be preferred.
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ENCISO, E., N. G. ALMARZA, S. MURAD, and M. A. GONZALEZ. "A non-equilibrium molecular dynamics approach to fluid transfer through microporous membranes." Molecular Physics 100, no. 14 (July 20, 2002): 2337–49. http://dx.doi.org/10.1080/00268970210124819.
Full textDissertations / Theses on the topic "Approach-to-equilibrium molecular dynamics (AEMD)"
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Dearman, Leslie R. "A New Approach to Non-Equilibrium Molecular Dynamics." Thesis, University of Reading, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.520095.
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Diarra, Cheick Oumar. "Modélisation par dynamique moléculaire ab initio du transport des excitons et du transport thermique dans les semiconducteurs organiques pour la collecte d'énergie." Electronic Thesis or Diss., Strasbourg, 2024. http://www.theses.fr/2024STRAD013.
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L'exciton joue un rôle clé dans le fonctionnement des cellules solaires organiques (OSCs). Comprendre sa dynamique dans les semiconducteurs organiques est essentiel, notamment pour améliorer la longueur de diffusion, une propriété déterminante pour la performance des hétérojonctions planaires, envisagées comme une alternative plus stable aux hétérojonctions en volume (BHJ). Dans la première partie de cette thèse, nous avons développé une approche méthodologique robuste et polyvalente pour évaluer la longueur de diffusion de l'exciton dans les semiconducteurs organiques. Cette approche, basée sur AIMD-ROKS, a été validée avec succès dans le cas du polymère P3HT. Elle a également été appliquée à l'accepteur NFA O-IDTBR, révélant des longueurs de diffusion prometteuses, mais encore insuffisantes pour les hétérojonctions planaires. Dans la deuxième partie de la thèse, le transfert de chaleur dans les semiconducteurs organiques a été exploré, élément crucial pour la performance des dispositifs thermoélectriques. Ces études se sont concentrées sur le P3HT, un matériau utilisé en thermoélectricité. Dans un premier temps, la conductivité thermique au sein des chaînes de P3HT a été étudiée, révélant l'influence de la longueur des chaînes de polymère. Ensuite, les transferts de chaleur entre ces chaînes ont également été examinésThe exciton plays a central role in the functioning of organic solar cells (OSCs). Understanding its dynamics in organic semiconductors is essential, particularly to optimize the diffusion length, a key property for the performance of planar heterojunctions, which are considered as a potentially more stable alternative to bulk heterojunctions (BHJ) in certain contexts. In the first part of this thesis, we developed a robust and versatile methodological approach to evaluate the exciton diffusion length in organic semiconductors. This method, based on AIMD-ROKS, was successfully validated for the P3HT polymer. It was also applied to the NFA O-IDTBR acceptor, revealing promising diffusion lengths, though still insufficient for planar heterojunctions. The second part of the thesis explores heat transfer in organic semiconductors, a crucial element for the performance of thermoelectric devices. These studies focused on P3HT, a material used in thermoelectricity. First, the thermal conductivity within P3HT chains was studied, revealing the influence of polymer chain length. Then, heat transfers between these chains were also examined
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Ni, Yuxiang. "Thermal contact resistance between molecular systems : an equilibrium molecular dynamics approach applied to carbon nanotubes, graphene and few layer graphene." Phd thesis, Ecole Centrale Paris, 2013. http://tel.archives-ouvertes.fr/tel-00969185.
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This thesis is devoted to the calculation of thermal contact resistance in various molecular systems based on carbon nanotubes (CNTs) and few layer graphene (FLG). This work has been performed through equilibrium molecular dynamics (EMD) simulations. We adopted the temperature difference fluctuations method in our EMD calculations. This method only needs the input of the temperatures of the subsystems whereas the heat flux, which is involved in all the other approaches, remains more difficult to compute in terms of simulation time and algorithm. Firstly, three cases were studied to validate this method, namely: (i) Si/Ge superlattices; (ii) diameter modulated SiC nanowires; and (iii) few-layer graphenes. The validity of the temperature difference fluctuations method is proved by equilibrium and non-equilibrium MD simulations. Then, by using this method, we show that an azide-functionalized polymer (HLK5) has a lower contact resistance with CNT than the one between CNT and PEMA, because HLK5 could form covalent bonds (C-N bonds) with CNT through its tail group azide, while only weak Van der Waals interactions exist in the case of CNT-PEMA contact. The data from our EMD simulations match with the results from experiments in a reasonable range. We then report the thermal contact resistance between FLG and a SiO2 substrate, which could be tuned with the layer number. Taking advantage of the resistive interface, we show that a SiO2 /FLG superlattices have a thermal conductivity as low as 0.30 W/mK, exhibiting a promising prospect in nano-scale thermal insulation. In the last part, we investigated the layer number dependence of the cross-plane thermal resistances of suspended and supported FLGs. We show that the existence of a silicon dioxide substrate can significantly decrease the cross-plane resistances of FLGs with low layer numbers, and the effective thermal conductivities were increased accordingly. The Frenkel-Kontorova model was introduced to explain the substrate-induced band gaps in FLG dispersion relations and the corresponding thermal energy transfer. The enhanced thermal conduction in the cross-plane direction is ascribed to the phonon radiation that occurs at the FLG-substrate interface, which re-distributes the FLG in-plane propagating energy to the cross-plane direction and to the substrate.
Book chapters on the topic "Approach-to-equilibrium molecular dynamics (AEMD)"
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Prigogine, Ilya, Eddy Kestemont, and Michel Mareschal. "The Approach to Equilibrium and Molecular Dynamics." In Microscopic Simulations of Complex Flows, 233–40. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4684-1339-7_15.
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Lampin, Evelyne, Pier Luca Palla, Hayat Zaoui, and Fabrizio Cleri. "Approach-to-Equilibrium Molecular Dynamics." In Nanostructured Semiconductors, 191–205. Jenny Stanford Publishing, 2017. http://dx.doi.org/10.1201/9781315364452-8.
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Bon Hoa, Gaston Hui, and Carmelo Di Primo. "Application of Pressure Relaxation to the Study of Substrate Binding to Cytochrome P-450cam versus Temperature, Pressure, and Viscosity." In High Pressure Effects in Molecular Biophysics and Enzymology. Oxford University Press, 1996. http://dx.doi.org/10.1093/oso/9780195097221.003.0015.
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The pressure-jump relaxation technique is a convenient and interesting means of studying rapid reversible reactions of biological systems. According to the change in reaction volume that accompanies a biochemical process, a rapid pressure change Δp produces a relative equilibrium shift ΔK/K, which is given by ΔlnK = AK/K = — (ΔV°/RT) Δp, where ΔV° is the reaction volume change. If the pressure change has a very short transition time, then relaxation kinetic measurements near equilibrium are possible, allowing the elucidation of reaction mechanisms through the detection of eventual reaction intermediates and the characterization of elementary kinetic and thermodynamic parameters. Our reversible pressure-jump method described in this chapter is capable of producing a sharp pressure change of ±20MPa in less than 3 milliseconds allowing the determination of relaxation rates in the time range of several milliseconds to several minutes at any final pressure up to 400 MPa, and in any viscosity solution. This technique was employed to study the binding kinetics of camphor and its analogues to bacterial cytochrome P-450cam as functions of temperature, pressure, and viscosity. The results obtained are discussed in terms of conformational dynamics of the protein associated with the entry and the exist of water molecules and specific interactions of the substrate1 with the apolar residues in the active site of cytochrome P-450cam. The binding of ligands or substrates to proteins can exhibit multistate kinetic behavior similar to transient-stale enzyme kinetics and isomerizations of proteins. The underlying elementary reaction mechanisms can be elucidated by the use of rapid mixing techniques. Usually a reaction is initiated by mixing the reactants as rapidly as possible, and the approach to equilibrium is monitored. This method has been adapted to the study of enzyme reaction mechanisms under extreme conditions of temperature and pressure (Hui Bon Hoa & Douzou, 1973; Balny et al., 1984). However, this approach is limited by the deadtime, the large amount of sample required, and difficulties in using the apparatus to study viscous solutions, such as Schlieren effects, caused by incomplete mixing in flow experiments. Relaxation techniques overcome these problems by the application of a physical perturbation to a system already at equilibrium.
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Nitzan, Abraham. "The Spin–Boson Model." In Chemical Dynamics in Condensed Phases. Oxford University Press, 2006. http://dx.doi.org/10.1093/oso/9780198529798.003.0018.
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In a generic quantum mechanical description of a molecule interacting with its thermal environment, the molecule is represented as a few level system (in the simplest description just two, for example, ground and excited states) and the environment is often modeled as a bath of harmonic oscillators. The resulting theoretical framework is known as the spin–boson model, a term that seems to have emerged in the Kondo problem literature (which deals with the behavior of magnetic impurities in metals) during the 1960s, but is now used in a much broader context. Indeed, it has become one of the central models of theoretical physics, with applications in physics, chemistry, and biology that range far beyond the subject of this book. Transitions between molecular electronic states coupled to nuclear vibrations, environmental phonons, and photon modes of the radiation field fall within this class of problems. The present chapter discusses this model and some of its mathematical implications. The reader may note that some of the subjects discussed in Chapter 9 are reiterated here in this more general framework. In Sections 2.2 and 2.9 we have discussed the dynamics of the two-level system and of the harmonic oscillator, respectively. These exactly soluble models are often used as prototypes of important classes of physical system. The harmonic oscillator is an exact model for a mode of the radiation field and provides good starting points for describing nuclear motions in molecules and in solid environments. It can also describe the short-time dynamics of liquid environments via the instantaneous normal mode approach. In fact, many linear response treatments in both classical and quantum dynamics lead to harmonic oscillator models: Linear response implies that forces responsible for the return of a system to equilibrium depend linearly on the deviation from equilibrium—a harmonic oscillator property! We will see a specific example of this phenomenology in our discussion of dielectric response in Section 16.9.
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Raff, Lionel, Ranga Komanduri, Martin Hagan, and Satish Bukkapatnam. "Empirical Potential-Energy Surfaces Fitting Using Feed forward Neural Networks." In Neural Networks in Chemical Reaction Dynamics. Oxford University Press, 2012. http://dx.doi.org/10.1093/oso/9780199765652.003.0012.
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When the system of interest becomes too complex to permit the use of ab initio methods to obtain the system potential-energy surfaces (PES), empirical potential surfaces are frequently employed to represent the force fields present in the system under investigation. In most cases, the functional forms present in these potentials are selected on the basis of chemical and physical intuitions. The parameters of the surface are frequently adjusted to fit a very small set of experimental data that comprise bond energies, equilibrium bond distances and angles, fundamental vibrational frequencies, and perhaps measured barrier heights to reactions of interest. Such potentials generally yield only qualitative or semiquantitative descriptions of the system dynamics. Several research groups have significantly improved the accuracy of the values of the experimental properties computed using empirical potential surfaces by fitting the chosen functional form for the potential to the force fields obtained from trajectories using ab initio Car-Parrinello molecular dynamics simulations. The fitting to the force fields is usually done using a least-squares fitting approach. This method has been employed by Izvekov et al. to obtain effective non-polarizable three-site force fields for liquid water. Carré et al. have employed such a procedure to obtain a new pair potential for silica. In their investigation, the vector of potential parameters was fitted using an iterative Levenberg-Marquardt algorithm. Tangney and Scandolo have also developed an interatomic force field for liquid SiO2 in which the parameters were fitted to the forces, stresses, and energies obtained from ab initio calculations. Ercolessi and Adams have used a quasi-Newtonian procedure to fit an empirical potential for aluminum to data obtained from first-principals computations. Empirical potentials can be improved by making the parameters parameterized functions of the coordinates defining the instantaneous positions of the atoms of the system. This approach has been successfully employed by numerous investigators The difficulty with this procedure is that the number of parameters that must be adjusted increases rapidly. Appropriate fitting of these parameters requires a much more extensive database. Finally, the actual fitting process can often be tedious, difficult, and time-consuming.
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Shahzad, Aamir, Zamar Ahmed, Muhammad Kashif, Amjad Sohail, Alina Manzoor, Fazeelat Hanif, Rabia Waris, and Sirag Ahmed. "Large Scale Simulations for Dust Acoustic Waves in Weakly Coupled Dusty Plasmas." In Advances in Fusion Energy Research - From Theory to Models, Algorithms, and Applications [Working Title]. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.108609.
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Dust acoustic wave of three-dimensional (3D) dusty plasmas (DPs) has been computed using equilibrium molecular dynamics (EMD) simulations for plasma parameters of Coulomb coupling strength (Γ) and Debye screening (κ). New simulations of wave properties such as longitudinal current correlation (LCC) CL(k, t) function have been investigated for 3D weakly DPs (WCDPs), for the first time. EMD results, CL (k, t) have been simulated for four normalized wave numbers (k = 0, 1, 2, and 3). Our simulations illustrate that the frequency and amplitude of oscillation vary with increasing of Γ and κ. Moreover, present simulations of CL (k, t) illustrate that the varying behavior has been observed for changing (Γ, κ) and system sizes (N). Current investigation illustrates that amplitude of wave oscillation increases with a decrease in Γ and N. However, there are slightly change in the value of CL (k, t) and its fluctuation increases with an increasing k. The obtained outcomes have found to be more acceptable than those that of previous numerical, theoretical, and experimental data. EMD simulation has been performed with an increasing sequence for WCDPs and it serves to benchmark improved approach for future energy generation applications.
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Chen, Gang. "Particle Description Of Transport Processes: Classical Laws." In Nanoscale Energy Transport And Conversion, 227–81. Oxford University PressNew York, NY, 2005. http://dx.doi.org/10.1093/oso/9780195159424.003.0006.
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Abstract We discussed in the previous chapter when we can ignore the coherence effects and treat heat carriers as individual particles without considering their phase information. In the next few chapters, we will describe how to deal with energy transfer under the particle picture. Most constitutive equations for macroscale transport processes, such as the Fourier law and the Newton shear stress laws, are obtained under such particle pictures. These equations are often formulated as laws summarized from experiments. In this chapter, we will see that most of the classical laws governing transport processes can be derived from a few fundamental principles. In chapter 4, we studied systems at equilibrium and developed the equilibrium distribution functions (Fermi-Dirac, Bose-Einstein, and Boltzmann distributions). The distribution function for a quantum state at equilibrium is a function of the energy of the quantum state, the system temperature, and the chemical potential. When the system is not at equilibrium, these distribution functions are no longer applicable. Ideally, we would like to trace the trajectory of all the particles in the system, as in the molecular dynamics approach that we will discuss in chapter 10. This approach, however, is not realistic for most systems, because they have a large number of atoms or molecules. Thus, we resort to a statistical description of the particle trajectory. In the statistical description we use nonequilibrium distribution functions, which depend not only on the energy and temperature of the system but also on positions and other variables. We will develop in this chapter the governing equations for the nonequilibrium distribution functions. In particular, we will rely on the Boltzmann equation, also called the Boltzmann transport equation. From the Boltzmann equation we will derive familiar constitutive equations such as the Fourier law, the Newton shear stress law, and the Ohm law.
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Dobson, C. M. "The Role of NMR Spectroscopy in Understanding How Proteins Fold." In Biological NMR Spectroscopy. Oxford University Press, 1997. http://dx.doi.org/10.1093/oso/9780195094688.003.0014.
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Proteins are synthesized within the cell on ribosomes. Although there is debate as to the beginnings of folding, it is clear that the major events in the folding process of a protein occur following departure from the ribosome. Folding may involve a series of auxiliary proteins, including molecular chaperones, and for extracellular proteins may occur in part following secretion from the cell itself (Ellis, 1994). Nevertheless, many proteins also fold efficiently and correctly in isolation, for example, following transfer from a denaturing medium to a medium in which the native state is thermodynamically stable (Anfinsen, 1973). It seems most unlikely, given the improbability that folding could occur in a finite time on a random search basis (Levinthal, 1968), that the principles behind the folding process differ fundamentally in the two situations (in vivo and in vitro). Studies of the molecular basis of protein folding are therefore appropriately initiated in vitro, where physical techniques capable of providing detailed structural information can be used most readily and where folding of molecules can be examined in isolation (Evans and Radford, 1994). It has long been recognized that NMR spectroscopy, with its ability to define protein structure and dynamics in solution, is ideally suited as a technique for studying the structural transitions that take place during folding. The rapidity of folding of small proteins under most conditions, however, has until recently limited its direct application in ‘real time’ kinetic studies. Early applications of NMR in folding studies therefore included investigations of the equilibrium between folded and unfolded states, and a search for stable intermediate species (Jardetzky et al., 1972). This approach has in fact become very important in recent years with the discovery that a wide range of stable partially structured states can be generated under carefully chosen conditions, and with the development of heteronuclear NMR techniques that make possible their detailed characterisation (Dobson, 1994). The most famous of these partially folded states are known as ‘molten globules’, compact species with extensive secondary structure but Sacking persistent tertiary interactions; these are of particular interest as they appeal to be closely linked to intermediates observed in kinetic refolding experiments (Ptitsyn, 1995).
Conference papers on the topic "Approach-to-equilibrium molecular dynamics (AEMD)"
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Kim, Changsung Sean. "Non-Equilibrium Molecular Dynamics Approach for Nano-Electro-Mechanical Systems: Nano-Fluidics and Its Applications." In ASME 2005 International Mechanical Engineering Congress and Exposition. ASMEDC, 2005. http://dx.doi.org/10.1115/imece2005-79628.
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A three-dimensional non-equilibrium molecular dynamics code has been developed and evaluated to provide fundamental understandings of nano-fluidics at molecular level. Intermolecular energy and force between fluid-fluid and fluid-wall particles were all included. Molecular dynamics results were verified by simulating both homogeneous and heterogeneous flows in a nano-tube and then compared with the classical Navier-Stokes solution with non-slip wall boundary conditions. At equilibration state, the macroscopic parameters were calculated using the statistical calculation. Liquid argon fluids within platinum walls were simulated for a homogeneous system. Also positively charged particles are mixed with water-like solvent particles to investigate the non-Newtonian behavior of the heterogeneous fluid. For an electrowetting phenomenon, a positive charged droplet moving on the negative charged ultra thin film was successfully simulated and compared with a macroscopic experiment. Nano-jetting mechanism was identified by simulating droplet ejection, breakup, wetting, and drying process in a consequent manner. In addition, conceptual nano/micropumps using electrowetting phenomenon are simulated. The present molecular dynamics approach showed its promising capability for the wide range of NEMS/MEMS applications
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Plummer, Gabriel, Mikhail I. Mendelev, and John W. Lawson. "Molecular Dynamics Simulations of Microstructural Effects on Austenite-Martensite Interfaces in NiTi." In SMST 2024. ASM International, 2024. http://dx.doi.org/10.31399/asm.cp.smst2024p0078.
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Abstract The formation and migration of austenite-martensite interfaces plays a key role in the reversible martensitic transformations of shape memory alloys (SMAs). How these interfaces interact with the SMA microstructure is a primary determining factor in important functional properties such as hysteresis and transformation span. Therefore, successful microstructural engineering of SMAs requires in-depth knowledge of interface behavior. The rapid nature of martensitic transformations makes experimental observations of moving interfaces challenging. Molecular dynamics (MD) simulation is a unique tool which can probe the atomic-scale details of austenite-martensite interfaces as they migrate and interact with different microstructural features. While MD simulations allow access to atomic-scale mechanisms, they are limited in time scale, typically to nanoseconds. This limitation creates problems when focusing on the entire transformation process in SMAs, specifically nucleation of new phases. To trigger nucleation on the nanosecond time scale, MD simulations must be performed so far from equilibrium that their relevance to experiment becomes questionable. Here, we demonstrate new MD simulation techniques to generate energetically preferred austenite-martensite interfaces in NiTi under near-equilibrium conditions. We then take advantage of this approach to probe interface behavior under conditions relevant to experiments. Our results demonstrate how austenite-martensite interfaces behave with dramatic differences in single crystals compared to more realistic microstructures containing features such as grain boundaries and precipitates. We identify trends in interface behavior which can be utilized to inform microstructural engineering approaches for SMAs.
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El Kadi, Khadije, Mohamed I. Hassan Ali, MD Didarul Islam, and Isam Janajreh. "Understanding Saline Water Droplet-Membrane Surface Interaction Using Molecular Dynamics Simulations." In ASME 2023 Heat Transfer Summer Conference collocated with the ASME 2023 17th International Conference on Energy Sustainability. American Society of Mechanical Engineers, 2023. http://dx.doi.org/10.1115/ht2023-106871.
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Abstract In this work, we utilize molecular dynamics (MD) simulations to investigate the interfacial characteristics of water droplet on a membrane surface. The MD approach allows us to probe the system dynamics and identify the fundamental mechanisms that govern the surface interactions at various conditions. Through simulating the droplet deposition process at thermodynamic equilibrium, we gain a comprehensive understanding of the interactions between the water droplet and the membrane surface at the atomic level. At different levels of water droplet salinity, results showed the strong influence of droplet salinity on surface tension and thus on wettability. Specifically, increasing salt concentration to brine water level was found to increase both droplet contact angle and droplet height by 49% and 62%, respectively, indicating reduced surface hydrophilicity. These simulations provide valuable insight into the complex interactions of multicomponent water mixtures, with potential implications in the fields of membrane technology and water purification.
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Saha, Sanjoy, and Li Shi. "Molecular Dynamics Simulation of Thermal Transport at Nanometer Size Point Contacts on a Planar Silicon Substrate." In ASME 2005 Summer Heat Transfer Conference collocated with the ASME 2005 Pacific Rim Technical Conference and Exhibition on Integration and Packaging of MEMS, NEMS, and Electronic Systems. ASMEDC, 2005. http://dx.doi.org/10.1115/ht2005-72308.
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A Non Equilibrium Molecular Dynamics (NEMD) simulation has been used to calculate the temperature distribution in the substrate side of a nanometer scale point contact on a planar silicon substrate with different doping concentrations and contact radii. The size of the non-uniform temperature zone was found to approach the average nearest-neighbor distance of impurity dopants when the contact radius was reduced below this distance. At a contact radius of 0.5 nm, the calculated spreading thermal resistance at the nano-point contact agrees with those obtained using two phonon transport models. At a contact radius between 1 nm and 6 nm, however, the spreading resistance from the NEMD is much larger than those from the two models that assume small deviation from the equilibrium distribution.
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Bharathi, Arvind Krishnasamy, and Adri van Duin. "Analysis of Thermal Transport in Zinc Oxide Nanowires Using Molecular-Dynamics Simulations With the ReaxFF Reactive Force-Field." In 2010 14th International Heat Transfer Conference. ASMEDC, 2010. http://dx.doi.org/10.1115/ihtc14-22733.
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The objective of this paper is to determine the thermal conductivity of Zinc Oxide nanowire by Steady State Non-equilibrium and Transient Non-equilibrium Molecular Dynamics (SS-NEMD and T-NEMD) simulations using the ReaxFF reactive force field [5]. While SS-NEMD uses an equilibrated system and statistical averaging; T-NEMD uses cooling/heating rates in order to calculate the conductivity. The validity of the methods is first verified using Argon as a test case. The thermal conductivity of Argon thus calculated is compared with those presented by Bhowmick and Shenoy [20]. We then study the effects of system size using SS-NEMD method while effects of periodic boundary conditions — 1D, 2D and bulk variation of conductivity with temperature are analyzed using T-NEMD simulations. The results obtained compare favorably with those measured experimentally [12, 13]. Thus the SS-NEMD and T-NEMD methods are alternatives to the traditional Green-Kubo approach. In conjunction with ReaxFF, they are computationally cheaper than the Green-Kubo method and can be used to determine the thermal conductivity of materials involved in surface chemistry reactions such as catalysis and sintering.
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Beretta, Gian Paolo, and Nicolas G. Hadjiconstantinou. "Steepest Entropy Ascent Models of the Boltzmann Equation: Comparisons With Hard-Sphere Dynamics and Relaxation-Time Models for Homogeneous Relaxation From Highly Non-Equilibrium States." In ASME 2013 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/imece2013-64905.
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We present a family of steepest entropy ascent (SEA) models of the Boltzmann equation. The models preserve the usual collision invariants (mass, momentum, energy), as well as the non-negativity of the phase-space distribution, and have a strong built-in thermodynamic consistency, i.e., they entail a general H-theorem valid even very far from equilibrium. This family of models features a molecular-speed-dependent collision frequency; each variant can be shown to approach a corresponding BGK model with the same variable collision frequency in the limit of small deviation from equilibrium. This includes power-law dependence on the molecular speed for which the BGK model is known to have a Prandtl number that can be adjusted via the power-law exponent. We compare numerical solutions of the constant and velocity-dependent collision frequency variants of the SEA model with the standard relaxation-time model and a Monte Carlo simulation of the original Boltzmann collision operator for hard spheres for homogeneous relaxation from near-equilibrium and highly non-equilibrium states. Good agreement is found between all models in the near-equilibrium regime. However, for initial states that are far from equilibrium, large differences are found; this suggests that the maximum entropy production statistical ansatz is not equivalent to Boltzmann collisional dynamics and needs to be modified or augmented via additional constraints or structure.
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Carey, V. P., and A. P. Wemhoff. "Disjoining Pressure Effects in Ultra-Thin Liquid Films in Micropassages: Comparison of Thermodynamic Theory With Predictions of Molecular Dynamics Simulations." In ASME 2005 International Mechanical Engineering Congress and Exposition. ASMEDC, 2005. http://dx.doi.org/10.1115/imece2005-80234.
Full textAbstract:
The concept of disjoining pressure, developed from thermodynamic and hydrodynamic analysis, has been widely used as a means of modeling the liquid-solid molecular force interactions in an ultra-thin liquid film on a solid surface. In particular, this approach has been extensively used in models of thin film transport in passages in micro evaporators and micro heat pipes. In this investigation, hybrid μPT molecular dynamics (MD) simulations were used to predict the pressure field and film thermophysics for an argon film on a metal surface. The results of the simulations are compared with predictions of the classic thermodynamic disjoining pressure model. The thermodynamic model provides only a prediction of the relation between vapor pressure and film thickness for a specified temperature. The MD simulations provide a detailed prediction of the density and pressure variation in the liquid film, as well as a prediction of the variation of the equilibrium vapor pressure variation with temperature and film thickness. Comparisons indicate that the predicted variations of vapor pressure with thickness for these two models are in close agreement. A modified thermodynamic model is developed which suggests that presence of a wall-affected layer tends to enhance the reduction of the equilibrium vapor pressure. However, the MD simulation results imply that presence of a wall layer has little effect on the vapor pressure. Implications of the MD simulation predictions for thin film transport in micro evaporators and heat pipes are also discussed.
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Esfarjani, Keivan, Gang Chen, and Asegun Henry. "First-Principles-Based Interatomic Potential for SI and Its Thermal Conductivity." In ASME/JSME 2011 8th Thermal Engineering Joint Conference. ASMEDC, 2011. http://dx.doi.org/10.1115/ajtec2011-44339.
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Based on first-principles density-functional calculations, we have developed and tested a force-field for silicon, which can be used for molecular dynamics simulations and the calculation of its thermal properties. This force field uses the exact Taylor expansion of the total energy about the equilibrium positions up to 4th order. In this sense, it becomes systematically exact for small enough displacements, and can reproduce the thermodynamic properties of Si with high fidelity. Having the harmonic force constants, one can easily calculate the phonon spectrum of this system. The cubic force constants, on the other hand, will allow us to compute phonon lifetimes and scattering rates. Results on equilibrium Green-Kubo molecular dynamics simulations of thermal conductivity as well as an alternative calculation of the latter based on the relaxation-time approximation will be reported. The accuracy and ease of computation of the lattice thermal conductivity using these methods will be compared. This approach paves the way for the construction of accurate bulk interatomic potentials database, from which lattice dynamics and thermal properties can be calculated and used in larger scale simulation methods such as Monte Carlo.
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Zhang, Qian, Jing Zhao, Xiaowei Wang, Jinlei liu, and Zengxiu Zhao. "Attosecond X-ray absorption spectroscopy of ionic dynamics induced by strong field ionization." In Compact EUV & X-ray Light Sources. Washington, D.C.: Optica Publishing Group, 2024. http://dx.doi.org/10.1364/euvxray.2024.jw4a.21.
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Real-time observation of electronic dynamics in ionic molecules induced by strong-field ionization (SFI) is essential for understanding the photoinduced chemical reactions and physical processes. The advent of ultrafast X-ray spectroscopy has opened new avenues for directly probing the electronic and nuclear dynamics in ions [1,2]. In a recent experiment [3], the population distribution of electronic states in air lasing of nitrogen ion was measured for the first time. Here we establish a theoretical approach to simulate the ionic dynamics, which simultaneously addresses strong-field ionization of the neutral molecules and electronic-vibrational coupled dynamics of the ions. We successfully reproduced the X-ray transient absorption spectra (XAS) of nitrogen ion observed in the experiment. By separating the contributions of different electronic states, our study revealed the important role of nuclear vibrational motion in strong-field induced non-equilibrium dynamics. It is found that the electronic population distributions strongly depend on the alignment angle of the molecular axis relative to the laser polarization. With the time-integrated XAS, we achieve the vibrational-resolved measurement of electronic state populations. The modulation of the absorbance with the time delay originates from the vibrational dynamics. Our work sheds light on ultrafast probing of ionic dynamics under strong laser field.
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Qiu, Bo, Hua Bao, and Xiulin Ruan. "Multiscale Simulations of Thermoelectric Properties of PBTE." In ASME 2008 3rd Energy Nanotechnology International Conference collocated with the Heat Transfer, Fluids Engineering, and Energy Sustainability Conferences. ASMEDC, 2008. http://dx.doi.org/10.1115/enic2008-53040.
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In this paper, thermoelectric properties of bulk PbTe are calculated using first principles calculations and molecular dynamics simulations. The Full Potential Linearized Augmented Plane Wave (FP-LAPW) method is first employed to calculate the PbTe band structure. The transport coefficients (Seebeck coefficient, electrical conductivity, and electron thermal conductivity) are then computed using Boltzmann transport equation (BTE) under the constant relaxation time approximation. Interatomic pair potentials in the Buckingham form are also derived using ab initio effective charges and total energy data. The effective interatomic pair potentials give excellent results on equilibrium lattice parameters and elastic constants for PbTe. The lattice thermal conductivity of PbTe is then calculated using molecular dynamics simulations with the Green-Kubo method. In the end, the figure of merit of PbTe is computed revealing the thermoelectric capability of this material, and the multiscale simulation approach is shown to have the potential to identify novel thermoelectric materials.