Journal articles: '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.

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Rudisill, J. W., and P. T. Cummings. "Non-equilibrium molecular dynamics approach to the rheology of model polymer fluids." Fluid Phase Equilibria 88 (August 1993): 99–113. http://dx.doi.org/10.1016/0378-3812(93)87104-9.

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Cartoixà, Xavier, Riccardo Dettori, Claudio Melis, Luciano Colombo, and Riccardo Rurali. "Thermal transport in porous Si nanowires from approach-to-equilibrium molecular dynamics calculations." Applied Physics Letters 109, no. 1 (July 4, 2016): 013107. http://dx.doi.org/10.1063/1.4955038.

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Hahn, Konstanze R., Claudio Melis, and Luciano Colombo. "Thermal transport in nanocrystalline graphene investigated by approach-to-equilibrium molecular dynamics simulations." Carbon 96 (January 2016): 429–38. http://dx.doi.org/10.1016/j.carbon.2015.09.070.

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Bouzid, Assil, Hayat Zaoui, Pier Luca Palla, Guido Ori, Mauro Boero, Carlo Massobrio, Fabrizio Cleri, and Evelyne Lampin. "Thermal conductivity of glassy GeTe4by first-principles molecular dynamics." Physical Chemistry Chemical Physics 19, no. 15 (2017): 9729–32. http://dx.doi.org/10.1039/c7cp01063j.

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Parsa, M. Reza, Aleksandra Pachalieva, and Alexander J. Wagner. "Validity of the molecular-dynamics-lattice-gas global equilibrium distribution function." International Journal of Modern Physics C 30, no. 10 (October 2019): 1941007. http://dx.doi.org/10.1142/s0129183119410079.

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The molecular-dynamics-lattice-gas (MDLG) method establishes a direct link between a lattice-gas method and the coarse-graining of a molecular dynamics (MD) approach. Due to its connection to MD, the MDLG rigorously recovers the hydrodynamics and allows to validate the behavior of the lattice-gas or lattice-Boltzmann methods directly without using the standard kinetic theory approach. In this paper, we show that the analytical definition of the equilibrium distribution function remains valid even for very high volume fractions.

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Begušić, Tomislav, Xuecheng Tao, Geoffrey A. Blake, and Thomas F. Miller. "Equilibrium–nonequilibrium ring-polymer molecular dynamics for nonlinear spectroscopy." Journal of Chemical Physics 156, no. 13 (April 7, 2022): 131102. http://dx.doi.org/10.1063/5.0087156.

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Two-dimensional Raman and hybrid terahertz-Raman spectroscopic techniques provide invaluable insight into molecular structures and dynamics of condensed-phase systems. However, corroborating experimental results with theory is difficult due to the high computational cost of incorporating quantum-mechanical effects in the simulations. Here, we present the equilibrium–nonequilibrium ring-polymer molecular dynamics (RPMD), a practical computational method that can account for nuclear quantum effects on the two-time response function of nonlinear optical spectroscopy. Unlike a recently developed approach based on the double Kubo transformed (DKT) correlation function, our method is exact in the classical limit, where it reduces to the established equilibrium-nonequilibrium classical molecular dynamics method. Using benchmark model calculations, we demonstrate the advantages of the equilibrium–nonequilibrium RPMD over classical and DKT-based approaches. Importantly, its derivation, which is based on the nonequilibrium RPMD, obviates the need for identifying an appropriate Kubo transformed correlation function and paves the way for applying real-time path-integral techniques to multidimensional spectroscopy.

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van Rooij, G. J., D. C. M. van den Bekerom, N. den Harder, T. Minea, G. Berden, W. A. Bongers, R. Engeln, M. F. Graswinckel, E. Zoethout, and M. C. M. van de Sanden. "Taming microwave plasma to beat thermodynamics in CO2 dissociation." Faraday Discussions 183 (2015): 233–48. http://dx.doi.org/10.1039/c5fd00045a.

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The strong non-equilibrium conditions provided by the plasma phase offer the opportunity to beat traditional thermal process energy efficiencies via preferential excitation of molecular vibrations. Simple molecular physics considerations are presented to explain potential dissociation pathways in plasma and their effect on energy efficiency. A common microwave reactor approach is evaluated experimentally with Rayleigh scattering and Fourier transform infrared spectroscopy to assess gas temperatures (exceeding 10⁴ K) and conversion degrees (up to 30%), respectively. The results are interpreted on a basis of estimates of the plasma dynamics obtained with electron energy distribution functions calculated with a Boltzmann solver. It indicates that the intrinsic electron energies are higher than is favorable for preferential vibrational excitation due to dissociative excitation, which causes thermodynamic equilibrium chemistry to dominate. The highest observed energy efficiencies of 45% indicate that non-equilibrium dynamics had been at play. A novel approach involving additives of low ionization potential to tailor the electron energies to the vibrational excitation regime is proposed.

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Martín-Platero, Antonio M., Eva Valdivia, Mercedes Maqueda, Inés Martín-Sánchez, and Manuel Martínez-Bueno. "Polyphasic Approach to Bacterial Dynamics during the Ripening of Spanish Farmhouse Cheese, Using Culture-Dependent and -Independent Methods." Applied and Environmental Microbiology 74, no. 18 (July 25, 2008): 5662–73. http://dx.doi.org/10.1128/aem.00418-08.

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ABSTRACT We studied the dynamics of the microbial population during ripening of Cueva de la Magahá cheese using a combination of classical and molecular techniques. Samples taken during ripening of this Spanish goat's milk cheese in which Lactococcus lactis and Streptococcus thermophilus were used as starter cultures were analyzed. All bacterial isolates were clustered by using randomly amplified polymorphic DNA (RAPD) and identified by 16S rRNA gene sequencing, species-specific PCR, and multiplex PCR. Our results indicate that the majority of the 225 strains isolated and enumerated on solid media during the ripening period were nonstarter lactic acid bacteria, and Lactobacillus paracasei was the most abundant species. Other Lactobacillus species, such as Lactobacillus plantarum and Lactobacillus parabuchneri, were also detected at the beginning and end of ripening, respectively. Non-lactic-acid bacteria, mainly Kocuria and Staphylococcus strains, were also detected at the end of the ripening period. Microbial community dynamics determined by temporal temperature gradient gel electrophoresis provided a more precise estimate of the distribution of bacteria and enabled us to detect Lactobacillus curvatus and the starter bacteria S. thermophilus and L. lactis, which were not isolated. Surprisingly, the bacterium most frequently found using culture-dependent analysis, L. paracasei, was scarcely detected by this molecular approach. Finally, we studied the composition of the lactobacilli and their evolution by using length heterogeneity PCR.

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ŠULC, PETR, ANDREAS WAGNER, and OLIVIER C. MARTIN. "QUANTIFYING SLOW EVOLUTIONARY DYNAMICS IN RNA FITNESS LANDSCAPES." Journal of Bioinformatics and Computational Biology 08, no. 06 (December 2010): 1027–40. http://dx.doi.org/10.1142/s0219720010005075.

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We re-examine the evolutionary dynamics of RNA secondary structures under directional selection towards an optimum RNA structure. We find that the punctuated equilibria lead to a very slow approach to the optimum, following on average an inverse power of the evolutionary time. In addition, our study of the trajectories shows that the out-of-equilibrium effects due to the evolutionary process are very weak. In particular, the distribution of genotypes is close to that arising during equilibrium stabilizing selection. As a consequence, the evolutionary dynamics leave almost no measurable out-of-equilibrium trace, only the transition genotypes (close to the border between different periods of stasis) have atypical mutational properties.

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Camiola, Vito Dario, and Valentina Tozzini. "Collective Mode Mining from Molecular Dynamics Simulations: A Comparative Approach." International Journal of Computational Methods 15, no. 03 (April 25, 2018): 1850108. http://dx.doi.org/10.1142/s0219876218501086.

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The evaluation of collective modes is fundamental in the analysis of molecular dynamics simulations. Several methods are available to extract that information, i.e., normal mode analysis, principal component and spectral analysis of trajectories, basically differing by the quantity considered as the nodal one (frequency, amplitude, or pattern of displacement) and leading to the definition of different kinds of collective excitations and physical spectral observables. The different views converge in the harmonic regime and/or for homo-atomic systems. However, for anharmonic and out of equilibrium dynamics, different quantities bring different information, and only their comparison can give a complete view of the system behavior. To allow such a comparative analysis, we review and compare the different approaches, applying them in diverse combinations to two examples of physical relevance: graphene and fullerene C[Formula: see text].

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Pachalieva, Aleksandra, and Alexander J. Wagner. "Molecular dynamics lattice gas equilibrium distribution function for Lennard–Jones particles." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 379, no. 2208 (August 30, 2021): 20200404. http://dx.doi.org/10.1098/rsta.2020.0404.

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The molecular dynamics lattice gas (MDLG) method maps a molecular dynamics (MD) simulation onto a lattice gas using a coarse-graining procedure. This is a novel fundamental approach to derive the lattice Boltzmann method (LBM) by taking a Boltzmann average over the MDLG. A key property of the LBM is the equilibrium distribution function, which was originally derived by assuming that the particle displacements in the MD simulation are Boltzmann distributed. However, we recently discovered that a single Gaussian distribution function is not sufficient to describe the particle displacements in a broad transition regime between free particles and particles undergoing many collisions in one time step. In a recent publication, we proposed a Poisson weighted sum of Gaussians which shows better agreement with the MD data. We derive a lattice Boltzmann equilibrium distribution function from the Poisson weighted sum of Gaussians model and compare it to a measured equilibrium distribution function from MD data and to an analytical approximation of the equilibrium distribution function from a single Gaussian probability distribution function. This article is part of the theme issue ‘Progress in mesoscale methods for fluid dynamics simulation’.

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Galliéro, Guillaume, Bernard Duguay, Jean-Paul Caltagirone, and François Montel. "Thermal diffusion sensitivity to the molecular parameters of a binary equimolar mixture, a non-equilibrium molecular dynamics approach." Fluid Phase Equilibria 208, no. 1-2 (June 2003): 171–88. http://dx.doi.org/10.1016/s0378-3812(03)00030-x.

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Heyes, D. M. "Transport coefficients of the Lennard–Jones fluid by molecular dynamics." Canadian Journal of Physics 64, no. 7 (July 1, 1986): 773–81. http://dx.doi.org/10.1139/p86-139.

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New nonequilibrium molecular dynamics (MD) calculations of the shear viscosity, bulk viscosity, and thermal conductivity are presented. Together with the self-diffusion coefficients obtained from equilibrium MD, the success of the Dymond–Batchinski expressions for the density and temperature dependence of these transport coefficients is demonstrated.The shear viscosity and self-diffusion coefficients are very good probes for the approach point of the solid-to-liquid phase change. The bulk viscosity and thermal conductivity are less useful in this respect.

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Rossouw, Debra, Roberto Olivares-Hernandes, Jens Nielsen, and Florian F. Bauer. "Comparative Transcriptomic Approach To Investigate Differences in Wine Yeast Physiology and Metabolism during Fermentation." Applied and Environmental Microbiology 75, no. 20 (August 21, 2009): 6600–6612. http://dx.doi.org/10.1128/aem.01251-09.

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ABSTRACT Commercial wine yeast strains of the species Saccharomyces cerevisiae have been selected to satisfy many different, and sometimes highly specific, oenological requirements. As a consequence, more than 200 different strains with significantly diverging phenotypic traits are produced globally. This genetic resource has been rather neglected by the scientific community because industrial strains are less easily manipulated than the limited number of laboratory strains that have been successfully employed to investigate fundamental aspects of cellular biology. However, laboratory strains are unsuitable for the study of many phenotypes that are of significant scientific and industrial interest. Here, we investigate whether a comparative transcriptomics and phenomics approach, based on the analysis of five phenotypically diverging industrial wine yeast strains, can provide insights into the molecular networks that are responsible for the expression of such phenotypes. For this purpose, some oenologically relevant phenotypes, including resistance to various stresses, cell wall properties, and metabolite production of these strains were evaluated and aligned with transcriptomic data collected during alcoholic fermentation. The data reveal significant differences in gene regulation between the five strains. While the genetic complexity underlying the various successive stress responses in a dynamic system such as wine fermentation reveals the limits of the approach, many of the relevant differences in gene expression can be linked to specific phenotypic differences between the strains. This is, in particular, the case for many aspects of metabolic regulation. The comparative approach therefore opens new possibilities to investigate complex phenotypic traits on a molecular level.

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Sharma, Bhanuday, Rakesh Kumar, Prateek Gupta, Savitha Pareek, and Ashish Singh. "On the estimation of bulk viscosity of dilute nitrogen gas using equilibrium molecular dynamics approach." Physics of Fluids 34, no. 5 (May 2022): 057104. http://dx.doi.org/10.1063/5.0088775.

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In this work, we present a study for the estimation of bulk viscosity using the equilibrium molecular dynamics-based Green–Kubo method. We have performed a parametric study to find optimal hyper-parameters to estimate bulk viscosity using the Green–Kubo method. Although similar studies exist for shear viscosity, none has been reported so far specifically for bulk viscosity. The expected uncertainty in bulk viscosity for a given length and number of molecular dynamics trajectories used in statistical averaging is determined. The effect of system size, temperature, and pressure on bulk viscosity has also been studied. The study reveals that the decay of autocorrelation function for bulk viscosity is slower than that for shear viscosity and hence requires a longer correlation length. A novel observation has been made that the autocorrelation length required for convergence in the Green–Kubo method for both shear and bulk viscosity of dilute nitrogen gas is of the same mean collision time length units irrespective of simulation pressure. However, when the temperature is varied, the required autocorrelation length remains unaffected for shear viscosity but increases slightly with temperature for bulk viscosity. The results obtained from the Green–Kubo method are compared with experimental and numerical results from the literature with special emphasis on their comparison with the results from the nonequilibrium molecular dynamics-based continuous expansion/compression method. Although the primary focus and novelty of this work are the discussion on bulk viscosity, a similar discussion on shear viscosity has also been added.

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Alvarez, H. Ariel, Andrés N. McCarthy, and J. Raúl Grigera. "A Molecular Dynamics Approach to Ligand-Receptor Interaction in the Aspirin-Human Serum Albumin Complex." Journal of Biophysics 2012 (November 21, 2012): 1–7. http://dx.doi.org/10.1155/2012/642745.

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In this work, we present a study of the interaction between human serum albumin (HSA) and acetylsalicylic acid (ASA, C9H8O4) by molecular dynamics simulations (MD). Starting from an experimentally resolved structure of the complex, we performed the extraction of the ligand by means of the application of an external force. After stabilization of the system, we quantified the force used to remove the ASA from its specific site of binding to HSA and calculated the mechanical nonequilibrium external work done during this process. We obtain a reasonable value for the upper boundary of the Gibbs free energy difference (an equilibrium thermodynamic potential) between the complexed and noncomplexed states. To achieve this goal, we used the finite sampling estimator of the average work, calculated from the Jarzynski Equality. To evaluate the effect of the solvent, we calculated the so-called “viscous work,” that is, the work done to move the aspirin in the same trajectory through the solvent in absence of the protein, so as to assess the relevance of its contribution to the total work. The results are in good agreement with the available experimental data for the albumin affinity constant for aspirin, obtained through quenching fluorescence methods.

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Schmied, Christian-Marcel, Aleksandr N. Mikheev, and Thomas Gasenzer. "Non-thermal fixed points: Universal dynamics far from equilibrium." International Journal of Modern Physics A 34, no. 29 (October 20, 2019): 1941006. http://dx.doi.org/10.1142/s0217751x19410069.

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In this article we give an overview of the concept of universal dynamics near non-thermal fixed points in isolated quantum many-body systems. We outline a non-perturbative kinetic theory derived within a Schwinger–Keldysh closed-time path-integral approach, as well as a low-energy effective field theory which enable us to predict the universal scaling exponents characterizing the time evolution at the fixed point. We discuss the role of wave-turbulent transport in the context of such fixed points and discuss universal scaling evolution of systems bearing ensembles of (quasi) topological defects. This is rounded off by the recently introduced concept of prescaling as a generic feature of the evolution towards a non-thermal fixed point.

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Capano, G., T. J. Penfold, M. Chergui, and I. Tavernelli. "Photophysics of a copper phenanthroline elucidated by trajectory and wavepacket-based quantum dynamics: a synergetic approach." Physical Chemistry Chemical Physics 19, no. 30 (2017): 19590–600. http://dx.doi.org/10.1039/c7cp00436b.

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On-the-fly excited state molecular dynamics is a valuable method for studying non-equilibrium processes in excited states and is beginning to emerge as a mature approach much like its ground state counterparts.

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Braudeau, Erik, and Rabi H. Mohtar. "Hydrostructural Pedology, Culmination of the Systemic Approach of the Natural Environment." Systems 9, no. 1 (January 22, 2021): 8. http://dx.doi.org/10.3390/systems9010008.

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The subject of this article is the dynamics of water in a soil pedostructure sample whose internal environment is subjected to a potential gradient created by the departure of water through surface evaporation. This work refers entirely to the results and conclusions of a fundamental theoretical study focused on the molecular thermodynamic equilibrium of the two aqueous phases of the soil pedostructure. The new concepts and descriptive variables of the hydro-thermodynamic equilibrium state of the soil medium, which have been established at the molecular level of the fluid phases of the pedostructure (water and air) in a previous article, are recalled here in the systemic paradigm of hydrostructural pedology. They allow access to the molecular description of water migration in the soil and go beyond the classical mono-scale description of soil water dynamics. We obtain a hydro-thermodynamic description of the soil′s pedostructure at different hydro-functional scale levels including those relating to the water molecule and its atoms. The experimental results show a perfect agreement with the theory, at the same time validating the systemic approach that was the framework.

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Kunene, Thokozane Justin, Lagouge Kwanda Tartibu, Sina Karimzadeh, Peter Ozaveshe Oviroh, Kingsley Ukoba, and Tien-Chien Jen. "Molecular Dynamics of Atomic Layer Deposition: Sticking Coefficient Investigation." Applied Sciences 12, no. 4 (February 19, 2022): 2188. http://dx.doi.org/10.3390/app12042188.

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This study focused on the atomic scale growth dynamics of amorphous Al2O3 films microscale structural relaxation. Classical Molecular Dynamics (MD) can not entirely model the challenging ALD dynamics due to the large timescales. The all-atom approach has rules based on deposition actions modelled MD relaxations that form as input to attain a single ALD cycle. MD relaxations are used to create a realistic equilibrium surface. This approach is fitting to this study as the investigation of the sticking coefficient is only at the first monolayer that includes the layering of a hydroxyl surface of alumina. The study provides insight between atomic-level numerical information and experimental measurements of the sticking coefficient related to the atomic layer deposition. The MD modeling was for the deposition of Al2O3, using trimethylaluminum (TMA) and water as precursors. The film thickness of 1.7 Å yields an initial sticking coefficient of TMA to be 4.257 × 10−3 determined from the slope of the leading front of the thickness profile at a substrate temperature of 573 K. This work adds to the knowledge of the kinetic nature of ALD at the atomic level. It provides quantitative information on the sticking coefficient during ALD.

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BÖYÜKATA, MUSTAFA. "MOLECULAR DYNAMICS STUDY OF Tin, Vn AND Crn CLUSTERS." Journal of Theoretical and Computational Chemistry 06, no. 01 (March 2007): 81–97. http://dx.doi.org/10.1142/s0219633607002873.

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Using a Morse type pair potential, molecular-dynamics simulations have been performed to investigate the atomic geometries, growing patterns, structural stabilities, energetics and magic sizes of Ti n, V n and Cr n (n = 2-50) clusters. Following rearrangement collision of the atom–cluster system in fusion process, and absorbing their energies step by step down to 0 K, possible optimal equilibrium geometries of the clusters have been generated to tackle the structural determination problem. This approach serves an efficient alternative to the growing path identification and the optimization techniques. It has been found that titanium, vanadium and chromium clusters prefer to form three-dimensional compact structures in the determined configurations and the appearances of medium sizes are, in general, five-fold symmetry on the spherical clusters. Moreover, relevant relations between atomic arrangements in the clusters and the magic sizes have been observed.

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Shahzad, Aamir, Muhammad Kashif, Tariq Munir, Muhammad Asif Shakoori, Maogang He, Sajid Bashir, and Qamar Ul Islam. "Studies of weak external force on thermal conductivity of complex liquids using homogenous perturbed simulations." High Temperatures-High Pressures 49, no. 5-6 (2020): 461–78. http://dx.doi.org/10.32908/hthp.v49.943.

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A modified Evan-Gillan homogenous perturbed scheme was employed to measure the thermal response and corresponding normalized plasma thermal conductivity (λ0) of strongly coupled dusty plasmas (SCDPs). Homogenous perturbed molecular dynamics (HPMD) approach was employed to analyze the efficiency and compared the obtained outcomes of perturbed heat flux vector to the outcomes computed through equilibrium molecular dynamics (EMD) approach. Our new outcomes show that the thermal response of heat energy current through HPMD and EMD approaches is an excellent agreement with each other for SCDPs at much low value of normalized external perturbation (F*). The obtained HPMD simulations demonstrate that the presented approach provides good outcomes with fast convergence and small system size for low-tointermediate plasma couplings (Γ) at very weak F*. It was found that the measured plasma λ0 outcomes at nearly equilibrium weak F* (= 0.00005) are in reasonable agreement with earlier results obtained from EMD, homogenous and inhomogeneous nonequilibrium molecular dynamics simulations and theoretical predictions and generally overpredicted the plasma λ0 by ~1%–~24% depending on the arrangement of plasma parameters (Г, к). It was shown that the HPMD is an excellent approach to calculate the plasma λ0 and to recognize the elementary patterns in 3D SCDPs.

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Mensitieri, Giuseppe, Giuseppe Scherillo, Pietro La Manna, and Pellegrino Musto. "Sorption Thermodynamics of CO2, H2O, and CH3OH in a Glassy Polyetherimide: A Molecular Perspective." Membranes 9, no. 2 (February 1, 2019): 23. http://dx.doi.org/10.3390/membranes9020023.

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In this paper, the sorption thermodynamics of low-molecular-weight penetrants in a glassy polyetherimide, endowed with specific interactions, is addressed by combining an experimental approach based on vibrational spectroscopy with thermodynamics modeling. This modeling approach is based on the extension of equilibrium theories to the out-of-equilibrium glassy state. Specific interactions are accounted for in the framework of a compressible lattice fluid theory. In particular, the sorption of carbon dioxide, water, and methanol is illustrated, exploiting the wealth of information gathered at a molecular level from Fourier-transform infrared (FTIR) spectroscopy to tailor thermodynamics modeling. The investigated penetrants display a different interacting characteristic with respect to the polymer substrate, which reflects itself in the sorption thermodynamics. For the specific case of water, the outcomes from molecular dynamics simulations are compared with the results of the present analysis.

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Mabotsa, Malebese, Justin Manango W. Munganga, and Adamu Shitu Hassan. "Mathematical modelling and optimal control of the transmission dynamics of enterovirus." Physica Scripta 97, no. 3 (February 7, 2022): 034002. http://dx.doi.org/10.1088/1402-4896/ac4f04.

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Abstract We propose a mathematical model for the transmission dynamics of enterovirus, with novelty of incorporating indirect transmission from the environment, inclusion of control interventions (sanitation and hygiene) and optimal control study. We prove that if the basic reproduction number  0 ≤ 1 , a suitable Lyapunov function is used to establish the global stability of the disease free equilibrium, in which case the infection will die out over time. Our analysis further establish the global stability of the endemic equilibrium based on the approach of Volterra-Lyapunov matrices if  0 > 1 . Our findings show that when  0 > 1 , the endemic equilibrium is globally asymptotically stable. In this case, the enterovirus will invade the population. It is shown that by reducing direct transmission rate by 80%, the basic reproduction number can be reduced below one and thus controlling the infection. Using optimal control, it is shown that the disease can be controlled within a shorter period of time as compared to minimizing the direct contact rate by 80%. Numerical simulations are provided to illustrate the results.

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35

Michalis, Vasileios K., Ioannis G. Economou, Athanasios K. Stubos, and Ioannis N. Tsimpanogiannis. "Phase equilibria molecular simulations of hydrogen hydrates via the direct phase coexistence approach." Journal of Chemical Physics 157, no. 15 (October 21, 2022): 154501. http://dx.doi.org/10.1063/5.0108738.

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We report the three-phase (hydrate–liquid water–vapor) equilibrium conditions of the hydrogen–water binary system calculated with molecular dynamics simulations via the direct phase coexistence approach. A significant improvement of ∼10.5 K is obtained in the current study, over earlier simulation attempts, by using a combination of modifications related to the hydrogen model that include (i) hydrogen Lennard-Jones parameters that are a function of temperature and (ii) the water–guest energy interaction parameters optimized further by using the Lorentz–Berthelot combining rules, based on an improved description of the solubility of hydrogen in water.

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Grifoni, Emanuele, GiovanniMaria Piccini, and Michele Parrinello. "Microscopic description of acid–base equilibrium." Proceedings of the National Academy of Sciences 116, no. 10 (February 14, 2019): 4054–57. http://dx.doi.org/10.1073/pnas.1819771116.

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Acid–base reactions are ubiquitous in nature. Understanding their mechanisms is crucial in many fields, from biochemistry to industrial catalysis. Unfortunately, experiments give only limited information without much insight into the molecular behavior. Atomistic simulations could complement experiments and shed precious light on microscopic mechanisms. The large free-energy barriers connected to proton dissociation, however, make the use of enhanced sampling methods mandatory. Here we perform an ab initio molecular dynamics (MD) simulation and enhance sampling with the help of metadynamics. This has been made possible by the introduction of descriptors or collective variables (CVs) that are based on a conceptually different outlook on acid–base equilibria. We test successfully our approach on three different aqueous solutions of acetic acid, ammonia, and bicarbonate. These are representative of acid, basic, and amphoteric behavior.

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Gao, Xubin, Qiuhui Pan, and Mingfeng He. "Transmission Dynamics of Resistant Bacteria in a Predator-Prey System." Computational and Mathematical Methods in Medicine 2015 (2015): 1–12. http://dx.doi.org/10.1155/2015/638074.

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This paper discusses the impact on human health caused by the addition of antibiotics in the feed of food animals. We use the established transmission rule of resistant bacteria and combine it with a predator-prey system to determine a differential equations model. The equations have three steady equilibrium points corresponding to three population dynamics states under the influence of resistant bacteria. In order to quantitatively analyze the stability of the equilibrium points, we focused on the basic reproduction numbers. Then, both the local and global stability of the equilibrium points were quantitatively analyzed by using essential mathematical methods. Numerical results are provided to relate our model properties to some interesting biological cases. Finally, we discuss the effect of the two main parameters of the model, the proportion of antibiotics added to feed and the predation rate, and estimate the human health impacts related to the amount of feed antibiotics used. We further propose an approach for the prevention of the large-scale spread of resistant bacteria and illustrate the necessity of controlling the amount of in-feed antibiotics used.

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Barazorda-Ccahuana, Haruna L., Vinicius Theiss-De-Rosso, Diego Ernesto Valencia, and Badhin Gómez. "Heat-Stable Hazelnut Profilin: Molecular Dynamics Simulations and Immunoinformatics Analysis." Polymers 12, no. 8 (August 5, 2020): 1742. http://dx.doi.org/10.3390/polym12081742.

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Heat treatment can modify the allergenic potential, reducing allergenicity in specific proteins. Profilins are one of the important hazelnut allergens; these proteins are considered panallergens due to their high capacity for cross-reactivity with other allergens. In the present work, we evaluated the thermostability of hazelnut profilin, combining molecular dynamics simulation and immunoinformatic techniques. This approach helped us to have reliable results in immunogenicity studies. We modeled Cor a 2 profilin and applied annealing simulation, equilibrium, and production simulation at constant temperatures ranging from 300 to 500 K using Gromacs software. Despite the hazelnut profilins being able to withstand temperatures of up to 400 K, this does not seem to reduce its allergenicity. We have found that profilin subjected to temperatures of 450 and 500 K could generate cross-reactivity with other food allergens. In conclusion, we note a remarkable thermostability of Cor a 2 at 400 K which avoids its structural unfolding.

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LIU, JIAN, FUDE NIE, JINSHAN LI, XIAOPING ZHAO, and TIENING HE. "MOLECULAR DYNAMICS STUDY OF ADSORPTION OF FLUORIC POLYMERS ON TATB SURFACE." Journal of Theoretical and Computational Chemistry 06, no. 01 (March 2007): 157–63. http://dx.doi.org/10.1142/s0219633607002800.

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Molecular dynamics simulation has been applied to study the adsorption process of PVDF/PCTFE copolymers on TATB (001) surfaces. The copolymers were formed by linking PVDF and PCTFE in 1:1 proportion as ABABAB pattern with the degree of polymerization N ranging from 10 to 200. The equilibrium time of each chain is several hundred picoseconds, and the adsorption energy E a increases with the distance H between the chain and the increased surface. Adsorption process occurs when H is below 10 Å, and E a tends to be zero as H becomes greater than 10 Å. Polymer's adsorbability is related to the length of the chain, and a longer chain is better than a short one. A short chain has more train conformation monomers than a long chain. Chain conformation changes greatly during the first hundred ps, and stabilizes after 150 ps. Monomers close to the TATB surface are easy to approach the surface, and the units far from the surface will approach the surface by chain torsion and bond rotation. The ratio of the number of train conformation monomers to the degree of polymerization N t /N increases with the increasing MD simulation time.

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Sarder, U., Alexander V. Evteev, Elena V. Levchenko, A. Kromik, I. V. Belova, and Graeme E. Murch. "Molecular Dynamics Study of Mass Transport Properties of Liquid Cu-Ag Alloys." Diffusion Foundations 9 (October 2016): 58–72. http://dx.doi.org/10.4028/www.scientific.net/df.9.58.

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In this study, mass transport properties of liquid Cu-Ag alloys are investigated over wide temperature and composition ranges. The calculations are performed within the framework of the Green-Kubo (GK) formalism by using equilibrium molecular dynamics (MD) simulations along with one of the most reliable embedded-atom method potentials for this system developed by [P. Williams et al.: Modell. Simul. Mater. Sci. Eng. vol. 14 (2006), p. 817]. The approach employed allows for evaluation of the components’ self-diffusion coefficients as well as the phenomenological coefficient for mass transport Lcc. The results obtained in this study can be used to predict the kinetics of solidification of real liquid Cu-Ag alloys.

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NEJAT PISHKENARI, HOSSEIN, and ALI MEGHDARI. "TEMPERATURE DEPENDENCE STUDY OF NONCONTACT AFM IMAGES USING MOLECULAR DYNAMICS SIMULATIONS." International Journal of Modern Physics: Conference Series 05 (January 2012): 418–32. http://dx.doi.org/10.1142/s2010194512002309.

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The effect of temperature on the noncontact atomic force microscopy (NC-AFM) surface imaging is investigated with the aid of molecular dynamics (MD) analysis based on the Sutton-Chen (SC) interatomic potential. Particular attention is devoted to the tip and sample flexibility at different temperatures. When a gold coated probe is brought close to the Au (001) surface at high temperatures, the tip and surface atoms are pulled together and their distance becomes smaller. The tip and sample atoms displacement varies in the different environment temperatures and this leads to the different interaction forces. Along this line, to study the effect of temperature on the resulting images, we have employed the well-known NC-AFM model and carried out realistic non-equilibrium MD 3D simulations of atomic scale imaging at different close approach positions to the surface.

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Atanasov, Ivailo S., and Marc Hou. "Non-Equilibrium Properties of Au-Pd Nanoparticles." Solid State Phenomena 172-174 (June 2011): 670–75. http://dx.doi.org/10.4028/www.scientific.net/ssp.172-174.670.

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We address the question of the evolution of a nanostructured system in a metastable state to equilibrium. To this purpose, we use the case study of the transition of an AucorePdshell nanoalloy cluster containing up to about 600 atoms toward the equilibrium Au segregated configuration. We start from a molecular dynamics approach with an embedded atom potential. The way the transition develops at low temperatures is found to be very sensitive to the cluster morphology and the way energy is exchanged with the environment. The transition of icosahedral inverse core-shell Au-Pd clusters is predicted to nucleate locally at the surface contrary to clusters with other morphologies, and starting at lower temperatures compared to them.

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pada Das, Krishna, Prodip Roy, Subhabrata Ghosh, and Somnath Maiti. "External Source of Infection and Nutritional Efficiency Control Chaos in a Predator–Prey Model with Disease in the Predator." Biophysical Reviews and Letters 12, no. 02 (June 2017): 87–115. http://dx.doi.org/10.1142/s1793048017500059.

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This paper deals with an eco-epidemiological approach with disease circulating through the predator species. Disease circulation in the predator species can be possible by contact as well as by external sources. Here, we try to discuss the role of external source of infection along with nutritional value on system dynamics. To establish our findings, we have worked out the local and global stability analysis of the equilibrium points with Hopf bifurcation analysis associated with interior equilibrium point. The ecological consequence by ecological basic reproduction number as well as the disease basic reproduction number or basic reproductive ratio are obtained and we have analyzed the community structure of the particular system with the help of ecological and disease basic reproduction numbers. Further we pay attention to the chaotic dynamics which is produced by disease circulating in predator species by contact. Our numerical simulations reveal that eco-epidemiological system without external source of infection induced chaotic dynamics for increasing force of infection due to contact, whereas in the presence of external source of infection, it exhibits stable solution. It is also observed that nutritional value can prevent chaotic dynamics. We conclude that chaotic dynamics can be controlled by the external source of infection as well as nutritional value. We apply basic tools of nonlinear dynamics such as Poincare section and maximum Lyapunov exponent to investigate chaotic behavior of the system.

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Kenkre, V. M., and M. Chase. "Approach to equilibrium of a quantum system and generalization of the Montroll–Shuler equation for vibrational relaxation of a molecular oscillator." International Journal of Modern Physics B 31, no. 20 (August 10, 2017): 1750244. http://dx.doi.org/10.1142/s0217979217502447.

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The approach to equilibrium of a quantum mechanical system in interaction with a bath is studied from a practical as well as a conceptual point of view. Explicit memory functions are derived for given models of bath couplings. If the system is a harmonic oscillator representing a molecule in interaction with a reservoir, the generalized master equation derived becomes an extension into the coherent domain of the well-known Montroll–Shuler equation for vibrational relaxation and unimolecular dissociation. A generalization of the Bethe–Teller result regarding energy relaxation is found for short times. The theory has obvious applications to relaxation dynamics at ultra-short times as in observations on the femtosecond time scale and to the investigation of quantum coherence at those short times. While vibrational relaxation in chemical physics is a primary target of the study, another system of interest in condensed matter physics, an electron or hole in a lattice subjected to a strong DC electric field that gives rise to well-known Wannier–Stark ladders, is naturally addressed with the theory. Specific system–bath interactions are explored to obtain explicit details of the dynamics. General phenomenological descriptions of the reservoir are considered rather than specific microscopic realizations.

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45

Correa, Andrea, Antonio De Nicola, Giuseppe Scherillo, Valerio Loianno, Domenico Mallamace, Francesco Mallamace, Hiroshi Ito, Pellegrino Musto, and Giuseppe Mensitieri. "A Molecular Interpretation of the Dynamics of Diffusive Mass Transport of Water within a Glassy Polyetherimide." International Journal of Molecular Sciences 22, no. 6 (March 12, 2021): 2908. http://dx.doi.org/10.3390/ijms22062908.

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The diffusion process of water molecules within a polyetherimide (PEI) glassy matrix has been analyzed by combining the experimental analysis of water sorption kinetics performed by FTIR spectroscopy with theoretical information gathered from Molecular Dynamics simulations and with the expression of water chemical potential provided by a non-equilibrium lattice fluid model able to describe the thermodynamics of glassy polymers. This approach allowed us to construct a convincing description of the diffusion mechanism of water in PEI providing molecular details of the process related to the effects of the cross- and self-hydrogen bonding established in the system on the dynamics of water mass transport.

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Mejía, Leopoldo, Ulrich Kleinekathöfer, and Ignacio Franco. "Coherent and incoherent contributions to molecular electron transport." Journal of Chemical Physics 156, no. 9 (March 7, 2022): 094302. http://dx.doi.org/10.1063/5.0079708.

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We numerically isolate the limits of validity of the Landauer approximation to describe charge transport along molecular junctions in condensed phase environments. To do so, we contrast Landauer with exact time-dependent non-equilibrium Green’s function quantum transport computations in a two-site molecular junction subject to exponentially correlated noise. Under resonant transport conditions, we find Landauer accuracy to critically depend on intramolecular interactions. By contrast, under nonresonant conditions, the emergence of incoherent transport routes that go beyond Landauer depends on charging and discharging processes at the electrode–molecule interface. In both cases, decreasing the rate of charge exchange between the electrodes and molecule and increasing the interaction strength with the thermal environment cause Landauer to become less accurate. The results are interpreted from a time-dependent perspective where the noise prevents the junction from achieving steady-state and from a fully quantum perspective where the environment introduces dephasing in the dynamics. Using these results, we analyze why the Landauer approach is so useful to understand experiments, isolate regimes where it fails, and propose schemes to chemically manipulate the degree of transport coherence.

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Singla, Anuradha, and Aditi Ray. "Predicting shock hugoniot and equation of state of single-crystal molybdenum by molecular dynamics simulation." IOP Conference Series: Materials Science and Engineering 1300, no. 1 (April 1, 2024): 012034. http://dx.doi.org/10.1088/1757-899x/1300/1/012034.

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Abstract In the present paper, we employ non-equilibrium molecular dynamics approach to simulate impact-induced shock propagation in single-crystal Molybdenum. Shock hugoniot, generated by simulation of impact with varied strength shows excellent agreement with experimental data in the strong shock regime. The resulting hugoniot parameters obtained by linear fitting of shock velocity vs. particle velocity data are then used to estimate ambient pressure Grüneisen coefficient. Finally Mie-Grüneisen equation of state (EOS) with hugoniot as reference state, is employed to express pressure-volume-energy relationship for [001] single-crystal Mo. The influence of different analytical forms for volume dependence of Grüneisen parameter on EOS is investigated.

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48

Simon, A., M. Rapacioli, G. Rouaut, G. Trinquier, and F. X. Gadéa. "Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 375, no. 2092 (March 20, 2017): 20160195. http://dx.doi.org/10.1098/rsta.2016.0195.

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We present dynamical studies of the dissociation of polycyclic aromatic hydrocarbon (PAH) radical cations in their ground electronic states with significant internal energy. Molecular dynamics simulations are performed, the electronic structure being described on-the-fly at the self-consistent-charge density functional-based tight binding (SCC–DFTB) level of theory. The SCC–DFTB approach is first benchmarked against DFT results. Extensive simulations are achieved for naphthalene , pyrene and coronene at several energies. Such studies enable one to derive significant trends on branching ratios, kinetics, structures and hints on the formation mechanism of the ejected neutral fragments. In particular, dependence of branching ratios on PAH size and energy were retrieved. The losses of H and C 2 H 2 (recognized as the ethyne molecule) were identified as major dissociation channels. The H/C 2 H 2 ratio was found to increase with PAH size and to decrease with energy. For , which is the most interesting PAH from the astrophysical point of view, the loss of H was found as the quasi-only channel for an internal energy of 30 eV. Overall, in line with experimental trends, decreasing the internal energy or increasing the PAH size will favour the hydrogen loss channels with respect to carbonaceous fragments. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

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Fan, Jing, Yuting Pan, Zhiqiang Gao, and Hongwei Qu. "Molecular Dynamic Simulations of the Physical Properties of Four Ionic Liquids." International Journal of Molecular Sciences 25, no. 20 (October 18, 2024): 11217. http://dx.doi.org/10.3390/ijms252011217.

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In this study, the molecular structure models of four ionic liquids were created, the reverse nonequilibrium molecular dynamics simulation (RNEMD) approach was used to predict their densities and viscosities, and their thermal conductivity was simulated using the non-equilibrium molecular dynamic simulation method (NEMD). The calculated results of ionic liquid densities were compared with the data in the literature; most of the variances are around 2.5%, and the maximum relative deviation was less than 6.27%; viscosity values were compared with the experimental data, with a maximum relative deviation of −8.96% and a minimum relative deviation of −2.72%. The simulated thermal conductivity has a good linear relationship with respect to temperature and pressure, which is in good agreement. This study provides a reference for molecular dynamics simulation to measure the physical properties of ionic liquids, which is important for the development of ionic liquids.

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Ziaja, B., E. Weckert, and T. Möller. "Statistical model of radiation damage within an atomic cluster irradiated by photons from free-electron-laser." Laser and Particle Beams 25, no. 3 (July 26, 2007): 407–14. http://dx.doi.org/10.1017/s0263034607000523.

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Here we report on the present status of our project on statistical modelling of charge dynamics within irradiated samples. Boltzmann statistical approach to model the radiation damage in samples irradiated by FEL photons is tested in a study case of a spherically symmetric xenon cluster. Qualitative agreement between the model predictions and the experimental data is found. The results obtained demonstrate the potential of the statistical method for describing the non-equilibrium dynamics of samples exposed to FEL radiation.

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Journal articles on the topic 'Approach-to-equilibrium molecular dynamics (AEMD)'

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