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Molecular dynamics method has been employed to study structures formed within a wide range of densities in a system of smoothed collapsing spheres located in a slitlike pore with a fixed thickness. It has been shown that, depending on the density, the profile of the system varies, and isolated layers are formed in it. The two-dimensional radial distribution functions and orientational parameters of each layer, as well as diffraction patterns, have been calculated for the system. It has been found that the phase state of the system strongly depends on its density; i.e., a passage takes place from a disordered state at low densities to a complex phase behavior with diverse combinations of crystalline phases at sufficiently high density values. [ABSTRACT FROM AUTHOR]

Equilibrium molecular dynamics (EMD) simulations have been executed to investigate the parallel (D║) and perpendicular (D┴) diffusion coefficients for three-dimensional (3D) strongly coupled (SC) electrorheological complex (dusty) plasmas (ERCPs). The effects of uniaxial (z-axis) AC electric field (MT) on dust grains have been investigated along with various combinations of plasma parameters (Γ, κ). The new outcomes obtained by mean squared displacement of Einstein relation show diffusion coefficients for low-intermediate to high plasma couplings (Γ) for varying MT. The D║ and D┴ at MT = 0.01 agree well with earlier available data obtained from the Green–Kubo and Einstein relation for 3D SC-Yukawa systems. The simulation data show that D║ increased with an increase in moderate MT strength and that D┴ decreased for the intermediate to large MT strength. Both (D║ and D┴) remained nearly constant for low MT values. The investigations show that the current EMD scheme is more efficient for nonideal gas-like, liquid-like, and solid-like states of SC-ERCPs. It has been demonstrated that present simulation outcomes extended the MT range up to 0.01 ≤ MT ≤ 10 to understand the diffusive and rheological behaviors of dusty plasma systems. [ABSTRACT FROM AUTHOR]

The effects of the branched structures of SDBS molecules on oil recovery are investigated by molecular dynamics method. The relative density of oil molecules shows that SDBS molecule with benzene ring located near the center of alkyl chain has the best effect on oil displacement. Dynamic trajectories show that the water and SDBS molecules gradually occupy the calcite surface and replace the oil droplets. In this process, more water molecules gather nearby the polar groups of SDBS, indicating that the polar group has a significant effect on the water infiltration and the formation of water channels. Contact angle between SDBS molecule and calcite surface indicates that compared to straight chains, the branched structure tends to spread on the calcite interface. Moreover, adsorption energies of the simulation systems further prove that as the aromatic ring is closer to the middle of the alkyl chain, the oil displacement effect is better. [ABSTRACT FROM AUTHOR]

We investigate systematically the effects of the inter-particle attraction on the structure and dynamical behaviors of glass-forming liquids via molecular dynamics simulations. We find that the inter-particle attraction does not influence the structure, but greatly affects the dynamics and dynamical heterogeneity of the system. After the system changes from a purely repulsive glass-forming liquid to an attractive one, the dynamics slows down and the dynamical heterogeneity becomes greater, which is found interestingly to be associated with larger cooperative rearrangement regions (CRRs). Additionally, the structures of CRRs are observed to be compact in attractive glass-forming liquids but string-like in purely repulsive ones. Our findings constitute an important contribution to the ongoing study of the role of attractions in properties of glasses and glass-forming liquids. [ABSTRACT FROM AUTHOR]

Structure and properties of model colloidal suspensions in bulk solutions have been investigated using classical molecular dynamics simulations. The system consists of spherical particles (macroscopic colloids and microscopic counterions and/or coions) in a continuum solvent and is described using the primitive model. Variations in different properties with system parameters (colloid size, charge, concentration etc.) have been investigated. An effective one-component model [Adelman SA. J. Chem. Phys. 1976;64:724–731] of the multicomponent suspension is used to calculate the effective colloid–colloid potential, which develops an attractive minimum with increase in charge, size and concentration of colloid. [ABSTRACT FROM AUTHOR]

Macroscale experiments show that a train of two immiscible liquid drops, a bislug, can spontaneously move in a capillary tube because of surface tension asymmetries. We use molecular dynamics simulation of Lennard-Jones fluids to demonstrate this phenomenon for NVT ensembles in submicron tubes. We deliberately tune the strength of intermolecular forces and control the velocity of bislug in different wetting and viscosity conditions. We compute the velocity profile of particles across the tube and explain the origin of deviations from the classical parabolae. We show that the self-generated molecular flow resembles the Poiseuille law when the ratio of the tube radius to its length is less than a critical value. [ABSTRACT FROM AUTHOR]

Structural and thermodynamic properties as well as diffusion coefficients of binary fluid mixtures with asymmetry in mass, size, charge and their combinations have been studied using classical molecular dynamics simulations. The fluid mixture is modelled as spherical particles interacting via the Weeks-Chandler-Andersen and Coulomb potential. The diameter, charge and mass of the fluid particles are in the range 6-60 Å, 1-10e and 1—500 amu, respectively. Systematic variations in pair-correlation functions, thermodynamic properties as well as the self-diffusion coefficient are found with the size, charge and mass ratio of the particles. The self-diffusion coefficient for systems having more than one type of asymmetry is calculated and expressed in terms of diffusion coefficients of systems with only one type of asymmetry. [ABSTRACT FROM AUTHOR]

The freezing-point shifts of Lennard-Jones (LJ) particles confined in a parallel slit porewhose size is less than 10 times the diameter of the LJ particle were studied. Using molecular dynamics simulation, the latent heat of freezing, specific volume, wall-liquid interfacial tension and wall-solid interfacial energywere obtained as functions of the slit width. We compare the freezing-point shifts predicted by the Gibbs-Thomson equation to those directly determined by cooling and heating simulations. Although both methods predicted the freezing points elevation in slit pores, the oscillation of the freezing-point shifts observed by molecular dynamics simulations could not be explained by the Gibbs-Thomson equation, even when the dependence of the physical properties on the pore size was considered. By assuming that the intermediate value between the freezing-point shift and themelting-point shift decreases to zero via a power function, the exponent of decay was calculated. [ABSTRACT FROM AUTHOR]

The surface wettability effect on fluid transport in nanoscale slit pores is quantitatively accessed by using non-equilibrium molecular dynamics (NEMD) simulation incorporating with density functional theory (DFT). In particular, the slip lengths of benzene steady flows under various wetting conditions are computed with NEMD simulations and a quasi-general expression is given, while the structural properties are investigated with DFT. By taking into account the inhomogeneity of fluid density inside pore, we find that the conventional flux enhancement rate is associated with both the molecule slipping and geometrical confinement, and it becomes drastically high in solvophobic pores especially when the pore size is of several fluid diameters. In good agreement with experimental results, we further show that the wettability effect competes with pore size effect in determining the flux after pore inner surface modification, and a high flux can be achieved when the deposited layer is solvophobic yet thin. © 2016 American Institute of Chemical Engineers AIChE J, 63: 1704-1714, 2017 [ABSTRACT FROM AUTHOR]

Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool that has enabled experimentalists to characterize molecular dynamics and kinetics spanning a wide range of time-scales from picoseconds to days. This review focuses on addressing the previously inaccessible supra-τc window (defined as τc < supra-τc < 40 μs; in which τc is the overall tumbling time of a molecule) from the perspective of local inter-nuclear vector dynamics extracted from residual dipolar couplings (RDCs) and from the perspective of conformational exchange captured by relaxation dispersion measurements (RD). The goal of the first section is to present a detailed analysis of how to extract protein dynamics encoded in RDCs and how to relate this information to protein functionality within the previously inaccessible supra-τc window. In the second section, the current state of the art for RD is analyzed, as well as the considerable progress toward pushing the sensitivity of RD further into the supra-τc scale by up to a factor of two (motion up to 25 μs). From the data obtained with these techniques and methodology, the importance of the supra-τc scale for protein function and molecular recognition is becoming increasingly clearer as the connection between motion on the supra-τc scale and protein functionality from the experimental side is further strengthened with results from molecular dynamics simulations. [ABSTRACT FROM AUTHOR]

The sophistication of the force fields, algorithms and hardware used for molecular dynamics (MD) simulations of proteins is continuously increasing. No matter how advanced the methodology, however, it is essential to evaluate the appropriateness of the structures sampled in a simulation by comparison with quantitative experimental data. Solution nuclear magnetic resonance (NMR) data are particularly useful for checking the quality of protein simulations, as they provide both structural and dynamic information on a variety of temporal and spatial scales. Here, various features and implications of using NMR data to validate and bias MD simulations are outlined, including an overview of the different types of NMR data that report directly on structural properties and of relevant simulation techniques. The focus throughout is on how to properly account for conformational averaging, particularly within the context of the assumptions inherent in the relationships that link NMR data to structural properties. [ABSTRACT FROM AUTHOR]

This study theoretically considers the motion of N identical inelastic particles between two oscillating walls. The particles' average energy increases abruptly at certain critical filling fractions, wherein the system changes into a solid-like phase with particles clustered in their compact form. Molecular dynamics simulations of the system show that the critical filling fraction is a decreasing function of vibration amplitude independent of vibration frequency, which is consistent with previous experimental results. This study considers the entire group of particles as a giant pseudo-particle with an effective size and an effective coefficient of restitution. The N-particles system is then analytically treated as a one-particle problem. The critical filling fraction's dependence on vibration amplitude can be explained as a necessary condition for a stable resonant solution. The fluctuation to the system's mean flow energy is also studied to show the relation between the granular temperature and the system phase. [ABSTRACT FROM AUTHOR]

The phenomenon of supercooling in metals—that is, the preservation of a disordered, fluid phase in a metastable state well below the melting point—has led to speculation that local atomic structure configurations of dense, symmetric, but non-periodic packing act as the main barrier for crystal nucleation. For liquids in contact with solids, crystalline surfaces induce layering of the adjacent atoms in the liquid and may prevent or lower supercooling. This seed effect is supposed to depend on the local lateral order adopted in the last atomic layers of the liquid in contact with the crystal. Although it has been suggested that there might be a direct coupling between surface-induced lateral order and supercooling, no experimental observation of such lateral ordering at interfaces is available. Here we report supercooling in gold-silicon (AuSi) eutectic droplets, enhanced by a Au-induced (6 × 6) reconstruction of the Si(111) substrate. In situ X-ray scattering and ab initio molecular dynamics reveal that pentagonal atomic arrangements of Au atoms at this interface favour a lateral-ordering stabilization process of the liquid phase. This interface-enhanced stabilization of the liquid state shows the importance of the solid–liquid interaction for the structure of the adjacent liquid layers. Such processes are important for present and future technologies, as fluidity and crystallization play a key part in soldering and casting, as well as in processing and controlling chemical reactions for microfluidic devices or during the vapour–liquid–solid growth of semiconductor nanowires. [ABSTRACT FROM AUTHOR]

Abstract  In this work, we study the temperature-induced development of “dynamically arrested” states in dense suspensions of “soft colloids” (multi-arm star polymers and/or block-copolymers micelles) by means of molecular dynamics (MD) simulations. Temperature increase in marginal solvents results in “soft sphere” swelling, dynamical arrest, and eventually crystallization. However, two distinct “dynamically arrested” states were found, one almost amorphous (“glassy”) and one with a considerable degree of crystallinity, yet lower than that of the fully equilibrated crystal. It is remarkable that even that latter state permitted self-diffusion in the timescale of the simulations, an effect that underlies the importance of the “ultra-soft” nature of inter-particle potential. The “number of connections” criterion for crystallinity proved to be very successful in identifying the ultimate thermodynamic trend from the very early stages of the α-relaxation. [ABSTRACT FROM AUTHOR]

An electrical double layer of a spherical macroion with single-, double-, and triple-charged counterions in aqueous solution of 1: 1 background electrolyte at different concentrations are studied by the molecular dynamics method for models with discrete and continuous surface charge distribution. Radial profiles of ion partial densities and the electric potential distribution in the double layer are calculated. The degree of counterion binding with a macroion is determined. The effect of water permittivity on the structure of electrical double layer is studied. [ABSTRACT FROM AUTHOR]

The structure and thermodynamics of the (100) and (111) disordered face-centred cubic (fcc) crystal/melt interfaces for a binary hard sphere system have been examined using molecular dynamics simulation. This study is an extension of previous work (Davidchack, R. L., and Laird, B. B., 1996, Phys. Rev. E, 54, R5905), in which preliminary data for the (100) interface were reported. Density and diffusion profiles on both fine and coarse grained scales are calculated and analysed, leading to the conclusion that equilibrium interfacial segregation is minimal in this system. [ABSTRACT FROM AUTHOR]

We study the properties of the ethylene glycol solutions and the conformational transitions of DNA segment in the ethylene glycol solutions by molecular dynamics simulations based on GROMACS. The hydrogen network structures of water–water and ethylene glycol–water are reinforced by ethylene glycol molecules when the concentrations of the solutions increase from 0% to 80%. As illustrated by the results, conformation of the double-stranded DNA in ethylene glycol solutions, although more compact, is similar to the structure of DNA in the aqueous solutions. In contrast, the DNA structure is an A–B hybrid state in the ethanol/water mixed solution. A fraying of terminal base-pairs is observed for the terminal cytosine. The ethylene glycol molecules preferentially form a ring structure around the phosphate groups to influence DNA conformation by hydrogen interactions, while water molecules tend to reside in the grooves. The repulsion between the negatively charged phosphate groups is screened by ethylene glycol molecules, preventing the repulsion from unwinding and extending the helix and thus making the conformation of DNA more compact. [ABSTRACT FROM AUTHOR]

The size-dependent melting behaviors and mechanisms of Ag nanoparticles (NPs) with diameters of 3.5–16 nm were investigated by molecular dynamics (MD). Two distinct melting modes, non-premelting and premelting with transition ranges of about 7–8 nm, for Ag NPs were demonstrated via the evolution of distribution and transition of atomic physical states during annealing. The small Ag NPs (3.5–7 nm) melt abruptly without a stable liquid shell before the melting point, which is characterized as non-premelting. A solid-solid crystal transformation is conducted through the migration of adatoms on the surface of Ag NPs with diameters of 3.5–6 nm before the initial melting, which is mainly responsible for slightly increasing the melting point of Ag NPs. On the other hand, surface premelting of Ag NPs with diameters of 8–16 nm propagates from the outer shell to the inner core with initial anisotropy and late isotropy as the temperature increases, and the close-packed facets {111} melt by a side-consumed way which is responsible for facets {111} melting in advance relative to the crystallographic plane {111}. Once a stable liquid shell is formed, its size-independent minimum thickness is obtained, and a three-layer structure of atomic physical states is set up. Lastly, the theory of point defect-pair (vacancy-interstitial) severing as the mechanism of formation and movement of the solid-liquid interface was also confirmed. Our study provides a basic understanding and theoretical guidance for the research, production and application of Ag NPs. [ABSTRACT FROM AUTHOR]