arXiv subjects

Yanting Wang

Publications and source records attributed to Yanting Wang.

50 records · Page 3Linked to original sources

arXiv2019

Poisson-Boltzmann theory with non-linear ion correlations

The Poisson-Boltzmann (PB) theory is widely used to depict ionic systems. As a mean-field theory, the PB theory neglects the correlation effect in the ionic atmosphere and leads to deviations from experimental results as the concentration or charge valance increases. A modified PB theory including ion correlation effect while retaining its simplicity is critical for many important applications in which ion correlation effect can be significant. In this paper, we present a new model to incorporate ion correlations into the original PB equation by utilizing the Green's function with a non-linear form of the self-energy, which is different from the linear self-energy equation obtained by the Field-Theoretic (FT) approach. Both equations are solved numerically and compared with our molecular dynamics (MD) simulation. The co-ion distribution calculated by the FT approach deviates significantly from the MD simulation, while our results for both counter-ion and co-ion distributions are justified by the MD simulation.

cond-mat.soft↗

arXiv2018

Percolation Phase Transition from Ionic Liquids to Ionic Liquid Crystals

As typical complex liquids, ionic liquids (ILs) exhibit phases beyond the description of simple liquid theories. In particular, with an intermediate cationic side-chain length, ILs can form the nanoscale segregated liquid (NSL) phase, which will eventually transform into the ionic liquid crystal (ILC) phase when the side chains are adequately long. However, the microscopic mechanism of this transformation is still unclear. In this work, by means of coarse-grained molecular dynamics simulation, we show that, with increasing cationic side-chain length, some local pieces of non-polar domains are gradually formed by side chains aligned in parallel inside the NSL phase, before an abrupt percolation phase transition happens when the system transforms into the ILC phase, manifesting that it is a critical phenomenon. Percolation phase transition is applied to ILs, providing new insights into many recent observations both in experiments and simulations.

cond-mat.soft↗

arXiv2016

Moderate Point: Balanced Entropy and Enthalpy Contributions in Soft Matter

Various soft materials share some common features, such as significant entropic effect, large fluctuations, sensitivity to thermodynamic conditions, and mesoscopic characteristic spatial and temporal scales. However, no quantitative definitions have yet been provided for soft matter, and the intrinsic mechanisms leading to their common features are unclear. In this work, from the viewpoint of statistical mechanics, we show that soft matter works in the vicinity of a specific thermodynamic state named moderate point, at which entropy and enthalpy contributions among substates along a certain order parameter are well balanced or have a minimal difference. Around the moderate point, the order parameter fluctuation, the associated response function, and the spatial correlation length maximize, which explains the large fluctuation, the sensitivity to thermodynamic conditions, and mesoscopic spatial and temporal scales of soft matter, respectively. Possible applications to switching chemical bonds or allosteric biomachines determining their best working temperatures are also discussed.

cond-mat.soft↗

arXiv2015

Equilibrium sampling by re-weighting non-equilibrium simulation trajectories

With the traditional equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space in complex systems, which are separated into some metastable conformational regions by high free energy barriers. The applied non-equilibrium process in simulations could enhance the transitions among these conformational regions, and the associated non-equilibrium effects can be removed by employing the Jarzynski equality (JE), then the global equilibrium distribution can be reproduced. However, the original JE requires the initial distribution of the non-equilibrium process is equilibrium, which largely limits the application of the non-equilibrium method in equilibrium sampling. By extending the previous method, the reweighted ensemble dynamics (RED), which re-weights many equilibrium simulation trajectories from arbitrary initial distribution to reproduce the global equilibrium, to non-equilibrium simulations, we present a method, named as re-weighted non-equilibrium ensemble dynamics (RNED), to generalize the JE in the non-equilibrium trajectories started from an arbitrary initial distribution, thus provide an efficient method to reproduce the equilibrium distribution based on multiple independent (short) non-equilibrium trajectories. We have illustrated the validity of the RNED in a one-dimensional toy model and in a Lennard-Jones system to detect the liquid-solid phase coexistence.

cond-mat.soft↗

arXiv2015

Jarzynski matrix equality: calculating free energy difference by non-equilibrium simulations with an arbitrary initial distribution

The Jarzynski equality (JE), which relates works of non-equilibrium trajectories to the free energy difference of the initial and final states of the non-equilibrium process, provides an efficient way to calculate free energies of systems in simulations and experiments. However, wider applications of the JE are limited by the requirement that the initial distribution of non-equilibrium trajectories must be equilibrium. Here we extend the JE to a matrix form, the Jarzynski matrix equality (JME), which transforms the free energies of metastable conformational regions in the initial system to that of final one. Therefore, we can calculate the free energies from non-equilibrium trajectories which started from an arbitrary initial distribution. We demonstrate the application of the JME in toy models, Lennard-Jones fluids, and polymer chain models, show its good efficiency in calculation of free energy with a satisfactory accuracy. The JME extends applications of the non-equilibrium method in estimate of free energy in complex system where the initial global equilibrium is difficult to reach.

cond-mat.soft↗

arXiv2015

Saturated Sodium Chloride Solution under an External Static Electric Field: a Molecular Dynamics Study

The behavior of saturated aqueous sodium chloride solutions under a constant external electric field (E) was studied by molecular dynamics (MD) simulation. Our dynamic MD simulations have indicated that the irreversible nucleation process towards crystallization is accelerated by a moderate E, but retarded or even prohibited under a stronger E, which can be understood by the competition between self-diffusion and drift motion. The former increases with E resulting in the acceleration of the nucleation process, and the latter tears oppositely charged ions more apart under a stronger E leading to the deceleration of nucleation. Moreover, our steady-state MD simulations have indicated that a first-order phase transition happens in saturated solutions only when the applied E is below a certain threshold Ec, and the ratio of crystallized ions does not change with the electric field. The magnitude of Ec increases with concentration, because larger clusters are easy to form in a more concentrated solution and require a stronger E to dissociate them.

cond-mat.soft↗

arXiv2015

Intrinsic Defect Formation in Peptide Self-Assembly

In contrast to extensively studied defects in traditional materials, we report here for the first time a systematic investigation of the formation mechanism of intrinsic defects in self-assembled peptide nanostructures. The Monte Carlo simulations with our simplified dynamic hierarchical model revealed that the symmetry breaking of layer bending mode at the two ends during morphological transformation is responsible for intrinsic defect formation, whose microscopic origin is the mismatch between layer stacking along the side-chain direction and layer growth along the hydrogen bond direction. Moreover, defect formation does not affect the chirality of the self-assembled structure, which is determined by the initial steps of the peptide self-assembly process.

cond-mat.soft↗

arXiv2014

One-dimensional steady transport by molecular dynamics simulation: Non-Boltzmann position distribution and non-Arrhenius dynamical behavior

A non-equilibrium steady state can be characterized by a nonzero but stationary flux driven by a static external force. Under a weak external force, the drift velocity is difficult to detect because the drift motion is feeble and submerged in the intense thermal diffusion. In this article, we employ an accurate method in molecular dynamics simulation to determine the drift velocity of a particle driven by a weak external force in a one-dimensional periodic potential. With the calculated drift velocity, we found that the mobility and diffusion of the particle obey the Einstein relation, whereas their temperature dependences deviate from the Arrhenius law. A microscopic hopping mechanism was proposed to explain the non-Arrhenius behavior. Moreover, the position distribution of the particle in the potential well was found to deviate from the Boltzmann equation in a non-equilibrium steady state. The non-Boltzmann behavior may be attributed to the thermostat which introduces and effective "viscous" drag opposite to the drift direction of the particle.

cond-mat.stat-mech↗

arXiv2014

Reversible Transient Nucleation in Ionic Solutions as the Precursor of Ion Crystallization

Molecular dynamics simulations for aqueous sodium chloride solutions were carried out at various concentrations. Supplementary to the Debye-Hückel theory, reversible transient nucleation of ions was observed even in dilute solutions. The average size of formed ion clusters and the lifetime of ion pairs increase with concentration until the saturation point, when ion clusters become stable and individual ions adjust their positions to form ordered lattice structures, leading to irreversible ion crystallization, which is beyond the description of the classical nucleation theory.

cond-mat.soft↗

arXiv2012

Diffusion-limited aggregation with polygon particles

Diffusion-limited aggregation (DLA) assumes that particles perform pure random walk at a finite temperature and aggregate when they come close enough and stick together. Although it is well known that DLA in two dimensions results in a ramified fractal structure, how the particle shape influences the formed morphology is still unclear. In this work, we perform the off-lattice two-dimensional DLA simulations with different particle shapes of triangle, quadrangle, pentagon, hexagon, and octagon, respectively, and compared with the results for circular particles. Our results indicate that different particle shapes only change the local structure, but have no effects on the global structure of the formed fractal cluster. The local compactness decreases as the number of polygon edges increases.

cond-mat.stat-mech↗

arXiv2005

Continuous Time Monte Carlo and Spatial Ordering in Driven Lattice Gases: Application to Driven Vortices in Periodic Superconducting Networks

We consider the two dimensional (2D) classical lattice Coulomb gas as a model for magnetic field induced vortices in 2D superconducting networks. Two different dynamical rules are introduced to investigate driven diffusive steady states far from equilibrium as a function of temperature and driving force. The resulting steady states differ dramatically depending on which dynamical rule is used. We show that the commonly used driven diffusive Metropolis Monte Carlo dynamics contains unphysical intrinsic randomness that destroys the spatial ordering present in equilibrium (the vortex lattice) over most of the driven phase diagram. A continuous time Monte Carlo (CTMC) is then developed, which results in spatially ordered driven states at low temperature in finite sized systems. We show that CTMC is the natural discretization of continuum Langevin dynamics, and argue that it gives the correct physical behavior when the discrete grid represents the minima of a periodic potential. We use detailed finite size scaling methods to analyze the spatial structure of the steady states. We find that finite size effects can be subtle and that very long simulation times can be needed to arrive at the correct steady state. For particles moving on a triangular grid, we find that the ordered moving state is a transversely pinned smectic that becomes unstable to an anisotropic liquid on sufficiently large length scales. For particles moving on a square grid, the moving state is a similar smectic at large drives, but we find evidence for a possible moving solid at lower drives. We find that the driven liquid on the square grid has long range hexatic order, and we explain this as a specifically non-equilibrium effect. We show that, in the liquid, fluctuations are diffusive in both the transverse and longitudinal directions.

cond-mat.stat-mech↗

arXiv2004

Surface Driven Bulk Reconstruction of Gold Nanorods

Molecular dynamic simulations are used to study the heating of a gold nanorod of 2624 atoms. We show that roughening of surface {110} facets leads to a shape transformation and structural rearrangement of surface and bulk atoms in the rod, in order to reach a more stable configuration. Our results show that the stability of the nanorod is governed by the free energetics of the surface facets.

cond-mat.stat-mech↗

arXiv2004

Melting of icosahedral gold nanoclusters from molecular dynamics simulations

Molecular dynamics simulations show that gold clusters with about 600--3000 atoms crystallize into a Mackay icosahedron upon cooling from the liquid. A detailed surface analysis shows that the facets on the surface of the Mackay icosahedral gold clusters soften but do not premelt below the bulk melting temperature. This softening is found to be due to the increasing mobility of vertex and edge atoms with temperature, which leads to inter-layer and intra-layer diffusion, and a shrinkage of the average facet size, so that the average shape of the cluster is nearly spherical at melting.

cond-mat.mtrl-sci↗

arXiv2004

Melting and Equilibrium Shape of Icosahedral Gold Nanoparticles

We use molecular dynamics simulations to study the melting of gold icosahedral clusters of a few thousand atoms. We pay particular attention to the behavior of surface atoms, and to the equilibrium shape of the cluster. We find that although the surface of the cluster remains ordered up to the melting T_m, the increasing mobility of vertex and edge atoms significantly soften the surface structure, leading to inter- and intra-layer diffusion, and shrinking of the average facet size, so that the average shape of the cluster is nearly spherical at melting.

cond-mat.mtrl-sci↗