Related papers: Escaping free-energy minima
We develop a framework for understanding the difference between strong and fragile behavior in the dynamics of glass-forming liquids from the properties of the potential energy landscape. Our approach is based on a master equation…
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased Molecular…
The multiple range random walk algorithm recently proposed by Wang and Landau [Phys. Rev. Lett. 86, 2050 (2001)] is adapted to the computation of free energy profiles for molecular systems along reaction coordinates. More generally, we show…
The dynamics of small-scale structures in free-surface turbulence is crucial to large-scale phenomena in natural and industrial environments. Here we conduct experiments on the quasi-flat free surface of a zero-mean-flow turbulent water…
In this paper, a statistical physical derivation of thermodynamically consistent fluid mechanical equations is presented for non-isothermal viscous molecular fluids. The coarse-graining process is based on (i) the adiabatic expansion of the…
Microscopic machines utilize free energy to create and maintain out-of-equilibrium organization in virtually all living things. Often this takes the form of converting the free energy stored in nonequilibrium chemical potential differences…
We present methods for exploratory studies of molecular dynamics using MATLAB. Such methods are not suitable for large scale applications, but they can be used for developement and testing of new types of interactions and other aspects of…
Simulations of colloidal suspensions consisting of mesoscopic particles and smaller species such as ions or depletants are computationally challenging as different length and time scales are involved. Here, we introduce a machine learning…
In this work we study the dynamic behaviour of compound shells of revolution partially filled with an ideal incompressible fluid based on boundary-value problems. New analytical mathematical model with corresponding discrete scheme for the…
We consider a stochastic many-body system where a source refills uniformly the empty sites of a hypercubic lattice, on which each particle is allowed to jump (symmetrically) onto neighboring vacant sites. In addition, there is a local {\it…
The exact time-dependent potential energy surface driving the nuclear dynamics was recently shown to be a useful tool to understand and interpret the coupling of nuclei, electrons, and photons, in cavity settings. Here we provide a detailed…
Using a Coarse-grained Molecular Dynamics (CMD) approach we study the apparent nonlinear dynamics of water molecules filling/emptying carbon nanotubes as a function of system parameters. Different levels of the pore hydrophobicity give rise…
This paper presents a continuous, information-theoretic extension of the Free Energy Principle through the concept of Markov blanket density, i.e., a scalar field that quantifies the degree of conditional independence between internal and…
Driving an inertial many-body system out of equilibrium generates complex dynamics due to memory effects and the intricate relationships between the external driving force, internal forces, and transport effects. Understanding the…
We present an accurate equation of state for water based on a simple microscopic Hamiltonian, with only four parameters that are well-constrained by bulk experimental data. With one additional parameter for the range of interaction, this…
We demonstrate the use of spatially encoded magnetic resonance to quantify ensemble dynamics of microscopic particles below the spatial resolution. By evaluating time series of k-space data-points, k-dependent motion patterns can be…
In this study, we utilize the many-body expansion (MBE) framework to decompose electronic structures into fragments by incrementing the virtual orbitals. Our work aims to accurately solve the ground and excited state energies of each…
Many-body dissipative particle dynamics is constructed to exhibit vapour-liquid coexistence, with a sharp interface, and a vapour phase of vanishingly small density. In this form, the model is an unusual example of a soft-sphere liquid with…
Multiple equilibrium states arise in many physical systems, including various types of liquid crystal structures. Having the ability to reliably compute such states enables more accurate physical analysis and understanding of experimental…
Molecular dynamics (MD) simulations have been carried out to investigate the slip of fluid in the lid driven cavity flow where the no-slip boundary condition causes unphysical stress divergence. The MD results not only show the existence of…