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We simulate the compression of a two-component Lennard-Jones liquid at a variety of constant temperatures using a molecular dynamics algorithm in an isobaric-isothermal ensemble. The viscosity of the liquid increases with pressure,…
Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which…
A new computational method for finite-temperature properties of strongly correlated electrons is proposed by extending the variational Monte Carlo method originally developed for the ground state. The method is based on the path integral in…
We discuss the temperature distribution in a two-dimensional, thermally unstable numerical simulation of the warm and cold gas in the Galactic disk, including the magnetic field, self-gravity, the Coriolis force, stellar energy injection…
In this work the high pressure region of the phase diagram of water has been studied by computer simulation by using the TIP4P/2005 model of water. Free energy calculations were performed for ices VII and VIII and for the fluid phase to…
Variational principles for magnetohydrodynamics (MHD) were introduced by previous authors both in Lagrangian and Eulerian form. In this paper we introduce simpler Eulerian variational principles from which all the relevant equations of…
We present a set of second-order, time-reversible algorithms for the isothermal (NVT) molecular-dynamics (MD) simulation of systems with mixed hard-core/continuous potentials. The methods are generated by combining real-time Nose'…
Markov chain Monte Carlo methods are primarily used for sampling from a given probability distribution and estimating multi-dimensional integrals based on the information contained in the generated samples. Whenever it is possible, more…
We propose a method, Temperature Integration, which allows an efficient calculation of free energy differences between two systems of interest, with the same degrees of freedom, which may have rough energy landscapes. The method is based on…
In a recent publication, Trentin et al employed Molecular Dynamics (MD) simulations for the theoretical study of the wetting of the different polymorphs of cellulose by water, using the widely employed TIP3P model of water. Here we show…
We present a differentiable formalism for learning free energies that is capable of capturing arbitrarily complex model dependencies on coarse-grained coordinates and finite-temperature response to variation of general system parameters.…
By using canonical Monte Carlo simulation, the liquid-vapor phase diagram, surface tension, interface width, and pressure for the Mie(n,m) model fluids are calculated for six pairs of parameters $m$ and $n$. It is shown that after certain…
Irreversible thermodynamics of simple fluids have been connected recently to the theory of dynamical systems and some interesting assumptions have been made about the nature of the associated invariant measures. We show that the tests of…
Using normalizing flows and reweighting, Boltzmann Generators enable equilibrium sampling from a Boltzmann distribution, defined by an energy function and thermodynamic state. In this work, we introduce Thermodynamic Interpolation (TI),…
Thermal fluctuations cause perturbations of fluid-fluid interfaces and highly nonlinear hydrodynamics in multiphase flows. In this work, we develop a novel multiphase smoothed dissipative particle dynamics model. This model accounts for…
Thermo-osmotic slip -- the flow induced by a thermal gradient along a surface -- is a well-known phenomenon, but curiously there is a lack of robust molecular-simulation techniques to predict its magnitude. Here, we compare three different…
Polycrystalline materials can be viewed as composites of crystalline particles or grains separated from one another by thin amorphous grain boundary (GB) regions. While GB have been exhaustively investigated at low temperatures, where these…
Torsional-space Monte Carlo simulations of flexible molecules are usually based on the assumption that all values of dihedral angles have equal probability in the absence of atomic interactions. In the present paper it is shown that this…
We develop a formulation of global thermodynamics for equilibrium systems under the influence of gravity. The free energy for simple fluids is extended to include a dependence on $(T, V, N, mgL)$, where $L$ represents the vertical system…
We present a simple model for the turbulent kinetic energy behavior of subsonic plasma turbulence undergoing isotropic three-dimensional compression, such as may exist in various inertial confinement fusion experiments or astrophysical…