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We present high-order variational Lagrangian finite element methods for compressible fluids using a discrete energetic variational approach. Our spatial discretization is mass/momentum/energy conserving and entropy stable. Fully implicit…
We propose a variational formulation for the nonequilibrium thermodynamics of discrete open systems, i.e., discrete systems which can exchange mass and heat with the exterior. Our approach is based on a general variational formulation for…
Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…
In this paper, we investigate if it occurs a phase transition for a system of classical dimers adsorbed on a 3-4 lattice in the thermodynamic limit. We define four types of bonds (denoted by the dimers activities adsorbed in her, $x$, $y$,…
A significant drawback of Lagrangian (particle-tracking) reactive transport models has been their inability to properly simulate interactions between solid and liquid chemical phases, such as dissolution and precipitation reactions. This…
We extend ring-polymer molecular dynamics (RPMD) to allow for the direct simulation of general, electronically non-adiabatic chemical processes. The kinetically constrained (KC) RPMD method uses the imaginary-time path-integral…
Recently we proposed a new constant-pressure molecular dynamics method for finite systems. In this paper, we discuss the current understanding of this method and its technique details. We also review the recent theoretical advances of…
We introduce a data-driven method for learning the equations of motion of mechanical systems directly from position measurements, without requiring access to velocity data. This is particularly relevant in system identification tasks where…
Systems switching between different dynamical phases is an ubiquitous phenomenon. The general understanding of such a process is limited. To this end, we present a general expression that captures fluctuations of a system exhibiting a…
Using an effective strongly coupled lattice QCD Hamiltonian and Wilson fermions we calculate the equation of state for cold and dense quark matter by constructing an ansatz which exactly diagonalizes the Hamiltonian to second order in field…
We use a mixture of a polymer and its dimer to control dynamics in a manner inspired by \emph{pinning} a fraction of the system. In our system of $\alpha$-methyl styrene, where the polymer has a glass transition at higher temperature than…
Fluctuating hydrodynamics based techniques have been developed in recent years for the simulation of Brownian motion of particles. These mesoscale simulation tools are viable approaches for problems where molecular dynamics simulations may…
This paper describes a method to do ab initio molecular dynamics in electronically excited systems within the random phase approximation (RPA). Using a dynamical variational treatment of the RPA frequency, which corresponds to the…
Using both atomistic and particle-based simulations, we investigate the current-driven dynamics of skyrmions on two-dimensional periodic substrates when there are multiple skyrmions per substrate minimum. At zero drive, the system forms…
The phoretic Brownian dynamics method is shown here to be an effective approach to simulate the properties of colloidal chemophoretic based systems. The method is then optimized to allow for the comparison with results from multiparticle…
We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are build on our previously developed…
We study quantum systems with broken symmetry that can be modelled as cyclic three-level atoms with coexisting one- and two-photon transitions. They can be selectively optically excited to any state. As an example, we show that left- and…
We introduce a lattice model of dimers with directional interactions as a paradigm of molecular fluids or strongly correlated Cooper pairs in electronic systems. The model supports an intermediate phase that is common to both systems. There…
We provide new insights into the contact Hamiltonian and Lagrangian formulations of dissipative mechanical systems. In particular, we state a new form of the contact dynamical equations, and we review two recently presented Lagrangian…
In this paper, we develop a Hamiltonian variational formulation for the nonequilibrium thermodynamics of simple adiabatically closed systems that is an extension of Hamilton's phase space principle in mechanics. We introduce the…