Related papers: Symplectic algorithm for constant-pressure molecul…
High-resolution simulations of particle-based kinetic plasma models typically require a high number of particles and thus often become computationally intractable. This is exacerbated in multi-query simulations, where the problem depends on…
A nonlinear analytical model for the pressure dynamics in a vacuum chamber, pumped with a sputter ion pump (SIP), is proposed, discussed and experimentally evaluated. The model describes the physics of the pumping mechanism of SIPs in the…
We describe a symplectic approach towards thermodynamics in which thermodynamic transformations are described by (symplectic) Hamiltonian dynamics. Upon identifying the spaces of equilibrium states with Lagrangian submanifolds of a…
In this work, we propose a nonlinear stabilization technique for scalar conservation laws with implicit time stepping. The method relies on an artificial diffusion method, based on a graph-Laplacian operator. It is nonlinear, since it…
We present a deterministic algorithm called contact density dynamics that generates any prescribed target distribution in the physical phase space. Akin to the famous model of Nos\'e-Hoover, our algorithm is based on a non-Hamiltonian…
In recent years, constant applied potential molecular dynamics has allowed to study the structure and dynamics of the electrochemical double-layer of a large variety of nanoscale capacitors. Nevertheless it remained impossible to simulate…
We present a new approach to carry out non-adiabatic molecular dynamics to study the carrier mobility in an organic monolayer. This approach allows the calculation of a 4802 atom system for 825 fs in about three hours using 51,744 computer…
Magnetic and electronic properties of the Hubbard model on the Bethe and fcc lattices in infinite dimensions have been investigated numerically on the basis of the dynamical coherent potential approximation (CPA) theory combined with the…
In this paper, we extend the energy-Casimir stability method for deterministic Lie-Poisson Hamiltonian systems to provide sufficient conditions for the stability in probability of stochastic dynamical systems with symmetries and…
With the rapid development of ultra-fast experimental techniques used for carrier dynamics in solid-state systems, a microscopic understanding of the related phenomena, particularly a first-principle calculation is highly desirable.…
The synchronized molecular dynamics simulation via macroscopic heat and momentum transfer is proposed for the non-isothermal flow behaviors of complex fluids. In this method, the molecular dynamics simulations are assigned to small fluid…
Atmospheric systems incorporating thermal dynamics must be stable with respect to both energy and entropy. While energy conservation can be enforced via the preservation of the skew-symmetric structure of the Hamiltonian form of the…
We propose in this work a second-order Langevin sampler for the isothermal-isobaric ensemble (the NPT ensemble), preserving a positive volume for the simulation box. We first derive the suitable equations of motion for particles to be…
In this note, we propose a symplectic algorithm for the stable manifolds of the Hamilton-Jacobi equations combined with an iterative procedure in [Sakamoto-van~der Schaft, IEEE Transactions on Automatic Control, 2008]. Our algorithm…
We study numerical methods for dissipative particle dynamics (DPD), which is a system of stochastic differential equations and a popular stochastic momentum-conserving thermostat for simulating complex hydrodynamic behavior at mesoscales.…
Hamiltonian and action principle (HAP) formulations of plasma physics are reviewed for the purpose of explaining structure preserving numerical algorithms. Geometric structures associated with and emergent from HAP formulations are…
Ab initio molecular dynamics (AIMD) simulations using hybrid density functionals and plane waves are of great interest owing to the accuracy of this approach in treating condensed matter systems. On the other hand, such AIMD calculations…
The Poisson-Nernst-Planck (PNP) equations are one of the most effective model for describing electrostatic interactions and diffusion processes in ion solution systems, and have been widely used in the numerical simulations of biological…
Symplectic integrators offer vastly superior performance over traditional numerical techniques for conservative dynamical systems, but their application to \emph{dissipative} systems is inherently difficult due to dissipative systems' lack…
Stochastic thermostats based on the Langevin equation, in which a system is coupled to an external heat bath, are popular methods for temperature control in molecular dynamics simulations due to their ergodicity and their ease of…