Related papers: Cell List Algorithms for Nonequilibrium Molecular …
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…
Human blood flow is a multi-scale problem: in first approximation, blood is a dense suspension of plasma and deformable red cells. Physiological vessel diameters range from about one to thousands of cell radii. Current computational models…
A fast and accurate computational scheme for simulating nonlinear dynamic systems is presented. The scheme assumes that the system can be represented by a combination of components of only two different types: first-order low-pass filters…
As an alternative to solving of Poisson equation in Particle-in-Cell methods, a new construction of current density exactly satisfying continuity equation in finite differences is developed. This procedure called density decomposition is…
We review a family of local algorithms that permit the simulation of charged particles with purely local dynamics. Molecular dynamics formulations lead to discretizations similar to those of ``particle in cell'' methods in plasma physics.…
The filtration of fluid in 2D porous medium is simulated by the molecular dynamics technique. The high concentration of fluid is created at the initial point in time and the number of fluid particles is investigated in all porous. The…
Normalizing flows (NFs) provide a powerful tool to construct an expressive distribution by a sequence of trackable transformations of a base distribution and form a probabilistic model of underlying data. Rotation, as an important quantity…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…
The conventional no-slip boundary condition leads to a non-integrable stress singularity at a moving contact line. This makes numerical simulations challenging, especially when capillary effects are essential for the dynamics of the flow.…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
Computational fluid dynamics lies at the heart of many issues in science and engineering, but solving the associated partial differential equations remains computationally demanding. With the rise of quantum computing, new approaches have…
This work presents a novel numerical investigation of the dynamics of free-boundary flows of viscoelastic liquid membranes. The governing equation describes the balance of linear momentum, in which the stresses include the viscoelastic…
In this work, algorithms for the parallel computation of three-body interactions in molecular dynamics are developed. While traversals for the computation of pair interactions are readily available in the literature, here, such traversals…
We present a quantum algorithm that analyzes time series data simulated by a quantum differential equation solver. The proposed algorithm is a quantum version of the dynamic mode decomposition algorithm used in diverse fields such as fluid…
We introduce a nonlinear stochastic model reduction technique for high-dimensional stochastic dynamical systems that have a low-dimensional invariant effective manifold with slow dynamics, and high-dimensional, large fast modes. Given only…
A molecular dynamics (MD) simulation of planar Couette flow is presented for the minimal channel in which turbulence structures can be sustained. Evolution over a single breakdown and regeneration cycle is compared to computational fluid…
A simple reweighting scheme is proposed for Monte Carlo simulations of interacting particle systems, permitting one to study various parameter values in a single study, and improving efficiency by an order of magnitude. Unlike earlier…
Living systems are capable of locomotion, reconfiguration, and replication. To perform these tasks, cells spatiotemporally coordinate the interactions of force-generating, "active" molecules that create and manipulate non-equilibrium…
Understanding active matter has led to new perspectives on biophysics and non-equilibrium dynamics. However, the development of numerical tools for simulating active fluids capable of incorporating non-trivial boundaries or inclusions has…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…