Related papers: A portable code for dissipative particle dynamics …
Real-life control tasks involve matters of various substances---rigid or soft bodies, liquid, gas---each with distinct physical behaviors. This poses challenges to traditional rigid-body physics engines. Particle-based simulators have been…
Dynamical decoupling (DD) is a popular technique for protecting qubits from the environment. However, unless special care is taken, experimental errors in the control pulses used in this technique can destroy the quantum information instead…
Understanding the complex viscoelastic properties of polymeric liquids remains a challenge in materials science and soft matter physics. Here, we present a simple and computationally efficient criterion for the topological constraints in…
We introduce a particle-based simulation method for granular material in interactive frame rates. We divide the simulation into two decoupled steps. In the first step, a relatively small number of particles is accurately simulated with a…
We study the motion of charged particles constrained to arbitrary two-dimensional curved surfaces but interacting in three-dimensional space via the Coulomb potential. To speed-up the interaction calculations, we use the parallel compute…
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the…
A 3D Cellular Automaton model developed by the authors to deal with the dynamics of N-body interactions has been adapted to investigate the head-on collision of two identical bound clusters of particles, and the ensuing process of…
In this paper, we present a 2D numerical model developed to simulate the dynamics of soft, deformable particles. To accommodate significant particle deformations, the particle surface is represented as a narrow shell composed of mass points…
Polymer-Attenuated Coulombic Self-Assembly (PACS) is a flexible experimental approach for generating crystals from simple colloidal building blocks. The central components are charged spherical particles coated with a polymer brush that…
In previous works it was shown that protein 3D-conformations could be encoded into discrete sequences called dominance partition sequences (DPS), that generated a linear partition of molecular conformational space into regions of molecular…
A finite-difference Micromagnetic simulation code written in MATLAB is presented with Graphics Processing Unit (GPU) acceleration. The high performance of Graphics Processing Unit (GPU) is demonstrated compared to a typical Central…
PolyMAPS is an open-source library that helps researchers to initialize LAMMPS molecular dynamics simulations. It introduces an integrated workflow by combining preparation, launching, visualization, and analysis into a single Jupyter…
We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three…
We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an…
In this work we study the tertiary structure of ionic surfactants when the pH in the system is modified using electrostatic dissipative particle dynamics simulations (DPD). The dependence with pH and kind of surfactant is presented. Our…
Quantum information processing requires overcoming decoherence---the loss of "quantumness" due to the inevitable interaction between the quantum system and its environment. One approach towards a solution is quantum dynamical decoupling---a…
Dissipative particle dynamics (DPD) and multi-particle collision (MPC) dynamics are powerful tools to study mesoscale hydrodynamic phenomena accompanied by thermal fluctuations. To understand the advantages of these types of mesoscale…
We present DiffTaichi, a new differentiable programming language tailored for building high-performance differentiable physical simulators. Based on an imperative programming language, DiffTaichi generates gradients of simulation steps…
We present a quasi-static finite element simulator for human face animation. We model the face as an actuated soft body, which can be efficiently simulated using Projective Dynamics (PD). We adopt Incremental Potential Contact (IPC) to…
In this study, we investigate the suitability of dissipative particle dynamics (DPD) simulations to predict the dynamics of polymer chains in dilute polymer solutions, where the chain is represented by a set of beads connected by almost…