相关论文: The ICC* Algorithm: A fast way to include dielectr…
We present an immersed boundary method to simulate the creeping motion of a rigid particle in a fluid described by the Stokes equations discretized thanks to a finite element strategy on unfitted meshes, called Phi-FEM, that uses the…
Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…
The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER,…
We introduce a numerical method for investigating interfacial flows coupled with frictional solid particles. Our method combines the lattice Boltzmann method (LBM) to model the dynamics of a two-component fluid and the discrete element…
The presence of surfactants alters the dynamics of viscous drops immersed in an ambient viscous fluid. This is specifically true at small scales, such as in applications of droplet based microfluidics, where the interface dynamics become of…
We present a highly efficient molecular dynamics scheme for calculating the concentration profile of dopants implanted in group-IV alloy, and III-V zinc blende structure materials. Our program incorporates methods for reducing computational…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
Currently, the study of systems confined within various materials, such as graphene and graphene oxide, for diverse applications such as water desalination, metal separation from water, battery cells, and high-efficiency capacitors, is very…
Realistic modeling of ionic systems necessitates taking explicitly account of many-body effects. In molecular dynamics simulations, it is possible to introduce explicitly these effects through the use of additional degrees of freedom. Here…
Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime…
In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing…
Ion transport through nanoscale channels and pores is pivotal to numerous natural processes and industrial applications. Experimental investigation of the kinetics and mechanisms of such processes is, however, hampered by the limited…
The Kinetic-Diffusion Monte Carlo (KDMC) method is a powerful tool for simulating neutral particles in fusion reactors. It is a hybrid fluid-kinetic method that is significantly faster than pure kinetic methods at the cost of a small bias…
Multiphase flow phenomena have been widely observed in the industrial applications, yet it remains a challenging unsolved problem. Three-dimensional computational fluid dynamics (CFD) approaches resolve of the flow fields on finer spatial…
Magnetic gels are soft elastic materials consisting of magnetic particles embedded in a polymer network. Their shape and elasticity can be controlled by an external magnetic field, which gives rise to both, engineering and biomedical…
Control Barrier Functions (CBFs) are a powerful tool for ensuring the safety of autonomous systems, yet applying them to nonholonomic robots in cluttered, dynamic environments remains an open challenge. State-of-the-art methods often rely…
Sorting cells based on their intrinsic properties is a highly desirable objective, since changes in cell deformability are often associated with various stress conditions and diseases. Deterministic lateral displacement (DLD) devices offer…
Machine learning force fields possess unprecedented potential in achieving both accuracy and efficiency in molecular simulations. Nevertheless, their application in organic systems is often hindered by structural collapse during simulation…
This work proposes four novel hybrid quadrature schemes for the efficient and accurate evaluation of weakly singular boundary integrals (1/r kernel) on arbitrary smooth surfaces. Such integrals appear in boundary element analysis for…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…