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Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
We investigate collisions of polar molecules in quasi-2D traps in the presence of an external electric field perpendicular to the collision plane. We use the quantum-defect model characterized by two dimensionless parameters: $y$ and $s$.…
This paper deals with the complex problem of how to simulate multiparticle contacts. The collision process is responsible for the transfer and dissipation of energy in granular media. A novel model of the interaction force between particles…
We present a simple, yet general, end-to-end deep neural network representation of the potential energy surface for atomic and molecular systems. This methodology, which we call Deep Potential, is "first-principle" based, in the sense that…
Starting from a model of an elastic medium, partial differential equations with the form of the coupled Einstein-Dirac-Maxwell equations are derived. The form of these equations describes particles with mass and spin coupled to…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
Quantifying the outcomes of cells collisions is a crucial step in building the foundations of a kinetic theory of living matter. Here, we develop a mechanical theory of such collisions by first representing individual cells as extended…
Molecular Dynamics method is based on solution of Newtonian differential equations of motion. A new very accurate and efficient time-reversible explicit integrator was derived on the basis of second order Tailor expansion of force. There is…
External biasing forces are often applied to enhance sampling in regions of phase space which would otherwise be rarely observed. While the typical goal of these experiments is to calculate the potential of mean force (PMF) along the…
Some commonly used approximations for complete fusion and breakup transmission coefficients in collisions of weakly bound projectiles at near barrier energies are assessed. We show that they strongly depend on the adopted classical…
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…
Isotropic pair potentials that are bounded at the origin have been proposed from time to time as models of the effective interaction between macromolecules of interest in the chemical physics of soft matter. We present a thorough study of…
The residual interaction for a meson-meson system is computed utilizing the cumulant, or cluster, expansion of the momentum-space time correlation matrix. The cumulant expansion serves to define asymptotic, or free, meson-meson operators.…
This paper gives a momentum-space representation of the Argonne V18 potential as an expansion in products of spin-isospin operators with scalar coefficient functions of the momentum transfer. Two representations of the scalar coefficient…
The paper deals with the analytical integration of interaction potentials between specific geometries such as disks, cylinders, rectangles, and rectangular prisms. Interaction potentials are modeled as inverse-power laws with respect to the…
Beyond the attractive strong potential needed for hadronic bound states, strong interactions are predicted to provide repulsive forces depending on the color charges involved. The repulsive interactions could in principle serve for particle…
Reactive molecular dynamics (MD) simulation is performed using a reactive force field (ReaxFF). To this end, we developed a new method to optimize the ReaxFF parameters based on a machine learning approach. This approach combines the…
The derivative expansion approach to the calculation of the interaction between two surfaces, is a generalization of the proximity force approximation, a technique of widespread use in different areas of physics. The derivative expansion…
We consider a discrete-continuum model of a biomembrane with embedded particles. While the membrane is represented by a continuous surface, embedded particles are described by rigid discrete objects which are free to move and rotate in…
The Lennard-Jones (LJ) potential is a cornerstone of Molecular Dynamics (MD) simulations and among the most widely used computational kernels in science. The potential models atomistic attraction and repulsion with century old prescribed…