Related papers: Undulations in a weakly interacting mechanically g…
In Molecular Dynamics (MD), the forces applied to atoms derive from potentials which describe the energy of bonds, valence angles, torsion angles, and Lennard-Jones interactions of which molecules are made. These de finitions are classic;…
We present a differentiable formalism for learning free energies that is capable of capturing arbitrarily complex model dependencies on coarse-grained coordinates and finite-temperature response to variation of general system parameters.…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
The motility of certain gram-negative bacteria is mediated by retraction of type IV pili surface filaments, which are essential for infectivity. The retraction is powered by a strong molecular motor protein, PilT, producing very high forces…
Several experiments have demonstrated the existence of an electro-mechanical effect in many biological tissues and hydrogels, and its actual influence on growth, migration, and pattern formation. Here, to model these interactions and…
Granular packings of non-convex or elongated particles can form free-standing structures like walls or arches. For some particle shapes, such as staples, the rigidity arises from interlocking of pairs of particles, but the origins of…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
A theoretical description of the weakly nonlinear and mode-dependent dynamics of a nanoscale beam that is under intrinsic tension is developed. A full analysis of the dynamic range of the beam over a wide range of conditions is presented.…
It has recently become possible to form molecules in ultracold gases of trapped alkali metal atoms. Once formed, the molecules may undergo elastic, inelastic and reactive collisions. Inelastic and reactive collisions are particularly…
We apply a recently developed model of cytoskeletal force generation to study a cell intrinsic contractility, as well as its response to external loading. The model is based on a non-equilibrium thermodynamic treatment of the…
We investigate the momentum-resolved spin and charge susceptibilities, as well as the chemical potential and double occupancy in the two-dimensional Hubbard model as functions of doping, temperature and interaction strength. Through these…
Presented here, is a technical manuscript that may form the basis of later published work. In it, we develop a statistical mechanical model to describe a closed loop plectoneme, applicable for when the closed loop is sufficiently…
We present an edge-based framework for the study of geometric elastic network models to model mechanical interactions in physical systems. We use a formulation in the edge space, instead of the usual node-centric approach, to characterise…
A scattering model is developed for ultracold molecular collisions, which allows inelastic processes, chemical reactions, and complex formation to be treated in a unified way. All these scattering processes and various combinations of them…
We implement molecular dynamics simulations in canonical ensemble to study the effect of confinement on a $2d$ crystal of point particles interacting with an inverse power law potential proportional to $r^{-12}$ in a narrow channel. This…
In this paper, we have studied, within a discrete WLC model, the spatial constraints in magnetic tweezers used in single molecule experiments. Two elements are involved: first, the fixed plastic slab on which is stuck the initial strand,…
Within a model where micrometer-size soft colloidal particles are viewed as liquid drops, we theoretically study the contact interaction between them. We compute the exact deformation energy across a broad range of indentations and for…
The formation of correlated structures is of importance in many diverse contexts such as strongly coupled plasmas, soft matter, and even biological mediums. In all these contexts the dynamics are mainly governed by electrostatic…
Lipid-bilayers are the fundamental constituents of the walls of most living cells and lipid vesicles, giving them shape and compartment. The formation and growing of pores in a lipid bilayer have attracted considerable attention from an…
We report, for the first time, some experimental observations regarding a new type of long range interaction between rigid particles that prevails when they are suspended in an soft elastic gel. A denser particle submerges itself to a…