Related papers: Dissipative electro-elastic network model of prote…
We describe and solve a discrete persistent chain model of protein binding on DNA, involving an extra sigma_i s at a site i of the DNA. This variable takes the value 1 or 0 depending on whether the site is occupied by a protein or not. In…
Spatial heterogeneity in the elastic properties of soft random solids is investigated via a two-pronged approach. First, a nonlocal phenomenological model for the elastic free energy is examined. This features a quenched random kernel,…
This paper presents an electromechanical analysis of the nonlinear static response and the superimposed small-amplitude wave characteristics in an infinite periodic compressible dielectric elastomer (DE) laminate subjected to electrostatic…
Dissipaton-equation-of-motion (DEOM) theory [Y. J. Yan, J. Chem. Phys. 140, 054105 (2014)] is an exact and nonperturbative many-particle method for open quantum systems. The existing dissipaton algebra treats also the dynamics of hybrid…
In this paper, an online multiscale model reduction method is presented for stochastic partial differential equations (SPDEs) with multiplicative noise, where the diffusion coefficient is spatially multiscale and the noise perturbation…
A three-dimensional simulation model is proposed here to study the erosive wear of structure caused by solid particles, which accounts for the accumulation of surface deformation and degradation during the erosion process. Although there…
The relation between thermal fluctuations and the mechanical response of a free membrane has been explored in great detail, both theoretically and experimentally. However, understanding this relationship for membranes, locally pinned by…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
We provide a detailed multiscale analysis of a system of particles interacting through a dynamical network of links. Starting from a microscopic model, via the mean field limit, we formally derive coupled kinetic equations for the particle…
In simulations of metallic interfaces, a critical aspect of metallic behavior is missing from the some of the most widely used classical molecular dynamics force fields. We present a modification of the embedded atom method (EAM) which…
Ensemble learning has proven effective in improving predictive performance and estimating uncertainty in neural networks. However, conventional ensemble methods often suffer from redundant parameter usage and computational inefficiencies…
Collagen networks provide the main structural component of most tissues and represent an important ingredient for bio-mimetic materials for bio-medical applications. Here we study the mechanical properties of stiff collagen networks derived…
We study kinks in the electronic dispersion of a generic strongly correlated system by dynamic mean-field theory (DMFT). The focus is on doped systems away from particle-hole symmetry where valence fluctuations matter potentially. Three…
We study the enzymatic degradation of an elastic fiber under tension using an an isotropic random-walk model, coupled with binding-unbinding reactions that weaken the fiber. The fiber is represented by a chain of elastic springs in series,…
We developed a deep generative model-based variational free energy approach to the equations of state of dense hydrogen. We employ a normalizing flow network to model the proton Boltzmann distribution and a fermionic neural network to model…
We simulate the electrical properties of a device realized by a G protein coupled receptor (GPCR), embedded in its membrane and in contact with two metallic electrodes through which an external voltage is applied. To this purpose, recently,…
Accurate protein structure prediction from amino-acid sequences is critical to better understanding the protein function. Recent advances in this area largely benefit from more precise inter-residue distance and orientation predictions,…
Sheared granular layers undergoing stick slip behavior are broadly employed to study the physics and dynamics of earthquakes. Here, a two dimensional implementation of the combined finite discrete element method (FDEM), which merges the…
The outcome of an epidemic is closely related to the network of interactions between the individuals. Likewise, protein functions depend on the 3D arrangement of their residues and on the underlying energetic interaction network. Borrowing…
The dynamics of a metallic particle confined between charged walls is studied. One wall is fixed and the other moves smoothly and periodically in time. Dissipation is considered by assuming a friction produced by the contact between the…