Related papers: An Electronically Non-Adiabatic Generalization of …
The equations of classical spin-orbit motion can be extended to a Hamiltonian system in 9-dimensional phase space by introducing a coupled spin-orbit Poisson bracket and a Hamiltonian function. After this extension and by establishing…
The mathematical formulation of the model for molecular movement of single motor proteins driven by cyclic biochemical reactions in an aqueous environment leads to a drifted Brownian motion characterized by coupled diffusion equations. In…
We present fully atomistic Molecular Dynamics simulation results on a main-chain polymer, 1,4-Polybutadiene, in the merging region of the $\alpha$- and $beta$-relaxations. A real space analysis reveals the occurrence of localized motions…
This paper leads with a random polymer model in $\Z^2$ having long-range self-repulsive interactions. By comparison with a long range one-dimensional ferromagnetic Ising model we shown that the polymer models we considered here undergo a…
Markov State Models (MSM) are widely used to elucidate dynamic properties of molecular systems from unbiased Molecular Dynamics (MD). However, the implementation of reweighting schemes for MSMs to analyze biased simulations, for example…
Cellular tissue behavior is a multiscale problem. At the cell level, out of equilibrium, biochemical reactions drive physical cell-cell interactions in a typical active matter process. Cell modeling computer simulations are a robust tool to…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
A general polarizable embedded (PE) quantum mechanics/molecular mechanics scheme for periodic systems is presented, describing mutual polarization of the two subsystems. The QM system, described with density functional theory (DFT), is…
Based on our experience in kinetic modeling of coupled multiple metabolic pathways we propose a generic rate equation for the dynamical modeling of metabolic kinetics. Its symmetric form makes the kinetic parameters (or functions) easy to…
Dynamic properties of molecular motors whose motion is powered by interactions with specific lattice bonds are studied theoretically with the help of discrete-state stochastic "burnt-bridge" models. Molecular motors are depicted as random…
We introduce an elliptic extension of Dyson's Brownian motion model, which is a temporally inhomogeneous diffusion process of noncolliding particles defined on a circle. Using elliptic determinant evaluations related to the reduced affine…
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…
A light-driven molecular motor system is investigated using a multi-state Brownian ratchet model described by a single effective coordinate with multiple electronic states in a dissipative environment. The rotational motion of the motor…
We investigate the Fano-Anderson model coupled to a large ensemble of spins under the influence of an external magnetic field. The interaction between the two spin systems is treated within a meanfield-approach and we assume an anisotropic…
Electron transfer is an important and fundamental process in chemistry, biology and physics, and has received significant attention in recent years. Perhaps one of the most intriguing questions concerns with the realization of the…
We theoretically describe the phenomenon of non-adiabatic spin dynamics, which occurs in a gas cell filled by alkali vapor in presence of a strong alternating magnetic field and pump light. Steep increase of the spin polarization occurs if…
Reduced-order models have long been used to understand the behavior of nonlinear partial differential equations (PDEs). Naturally, reduced-order modeling techniques come at the price of computational accuracy for a decrease in computation…
Dynamics of a discrete polymer in time-dependent external potentials is studied with the master equation approach. We consider both stochastic and deterministic switching mechanisms for the potential states and give the essential equations…
In this paper a formalism for studying the dynamics of quantum systems coupled to classical spin environments is reviewed. The theory is based on generalized antisymmetric brackets and naturally predicts open-path off-diagonal geometric…
Hybrid dynamical systems characterized by discrete switching of smooth dynamics have been used to model various rhythmic phenomena. However, the phase reduction theory, a fundamental framework for analyzing the synchronization of…