相关论文: Modeling truncated hemoglobin vibrational dynamics
We review two important non-perturbative approaches for extracting the physics of low-dimensional strongly correlated quantum systems. Firstly, we start by providing a comprehensive review of non-Abelian bosonization. This includes an…
We present analytical results (up to a numerical diagonalization of a real symmetric matrix) for a set of time- and ensemble-average physical observables in the non-Hookean Gaussian Network Model (GNM) - a generalization of the Rouse model…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
Self Consistent Normal Mode Analysis (SCNMA) is applied to heme c type cytochrome f to study temperature dependent protein motion. Classical Normal Mode Analysis (NMA) assumes harmonic behavior and the protein Mean Square Displacement (MSD)…
We employ the Distance Matrix method to investigate metabasin dynamics in supercooled water. We find that the motion of the system consists in the exploration of a finite region of configuration space (enclosing several distinct local…
In this paper, we present a method for the Hamiltonian simulation in the context of eigenvalue estimation problems which improves earlier results dealing with Hamiltonian simulation through the truncated Taylor series. In particular, we…
A simple model to investigate the long time dynamics of glass-formers is presented and applied to study a Lennard-Jones system in supercooled and glassy phases. According to our model, the point representing the system in the…
An accurate description of the nonequilibrium dynamics of systems with coupled spin and bosonic degrees of freedom remains theoretically challenging, especially for large system sizes and in higher than one dimension. Phase space methods…
We study the dynamics of condensation for a stochastic continuous mass transport process defined on a one-dimensional lattice. Specifically we introduce three different variations of the truncated random average process. We generalize…
Simple coarse-grained models, such as the Gaussian Network Model, have been shown to capture some of the features of equilibrium protein dynamics. We extend this model by using atomic contacts to define residue interactions and introducing…
Coarse-grained (CG) molecular dynamics enables simulations of atomic systems such as biomolecules at timescales inaccessible to all-atom (AA) methods, but existing CG neural potentials trained via force matching capture only the gradient of…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
Transient bonds between fast linkers and slower particles are widespread in physical and biological systems. In spite of their diverse structure and function, a commonality is that the linkers diffuse on timescales much faster compared to…
We study Hamiltonian truncation in boosted frames. We consider the thermal and magnetic field deformations of the 2d Ising model using TCSA at finite momentum. We find that even with moderate momenta, the spectrum and time-dependent…
The mathematical modelling of biological systems has historically followed one of two approaches: comprehensive and minimal. In comprehensive models, the involved biological pathways are modelled independently, then brought together as an…
We study quench dynamics of the Bose-Hubbard model by exact diagonalization. Initially the system is at thermal equilibrium and of a finite temperature. The system is then quenched by changing the on-site interaction strength $U$ suddenly.…
Understanding the equilibrium properties and out of equilibrium dynamics of quantum field theories are key aspects of fundamental problems in theoretical particle physics and cosmology. However, their classical simulation is highly…
This article studies typical dynamics and fluctuations for a slow-fast dynamical system perturbed by a small fractional Brownian noise. Based on an ergodic theorem with explicit rates of convergence, which may be of independent interest, we…
The Hubbard model is a prototype for strongly correlated electrons in condensed matter, for molecules and fermions or bosons in optical lattices. While the equilibrium properties of these systems have been studied in detail, the excitation…
A scaling analysis within a model of hierarchically constrained dynamics is shown to reproduce the main features of non-exponential relaxation observed in kinetic studies of carbonmonoxymyoglobin.