相关论文: Modeling truncated hemoglobin vibrational dynamics
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…
Twisted bilayer graphene (TBG) has drawn significant interest due to recent experiments which show that TBG can exhibit strongly correlated behavior such as the superconducting and correlated insulator phases. Much of the theoretical work…
We study dynamics of freely cooling granular gases in two-dimensions using large-scale molecular dynamics simulations. We find that for dilute systems the typical kinetic energy decays algebraically with time, E(t) ~ t^{-1}, in the long…
Topologically stabilized polymer conformations observed in melts of nonconcatenated polymer rings and crumpled globules, are considered to be a good candidate for the description of the spatial structure of mitotic chromosomes. Despite…
Coupled quantum harmonic oscillators, studied by many authors using many different techniques over the decades, are frequently used toy-models to study open quantum systems. In this manuscript, we explicitly study the simplest oscillator…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
We investigate the dynamics of atomic and molecular bosons weakly coupled via Feshbach detuning in the presence of Gaussian white noise. The time-evolution of the population imbalance between the two species, as well as the coherence of the…
Glauber dynamics of a bond-diluted Ising model on a Bethe lattice (a random graph with fixed connectivity) is investigated by an approximate theory which provides exact results for equilibrium properties. The time-dependent solutions of the…
Exact spectral truncations of the unforced, inviscid Burgers-Hopf equation are Hamiltonian systems with many degrees of freedom which exhibit intrinsic stochasticity and coherent scaling behavior. For this reason recent studies have…
A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the…
The analysis of single particle trajectories plays an important role in elucidating dynamics within complex environments such as those found in living cells. However, the characterization of intracellular particle motion is often confounded…
We study the dynamics of gene activities in relatively small size biological networks (up to a few tens of nodes), e.g. the activities of cell-cycle proteins during the mitotic cell-cycle progression. Using the framework of deterministic…
We present a computer-assisted approach to coarse-graining the evolutionary dynamics of a system of nonidentical oscillators coupled through a (fixed) network structure. The existence of a spectral gap for the coupling network graph…
Small signal analysis is a special case of analytical approaches using Taylor expansions of power system differential equations with the truncation performed at order one. The truncated Taylor expansions (TTEs) at higher orders can lead to…
We present an analytical approximation for nonlinear dynamics of trapped Bose-co ndensed gases. The new approximation is a substantial improvement over the Thomas-Fermi approximation and is shown to be applicable for systems with a rather…
We analyze the equilibrium fluctuations of the density, current and tagged particle in symmetric exclusion with a slow bond. The system evolves in the one-dimensional lattice and the jump rate is everywhere equal to one except at the slow…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
Balanced truncation (BT) is a model reduction method that utilizes a coordinate transformation to retain eigen-directions that are highly observable and reachable. To address realizability and scalability of BT applied to highly stiff and…
We study the complex quantum dynamics of a system of many interacting atoms in an elongated anharmonic trap. The system is initially in a Bose-Einstein condensed state, well described by Thomas-Fermi profile in the elongated direction and…