Related papers: Size limits sensitivity in all kinetic schemes
Hysteresis is a nonlinear phenomenon with memory effects, where a system's output depends on both its current state and past states. It is prevalent in various physical and mechanical systems, such as yielding structures under seismic…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
We report the results of a numerical study of nonequilibrium steady states for a class of Hamiltonian models. In these models of coupled matter-energy transport, particles exchange energy through collisions with pinned-down rotating disks.…
The mutation and selection of regulatory DNA sequences is presented as an ideal model system of molecular evolution where genotype, phenotype, and fitness can be explicitly and independently characterized. In this theoretical study, we…
In order to increase the efficiency of the computer simulation of biological molecules, it is very common to impose holonomic constraints on the fastest degrees of freedom; normally bond lengths, but also possibly bond angles. However, as…
In this paper we study a simple stochastic version of the Hopfield-Ninio kinetic proofreading model. The model is characterized by means of two parameters, the unbinding time, which depends on the binding energy between a ligand and a…
Size and shape are critical discriminators between molecular species and states. We describe a micro-chip based high-throughput imaging approach offering rapid and precise determination of molecular properties under native solution…
We consider $N$ bosons in a box in $\mathbb {R}^d$ with volume $N/\rho$ under the influence of a mutually repellent pair potential. The particle density $\rho\in (0,\infty)$ is kept fixed. Our main result is the identification of the…
Engineering molecular systems that exhibit complex behavior requires the design of kinetic barriers. For example, an effective catalytic pathway must have a large barrier when the catalyst is absent. While programming such energy barriers…
In the first part of this paper we give a short review of the hierarchy of stochastic models, related to physical chemistry. In the basement of this hierarchy there are two models --- stochastic chemical kinetics and the Kac model for…
We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…
Myosin motors are fundamental biological actuators, powering diverse mechanical tasks in eukaryotic cells via ATP hydrolysis. Recent work revealed that myosin's velocity-dependent detachment rate can bridge actomyosin dynamics to macroscale…
Small thermodynamic systems exhibit peculiar behavior different from that observed in long-scale systems. Non-equilibrium processes taking place in those systems are strongly influenced by the presence of fluctuations which can be large.…
We analyse the asymptotic behavior for kinetic models describing the collective behavior of animal populations. We focus on models for self-propelled individuals, whose velocity relaxes toward the mean orientation of the neighbors. The…
Hysteresis, with rich dynamical behaviors-especially in interacting systems-has drawn broad research interest. Yet its dynamic scalings across time scales lack a unified description, and their transitions remain unclear. Here, we study the…
The concept of equilibrium is a general tool to fill the gap between macroscopic and mesoscopic information, both within kinetic systems and kinetic schemes. This work explores the use of equilibria to devise numerical boundary conditions…
We show that active transport processes in biological systems can be understood through a local equilibrium description formulated at the mesoscale, the scale to describe stochastic processes. This new approach uses the method established…
We define a DNA as a sequence of $1, 2$'s and embed it on a path of Cayley tree in such a way that each vertex of the Cayley tree belongs only to one of DNA and each DNA has its own countably many set of neighboring DNAs. The Hamiltonian of…
The associative interaction, such as hydrogen bonding, can bring about versatile functionalities to polymer systems, which has been investigated by tremendous researches, but the fundamental understanding on association process is still…
Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…