Related papers: Mechanics, Energetics, Entropy and Kinetics of a B…
The influence of repeated thermal cycling on mechanical properties, structural relaxation, and evolution of the potential energy in binary glasses is investigated using molecular dynamics simulations. We consider a binary mixture with…
A kinetic equation for a dilute gas of hard spheres confined between two parallel plates separated a distance smaller than two particle dimeters is derived. It is a Boltzmann-like equation, which incorporates the effect of the confinement…
The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic…
Proteins are intricate molecular machines whose complexity arises from the heterogeneity of the amino acid building blocks and their dynamic network of many-body interactions. These nanomachines gain function when put in the context of a…
Protein conformational changes are activated processes essential for protein functions. Activation in a protein differs from activation in a small molecule in that it involves directed and systematic energy flows through preferred channels…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
Motor proteins are active enzyme molecules that play a crucial role in many biological processes. They transform the chemical energy into the mechanical work and move unidirectionally along rigid cytoskeleton filaments. Single-molecule…
Kinetic traps are a notorious problem in equilibrium statistical mechanics, where temperature quenches ultimately fail to bring the system to low energy configurations. Using multifarious self-assembly as a model system, we introduce a…
When examining dynamics occurring at non-zero temperatures, both energy and entropy must be taken into account while describing activated barrier crossing events. Furthermore, good reaction coordinates need to be constructed to describe…
In this conceptual paper we propose to explore the analogy between ontic/epistemic description of quantum phenomena and interrelation between dynamics of conformational and functional states of proteins. Another new idea is to apply theory…
We study the effect of membrane proteins on the shape, composition and thermodynamic stability of the surrounding membrane. When the coupling between membrane composition and curvature is strong enough the nearby composition and shape both…
Strand displacement and tile assembly systems are designed to follow prescribed kinetic rules (i.e., exhibit a specific time-evolution). However, the expected behavior in the limit of infinite time--known as thermodynamic equilibrium--is…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
The lifetime of protein domains and ligand-receptor complexes under force is crucial for mechanosensitive functions, while many aspects of how force affects the lifetime still remain poorly understood. Here, we report a new analytical…
In Part I of this article we have developed a novel mechanobiological model of a Tissue Engineering process that accounts for the mechanisms through which an isotropic or anisotropic adherence condition regulates the active functions of the…
We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of proteins, in spite of the fact that the phosphorylation-state…
We consider several multiscale-in-time kinetic Monte Carlo models, in which some variables evolve on a fast time scale, while the others evolve on a slow time scale. In the first two models we consider, a particle evolves in a…
In systems with detailed balance, the stationary distribution and the equilibrium distribution are identical, creating a clear connection between energetic and entropic quantities. Many driven systems violate detailed balance and still pose…
We computationally study suspensions of slow and fast active Brownian particles that have undergone motility induced phase separation and are at steady state. Such mixtures, of varying non-zero activity, remain largely unexplored even…
On the basis of information theory, a new formalism of classical non-relativistic mechanics of a mass point is proposed. The particle trajectories of a general dynamical system defined on an (1+n)-dimensional smooth manifold are treated…