相关论文: Master curve of boosted diffusion for ten catalyti…
In a conformational nonequilibrium steady state (cNESS), enzyme turnover is modulated by the underlying conformational dynamics. Based on a discrete kinetic network model, we use the integrated probability flux balance method to derive the…
Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…
A fully quantum multiphonon up-pumping model is proposed to characterize coherent energy transfer in energetic materials (EMs) subjected to external shock. After eliminating the degrees of freedom of the phonon bath within a mean-field…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
We use a large single particle tracking data set to analyze the short time and small spatial scale motion of quantum dots labeling proteins in cell membranes. Our analysis focuses on the jumps which are the changes in the position of the…
Excitability is an attribute of life, and is a driving force in the descent of complexity. Cellular electrical activity as realized by membrane proteins that act as either channels or transporters is the basis of excitability. Electrical…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
Predicting enzyme kinetic parameters quantifies how efficiently an enzyme catalyzes a specific substrate under defined biochemical conditions. Canonical parameters such as the turnover number ($k_\text{cat}$), Michaelis constant…
The stochastic driving force exerted by a single molecular motor (e.g., a kinesin, or myosin) moving on a periodic molecular track (microtubule, actin filament, etc.) is discussed from a general viewpoint open to experimental test. An…
Bacterial motility, and in particular repulsion or attraction towards specific chemicals, has been a subject of investigation for over 100 years, resulting in detailed understanding of bacterial chemotaxis and the corresponding sensory…
Diffusion in living tissues governs essential physiological processes and is well studied within cells. Yet how extracellular molecular motion emerges from the structural complexity of tissues remains unresolved. In the brain, molecules…
All living cells transport molecules and ions across membranes, often against concentration gradients. This active transport requires continual energy expenditure and is clearly a nonequilibrium process for which standard equilibrium…
Cells are often considered input-output devices that maximize the transmission of information by converting extracellular stimuli (input) via signaling pathways (communication channel) to cell behavior (output). However, in biological…
When two binary solutions are separated by a permeable barrier, the individual species typically diffuse and mix, dissipating their chemical potential gradients. However, we use model lattice simulations to show that single-file…
We study a Michaelis-Menten reaction for a single two-state enzyme molecule, whose transition rates between the two conformations are modulated by an harmonically oscillating external force. In particular, we obtain a range of optimal…
Aerotaxis is the particular form of chemotaxis in which oxygen plays the role of both the attractant and the repellent. Aerotaxis occurs without methylation adaptation, and it leads to fast and complete aggregation toward the most favorable…
We consider the diffusion and spreading of chainlike molecules on solid surfaces. We first show that the steep spherical cap shape density profiles, observed in some submonolayer experiments on spreading polymer films, imply that the…
Multiple experiments show that various submicron particles such as magnetosomes, RNA messengers, viruses, and even much smaller nanoparticles such as globular proteins diffuse anomalously slow in viscoelastic cytosol of living cells. Hence,…
Normal molecular dynamics simulations are usually unable to simulate chemical reactions due to the low probability of forming the transition state. Therefore, enhanced sampling methods are implemented to accelerate the occurrence of…
A microscopic model for thermal excitation of vibrational ground state of a molecule interacting with a condensed medium is developed. The master equation for evolution of occupancies of the vibrational levels is derived. The rate constant…