Related papers: ATP binding to a multisubunit enzyme: statistical …
The hyperbolic dependence of catalytic rate on substrate concentration is a classical result in enzyme kinetics, quantified by the celebrated Michaelis-Menten equation. The ubiquity of this relation in diverse chemical and biological…
Under the most common experimental conditions, the adsorption of proteins to solid surfaces is an spontaneous process that leads to a rather compact layer of randomly oriented molecules. Due to the importance of this process for the…
Spatial organization in metabolic pathways can arise from the interplay between enzymatic reaction kinetics and diffusion-driven instabilities. In this work we investigate how reversible enzyme--substrate binding influences pattern…
Structural dynamics of macromolecules is critical to their structural-function relationship. Cryogenic electron microscopy (CryoEM) provides snapshots of vitrified protein at different compositional and conformational states, and the…
A thermodynamic-like formalism is developed for superstatistical systems based on conditional entropies. This theory takes into account large-scale variations of intensive variables of systems in nonequilibrium stationary states. Ordinary…
The most complicated phenomena of equilibrium statistics, phase separations and transitions of various order and critical phenomena, can clearly and sharply be seen even for small systems in the topology of the curvature of the…
A model for the thermodynamics of a quantum heat bath is introduced. Under the assumption that the bath molecules have finitely many degrees of freedom and are weakly interacting, we present a general derivation of the equation of state of…
Polymerization dynamics of single actin filaments is investigated theoretically using a stochastic model that takes into account the hydrolysis of ATP-actin subunits, the geometry of actin filament tips, the lateral interactions between the…
Development of thermodynamic induction up to second order gives a dynamical bifurcation for thermodynamic variables and allows for the prediction and detailed explanation of nonequilibrium phase transitions with associated spontaneous…
Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can…
We derive a formulation of the First Law of nonequilibrium thermodynamics for biological information-processing systems by partitioning entropy in the Second Law into microscopic and mesoscopic components and by assuming that natural…
Situations where a spontaneous process of energy or matter transfer is enhanced by an external device are widespread in nature (human sweating system, enzyme catalysis, facilitated diffusion across bio-membranes, industrial heat…
A model for the processive movement of dynein is presented based on experimental observations available. In the model, the change from strong microtubule-binding to weak binding of dynein is determined naturally by the variation of the…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
A quantum model on the chemically and physically induced pluripotency in stem cells is proposed. Based on the conformational Hamiltonian and the idea of slow variables (molecular torsions) slaving fast ones the conversion from the…
We brief{}ly review the connection between statistical mechanics and thermodynamics. We show that, in order to satisfy thermodynamics and its Legendre transformation mathematical frame, the celebrated Boltzmann-Gibbs~(BG) statistical…
Cellulases hold great promise for the production of biofuels and biochemicals. However, they are modular enzymes acting on a complex heterogeneous substrate. Because of this complexity, the computational prediction of their catalytic…
We show through a nonlinear Fokker-Planck formalism, and confirm by molecular dynamics simulations, that the overdamped motion of interacting particles at T=0, where T is the temperature of a thermal bath connected to the system, can be…
Collective sensing by interacting cells is observed in a variety of biological systems, and yet a quantitative understanding of how sensory information is collectively encoded is lacking. Here we investigate the ATP-induced calcium dynamics…
In living cells, protein-rich condensates can wet the cell membrane and surfaces of membrane-bound organelles. Interestingly, many phase-separating proteins also bind to membranes leading to a molecular layer of bound molecules. Here we…