Related papers: Cooperative Function with Thermal Fluctuations in …
A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical…
We present two simplified models of protein dynamics based on Langevin's equation of motion in a viscous medium. We explore the effect of the potential energy function's symmetry on the kinetics and thermodynamics of simulated folding. We…
At zero temperature, spring networks with connectivity below Maxwell's isostatic threshold undergo a mechanical phase transition from a floppy state at small strains to a rigid state for applied shear strain above a critical strain…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
We study experimentally the thermal fluctuations of energy input and dissipation in a harmonic oscillator driven out of equilibrium, and search for Fluctuation Relations. We study transient evolution from the equilibrium state, together…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
Recent advances in designing meta-materials have demonstrated that global mechanical properties of disordered spring networks can be tuned by selectively modifying only a small subset of bonds. Here, using a computationally-efficient…
A new network model is proposed to describe the $1/f^\alpha$ resistance noise in disordered materials for a wide range of $\alpha$ values ($0< \alpha < 2$). More precisely, we have considered the resistance fluctuations of a thin resistor…
A statistical mechanical distance constraint model (DCM) is presented that explicitly accounts for network rigidity among constraints present within a system. Constraints are characterized by local microscopic free energy functions.…
Cooperative binding affects many processes in biology, but it is commonly addressed only in equilibrium. In this work we explore dynamical cooperativity in driven systems, where the cooperation occurs because some of the bonds change the…
The freely jointed chain is often applied to model the thermodynamics of single polymer chains, but the traditional formulation of the model lacks internal energy changes due to bond stretching. For this reason, the extensible freely…
We consider two types of fluctuations in the mass-action equilibrium in protein binding networks. The first type is driven by relatively slow changes in total concentrations (copy numbers) of interacting proteins. The second type, to which…
We study the elasticity of thermalized spring networks under an applied bulk strain. The networks considered are sub-isostatic random-bond networks that, in the athermal limit, are known to have vanishing bulk and linear shear moduli at…
Fluctuations in conjugate thermodynamic variables are studied using the cross-correlation function. A new procedure is given enabling the derivation of fluctuation formulas for a system in equilibrium. Specifically, the cross-correlation…
We consider equilibrium folding transitions in lattice protein models with and without side chains. A dimensionless measure, $Omega_{c}$, is introduced to quantitatively assess the degree of cooperativity in lattice models and in real…
The origin of stochastic fluctuations in gene expression has received considerable attention recently. Fluctuations in gene expression are particularly pronounced in cellular systems because of the small copy number of species undergoing…
Many different processes take place to facilitate lubrication of the joints functioning in human locomotion system. The main purpose of this is to avoid destroying the articular cartilage. Viscoelastic properties of the joints system are…
Allostery is a fundamental property of proteins that represents the functional coupling between distantly located sites. In different manifestations, this property underlies signal transduction, gene expression, and regulation -- elementary…