Related papers: A Three-State Thermodynamically Consistent Cross-B…
Despite the great success of the Huxley sliding filament model proposed half a century ago for actin-myosin linkages (cross-bridges), it fails to explain the force-velocity behavior of stretching skeletal muscles. Huxley's two-state kinetic…
We describe in this paper a crossbridge model in which an attached crossbridge behaves like a linear spring with a variable rest length. We assume in particular that the rest length has a linear force-velocity relation, and that the force…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
In this paper we report, clarify and broaden various recent efforts to complement the chemistry-centered models of force generation in muscles by mechanics-centered models. The physical mechanisms of interest can be grouped into two…
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
In this paper, we examine how to build coarse-grain transport models consistently from the kinetic to fluid regimes. The internal energy of the gas particles is described through a state-to-state approach. A kinetic equation allows us to…
We study the thermodynamic behavior of a model protein with 54 amino acids that is designed to form a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid, and has the…
We present a thermodynamically consistent energetic variational model for active nematics driven by ATP hydrolysis, with a focus on the coupling between chemical reactions and mechanical dynamics. Extending the classical Toner-Tu framework,…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
This study address the computational determination of catalytic reaction rates by moving beyond traditional Transition State Theory (TST), addressing its limitations in complex systems. The Hill relation framework, integrated with Adaptive…
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…
The adhesive and frictional response of an AFM tip connected to a substrate through supramolecular host-guest complexes is investigated by dynamic Monte Carlo simulations. The variation of the pull-off force with the unloading rate recently…
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a…
We discuss the force-velocity relations obtained in a two-state crossbridge model for molecular motors. They can be calculated analytically in two limiting cases: for a large number and for one pair of motors. The effect of the…
We present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state. The free-energy barrier separating the native and unfolded…
Single-molecule force spectroscopy has opened a new field of research in molecular biophysics and biochemistry. Pulling experiments on individual proteins permit us to monitor conformational transitions with high temporal resolution and…
Molecular dynamics simulations of frictional sliding in an Atomic Force Microscope (AFM) show a clear dependence of superlubricity between incommensurate surfaces on tip compliance and applied normal force. While the kinetic friction…
We propose a theory based on non-equilibrium thermodynamics to describe the mechanical behavior of an active polymer gel created by the inclusion of molecular motors in its solvent. When activated, these motors attach to the chains of the…
The influence of the stress state on the cross-slip rate in Al was analyzed by means of molecular dynamics simulations and transition state theory. The activation energy barrier in the absence of thermal energy was determined through the…