Related papers: New force replica exchange method and protein fold…
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…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
Mechanical unfolding of polyproteins by force spectroscopy provides valuable insight into their free energy landscapes. Most phenomenological models of the unfolding process are two-state and/or one dimensional, with the details of the…
Mechanical unfolding of the fourth domain of Distyostelium discoideum filamin (DDFLN4) was studied in detail using the C$_{\alpha}$-Go model. We show that unfolding pathways of this protein depend on the pulling speed. The agreement between…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
An Ising--like model of proteins is used to investigate the mechanical unfolding of the Green Fluorescent Protein along different directions. When the protein is pulled from its ends, we recover the major and minor unfolding pathways…
A new theoretical survey of proteins' resistance to constant speed stretching is performed for a set of 17 134 proteins as described by a structure-based model. The proteins selected have no gaps in their structure determination and consist…
We investigate the growth of a branched actin network under load. Using a combination of simulations and theory, we show that the network adapts to the load and exhibits two regimes: a finite velocity at low stress, followed by a power-law…
We study the mechanical unfolding pathways of the $FnIII_{10}$ domain of fibronectin by means of an Ising--like model, using both constant force and constant velocity protocols. At high forces and high velocities our results are consistent…
The nanomechanical response of a folded single protein, the natural nanomachine responsible for myriad biological processes, provides insight into its function. The conformational flexibility of a folded state, characterized by its…
We show that the interplay between spin-changing collisions and quadratic Zeeman coupling provides a novel mechanism for the formation of repulsively bound composites in high-spin fermions, which we illustrate by considering spin flips in…
A finite element framework is presented for the analysis of crack-tip phenomena in an elastic material containing a single edge crack under compressive loading. The mechanical response of the material is modeled by a nonlinear constitutive…
The flexibility and the extension along the direction of the force are shown to be related to the bubble number fluctuation and the average number of bubbles respectively, when the strands of the DNA are subjected to a force along the same…
Mechanically induced unfolding of passive crosslinkers is a fundamental biological phenomenon encountered across the scales from individual macro-molecules to cytoskeletal actin networks. In this paper we study a conceptual model of…
Proteins are translated from the N- to the C-terminus, raising the basic question of how this innate directionality affects their evolution. To explore this question, we analyze 16,200 structures from the protein data bank (PDB). We find…
Using a simple hydrophobic/polar protein model, we perform a Monte Carlo study of the thermodynamics and kinetics of binding to a target structure for two closely related sequences, one of which has a unique folded state while the other is…
The mechanical unfolding of proteins is investigated by extending the Wako-Saito-Munoz-Eaton model, a simplified protein model with binary degrees of freedom, which has proved successful in describing the kinetics of protein folding. Such a…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
Force-based multiphysics coupling methods have become popular since they provide a simple and efficient coupling mechanism, avoiding the difficulties in formulating and implementing a consistent coupling energy. They are also the only known…
Superradiant phase transitions from cavity light-matter coupling have been widely explored across platforms. Here, we report a unilateral critical endpoint (UCEP) and a tricritical point (TCP) in the phase diagram of the cavity-coupled…