Related papers: Multiple barriers in forced rupture of protein com…
To explain the observed dynamics in equilibrium single-molecule measurements of biomolecules, the experimental observable is often chosen as a putative reaction coordinate along which kinetic behavior is presumed to be governed by diffusive…
We consider the influence of the Fermi statistics of nucleons on the binding energy of a new type of nuclear structures such as fractal nuclear clusters (fractal isomers of nuclei). It is shown that the fractal nuclear isomers possess a…
Using a beta-hairpin protein as a representative example of two-state folders, we studied how the exploration of native-like states affects the folding kinetics. It has been found that the first-passage time (FPT) distributions are…
Many processes in chemistry, physics, and biology involve rare events in which the system escapes from a metastable state by surmounting an activation barrier. Examples range from chemical reactions, protein folding, and nucleation events…
With potential relevance to biomechanics, an interesting problem in statistical mechanics not previously solved is a binary mechanical model system. Discrete chemical states of proteins are often associated with discrete metastable…
Hydrostatic pressure is a common perturbation to probe the conformations of proteins. There are two common forms of pressure dependent potentials of mean force (PMFs) derived from hydrophobic molecules available for the coarse grained…
Engineering molecular systems that exhibit complex behavior requires the design of kinetic barriers. For example, an effective catalytic pathway must have a large barrier when the catalyst is absent. While programming such energy barriers…
The forces that mixtures of motorized and passive crosslinking proteins collectively generate between cytoskeletal filaments within our cells are the key drivers of active cellular mechanics. Despite their importance, a unified theory to…
Based on the trajectories of the separation between water molecule pairs from MD simulations, we investigate the bond breakage dynamics in bulk water. From the spectrum of mean first-passage times, the Fokker-Planck equation allows us to…
Single molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in…
Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by…
This paper deals with the theoretical and numerical analysis of dynamic fracture of dissimilar chain consisting of masses lined by springs. Such a structure exhibits quite different dynamic properties in comparison with a symmetrical…
In this letter, the possible dynamic scaling properties of protein molecules in folding are investigated theoretically by assuming that the protein molecules are percolated networks. It is shown that the fractal character and the fractal…
The breakup dynamics of viscous liquid bridges on solid surfaces is studied experimentally. It is found that the dynamics bears similarities to the breakup of free liquid bridges in the viscous regime. Nevertheless, the dynamics is…
The influence on the fusion process of coupling to collective degrees of freedom has been explored. The significant enhancement of he fusion cross setion at sub-barrier energies was understood in terms of the dynamical processes arising…
Dynamic force spectroscopy (DFS) is an experimental technique that is commonly used to assess information of the strength, energy landscape, and lifetime of noncovalent bio-molecular interactions. DFS traditionally requires an applied force…
Fracture resistance of blood clots plays a crucial role in physiological hemostasis and pathological thromboembolism. Although recent experimental and computational studies uncovered the poro-viscoelastic property of blood clots and its…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
Experimental studies of systems containing active proteins that undergo conformational changes driven by catalytic chemical reactions have shown that the diffusion coefficients of passive tracer particles and active molecules are larger…
Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound and unbound conformations of six proteins to explore their…