Related papers: Ab-initio force prediction for single molecule for…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
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…
We have studied the separation of a double stranded DNA (dsDNA), which is driven either by the temperature or force. By monitoring the probability of opening of entire base pairs along the chain, we show that the opening of a dsDNA depends…
The single-nucleon potential in hot nuclear matter is investigated in the framework of the Brueckner theory by adopting the realistic Argonne V18 or Nijmegen 93 two-body nucleon-nucleon interaction supplemented by a microscopic three-body…
A model of self avoiding walks with suitable constraint has been developed to study the effect of temperature on a single stranded DNA (ssDNA) in the constant force ensemble. Our exact calculations for small chains show that the extension…
The self-affine mode of ice softening during friction is investigated within the rheological model for viscoelastic medium approximation. The different modes of ice rubbing, determined by formation of surface liquid-like layer, are studied.…
Little is known about mechanics underlying the interaction among platelets during activation and aggregation. Although the strength of a blood thrombus has likely major biological importance, no previous study has measured directly the…
Free energy perturbation (FEP) is considered the gold-standard simulation method for estimating small molecule binding affinity, a quantity of vital importance to drug discovery. The accuracy of FEP critically depends on an accurate model…
Theories that are used to extract energy-landscape information from single-molecule pulling experiments in biophysics are all invariably based on Kramers' theory of thermally-activated escape rate from a potential well. As is well known,…
Electronic-vibrational coupling in single-molecule junctions may result in current-induced bond rupture and is thus an important mechanism for the stability of molecular junctions. We use the hierarchical quantum master equation (HQME)…
Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a…
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…
We examine the thermally-induced fracture of an unstrained polymer chain of discrete segments coupled by an anharmonic potential by means of Molecular Dynamics simulation with a Langevin thermostat. Cases of both under- and over-damped…
Atom probe tomography is frequently employed to characterize the elemental distribution in solids with atomic resolution. Here we review and discuss the potential of this technique to locally probe chemical bonds. Two processes characterize…
It is predicted that in force microscopy the quantum fluctuations responsible for the Casimir force can be directly observed as temperature-independent force fluctuations having spectral density $9\pi/(40\ln(4/e)) \hbar \delta k$, where…
The remarkable accuracy and versatility of single-molecule techniques make possible new measurements that are not feasible in bulk assays. Among these, the precise estimation of folding free energies using fluctuation theorems in…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
Recently, a new class of carbon allotrope called protomene was proposed. This new structure is composed of sp2 and sp3 carbon-bonds. Topologically, protomene can be considered as an sp3 carbon structure (~80% of this bond type) doped by sp2…
We present molecular dynamics simulations of the SPC/E model of water to probe the dynamic properties at temperatures from 350 K down to 190 K and pressures from 2.5GPa (25kbar) down to -300MPa (-3kbar). We compare our results with those…
Measurement of the life time of attachments formed by a single microtubule (MT) with a single kinetochore (kt) {\it in-vitro} under force-clamp conditions had earlier revealed a catch-bond-like behavior. In the past the physical origin of…