Related papers: Force Feedback Effects on Single Molecule Hopping …
We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and continuous trajectory segments between replica…
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…
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 concept of critical ambient pressure is introduced. The particle escapes from its trap when the ambient pressure becomes comparable with or smaller than a critical value, even if the particle motion is cooled by one of the feedback (or…
Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…
We present a theoretical investigation of thermal fluctuation statistics in a molecular motor. Energy transfer in the motor is described using a multidimensional discrete master equation with nearest-neighbor hopping. In this theory, energy…
It is important to understand how protein folding and evolution influences each other. Several studies based on entropy calculation correlating experimental measurement of residue participation in folding nucleus and sequence conservation…
We consider reversible breaking of adhesion bonds or folding of proteins under the influence of a constant external force. We discuss the stochastic properties of the unbinding/rebinding events and analyze their mean number and their…
Single molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse…
The energy dependent thermoelectric response of a single molecule contains valuable information about its transmission function and its excited states. However, measuring it requires devices that can efficiently heat up one side of the…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…
Metal-organic frameworks (MOFs) are promising materials for gas sensing but are often limited to single-use detection. We demonstrate a hybridization strategy synergistically deploying conductive MOFs (cMOFs) and conductive polymers (cPs)…
We investigate the exchange bias and training effects in the FM/AF heterostructures using a unified Monte Carlo dynamical approach. This real dynamical method has been proved reliable and effective in simulating dynamical magnetization of…
Although known that single domain proteins fold and unfold by parallel pathways, demonstration of this expectation has been difficult to establish in experiments. Unfolding rate, $k_\mathrm{u}(f)$, as a function of force $f$, obtained in…
We investigate the coupling between interstitial medium and granular particles by studying the hopper flow of dry and submerged system experimentally and numerically. In accordance with earlier studies, we find, that the dry hopper empties…
Large-scale three dimensional molecular dynamics simulations of hopper flow are presented. The flow rate of the system is controlled by the width of the aperture at the bottom. As the steady-state flow rate is reduced, the force…
We present a unified framework for folding kinetics of proteins and RNA. The basis for this framework relies on the notion of topological frustration, which gives rise to several competing basins of attraction (CBA) in addition to 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…
Hill function is one of the widely used gene transcription regulation models. Its attribute of fitting may result in a lack of an underlying physical picture, yet the fitting parameters can provide information about biochemical reactions,…
We present a highly efficient method to directly simulate the photodissociation followed by Coulomb explosion of methyl iodide. In order to achieve statistical reliability, more than 40,000 trajectories are calculated on accurate potential…