Related papers: A two-state kinetic model for the unfolding of sin…
We summarize the recent simulation progress of micromanipulation experiments on RNAs. Our work mainly consults with two important small RNAs unfolding experiments carried out by Bustamante group. Our results show that, in contrast to…
In typical single-molecule force spectroscopy experiments the mechanical unfolding of molecular complexes or biomolecules is studied applying a force ramp to one end of the system while the other end is kept fixed in space. The…
We construct a mathematical model for a diffusiophoretic motion of a deformable droplet, which is floating on a liquid surface and is driven by the surface tension gradient originating from the surface concentration field of the chemicals…
In the global framework of finding an axiomatic derivation of nonequilibrium Statistical Mechanics from fundamental principles, such as the maximum path entropy -- also known as Maximum Caliber principle -- , this work proposes an…
Replication through cell division is one of the most fundamental processes of life and a major driver of dynamics in systems ranging from bacterial colonies to embryogenesis, tissues and tumors. While regulation often plays a role 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…
The Metropolis Monte Carlo (MC) method is used to extract reaction kinetics from a given equilibrium distribution of states of a complex system. The approach is illustrated by the folding/unfolding reaction for two proteins - a model…
We study numerically the behavior of RNA secondary structures under influence of a varying external force. This allows to measure the work $W$ during the resulting fast unfolding and refolding processes. Here, we investigate a medium-size…
We introduce a simple enhanced sampling approach for the calculation of free energy differences and barriers along a one-dimensional reaction coordinate. First, a small number of short nonequilibrium simulations are carried out along the…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
We propose a simple approach, based on the minimization of the total (entropic plus unfolding) energy of a two-state system, describing the stretch-induced unfolding of macromolecules (proteins, silks, nanopolymers, DNA/RNA). The model is…
The mechanical unfolding of an engineered protein composed of eight domains of Ig27 is investigated by using atomic force microscopy. Exploiting a fluctuation relation, the equilibrium free energy as a function of the molecule elongation is…
Single-molecule force spectroscopy experiments, as well as a number of other physical systems, are governed by thermally activated transitions out of a metastable state under the action of a steadily increasing external force. The main…
In single-molecule force spectroscopy experiments, the dependence of the mean unfolding force on the loading rate is used for obtaining information about the energetic and dynamic properties of the system under study. However, it is crucial…
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 semiclassical model, based on a solution of the Vlasov equation for finite systems with moving-surface, is employed to study the isoscalar dipole modes in nuclei. It is shown that, by taking into account the surface degree of freedom, it…
The local balance equations for the density, momentum, and energy of a dilute gas of elastic or inelastic hard spheres, strongly confined between two parallel hard plates are obtained. The starting point is a Boltzmann-like kinetic…
A system of a solvated canonical B-DNA of 12 base pairs with the specified sequence is initially equilibrated in a state of zero external force $f$ acting on it. After equilibration, a switching experiment is performed over the system by…
According to the second law of thermodynamics, for every transformation performed on a system which is in contact with an environment of fixed temperature, the extracted work is bounded by the decrease of the free energy of the system.…
In this paper, we analyze dissipative diamagnetism, arising due to dissipative cyclotron motion in two dimensions, in the light of the quantum counterpart of energy equipartition theorem. We consider a charged quantum particle moving in a…