Related papers: Multiple barriers in forced rupture of protein com…
Identifying minimal and informative feature sets is a central challenge in data analysis, particularly when few data points are available. Here we present a theoretical analysis of an unsupervised feature selection pipeline based on the…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
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…
A phenomenological model for the unbinding transition of multi-component fluid membranes is proposed, where the unbinding transition is described using a theory analogous to Flory-Huggins theory for polymers. The coupling between the…
Epithelization, the process whereby an epithelium covers a cell-free surface, is not only central to wound healing but also pivotal in embryonic morphogenesis, regeneration, and cancer. In the context of wound healing, the epithelization…
In various cellular processes, biofilaments like F-actin and F-tubulin are able to exploit chemical energy associated to polymerization to perform mechanical work against an external load. The force-velocity relationship quantitatively…
Theoretical studies of stretching proteins with slipknots reveal a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This behavior arises as a consequence of the existence of alternative…
Recent observations of the growth of protein crystals have identified two different growth regimes. At low supersaturation, the surface of the crystal is smooth and increasing in size due to the nucleation of steps at defects and the…
Recent experimental studies have observed a surprisingly wide range of strengths in polycrystalline graphene. Previous computational investigations of graphene tilt boundaries have highlighted the role of interfacial topology in determining…
Through experiments, we idealise a plant leaf as a flexible, thin, rectangular plate clamped at the midpoint and positioned perpendicular to an airflow. Flexibility of the structure is considered as an advantage at moderate flow speed…
Force-clamp spectroscopy reveals the unfolding and disulfide bond rupture times of single protein molecules as a function of the stretching force, point mutations and solvent conditions. The statistics of these times reveal whether the…
The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed…
We present a new theory for modeling forced indentation spectral lineshapes of biological particles, which considers non-linear Hertzian deformation due to an indenter-particle physical contact and bending deformations of curved beams…
Many of the cell membrane vital functions are achieved by the self-organization of the proteins and biopolymers embedded in it. The protein dynamics are in part determined by its drag. A large number of these proteins can polymerize to form…
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…
The microscopic studies on nuclear fission require the evaluation of the potential energy surface as a function of the collective coordinates. A reasonable choice of constraints on multipole moments should be made to describe the topography…
A recent experimental study reports on measuring the temporal duration and the spatial extent of failed attempts to cross an activation barrier (i.e., "loops") for a folding transition in a single molecule and for a Brownian particle…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
We propose algorithms for determining both lower and upper bounds for the energy barriers encountered by a flux line in moving through a two-dimensional random potential. Analytical arguments, supported by numerical simulations, suggest…
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…