Related papers: Falling chains as variable mass systems: theoretic…
Biofilament-motor protein complexes are ubiquitous in biology and drive the transport of cargo vital for many fundamental cellular processes. As they move, motor proteins exert compressive forces on the filaments to which they are attached,…
The thermally assisted detachment of a self-avoiding polymer chain from an adhesive surface by an external force applied to one of the chain ends is investigated. We perform our study in the "fixed height" statistical ensemble where one…
We investigate the behaviour of a chain of interacting Brownian particles with one end fixed and the other moving away at slow speed, in the limit of small noise. The interaction between particles is through a pairwise potential with finite…
We show that, in conserved-mass transport processes, the steady-state distribution of mass in a subsystem is uniquely determined from the functional dependence of variance of the subsystem mass on its mean, provided that joint mass…
It is common to study polymer physics through the use of idealized single-chain models, and the most popular of these is the freely jointed chain model. In certain thermodynamic ensembles, statistical mechanical treatment of this model is…
We propose a continuum theory to model the Mullins effect, which is ubiquitously observed in polymer composites. In the theory, the softening of the materials during the stretching process is accounted for by considering the delamination of…
The protein folding is regarded as a quantum transition between torsion states on polypeptide chain. The deduction of the folding rate formula in our previous studies is reviewed. The rate formula is generalized to the case of frequency…
The energy for protein folding arises from multiple sources and is not large in total. In spite of the many specific successes of energy landscape and other approaches, there still seems to be some missing guiding factor that explains how…
The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling…
Biopolymer Networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the mechanical response of a model biopolymer network due to the active…
It has been established that the entangled polymer dynamics can be reasonably described by single chain models such as tube and slip-link models. Although the entanglement effect is a result of the hard-core interaction between chains,…
Granular materials transmit stress via a network of force chains. Despite the importance of these chains to characterizing the stress state and dynamics of the system, there is no common framework for quantifying their their properties.…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The…
The general theoretical ground for the models based on the compact angle coordinates is presented. It is observed that the proper dependence on compact coordinates has to be through the group elements and is achieved most naturally in a…
In Variational Analysis, VU-theory provides a set of tools that is helpful for understanding and exploiting the structure of nonsmooth functions. The theory takes advantage of the fact that at any point, the space can be separated into two…
We investigate the dependence of the displacements of a molecular motor embedded inside a glassy material on its folding characteristic time. We observe two different time regimes. For slow foldings (regime I) the diffusion evolves very…
The dynamical response of a tethered semiflexible polymer with self-attractive interactions and subjected to an external force field is numerically investigated by varying stiffness and self-interaction strength. The chain is confined in…
We present a numerical model for a two dimensional (2D) granular assembly, falling in a rectangular container when the bottom is removed. We observe the occurrence of cracks splitting the initial pile into pieces, like in experiments. We…
This paper presents a reduced-order model for the Reynolds equation for deformable structure and large displacements. It is based on the model established in [11] which is piece-wise linearized using two different methods. The advantages…