Related papers: Protein viscoelastic dynamics: a model system
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
The present article is concerned with modelling the viscoelastic behavior of Polydimethylsiloxane (PDMS) in large-strain regime. Starting from the basic principles of thermodynamics, an incremental variational formulation is derived. Within…
In Part I of this contribution, a systematic coarse-grained description of the dynamics of a weakly-bending semiflexible polymer was developed. Here, we discuss analytical solutions of the established deterministic partial…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
In this article, we study the dynamics of a nonlinear system governed by an ordinary differential equation under the combined influence of fast periodic sampling with period $\delta$ and small jump noise of size $\varepsilon, 0<…
We introduce a system where an elastic lattice of particles is moved slowly at a constant velocity under the influence of a local external potential, construct a rigid-body model through simplification processes, and show that the two…
A theoretical description of the weakly nonlinear and mode-dependent dynamics of a nanoscale beam that is under intrinsic tension is developed. A full analysis of the dynamic range of the beam over a wide range of conditions is presented.…
Robust oscillations play crucial roles in a wide variety of biological processes and are often generated by deterministic mechanisms. However, stochastic fluctuations often generate complex perturbations of these deterministic oscillations,…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Self-assembled linear structures like giant cylindrical micelles or discotic molecules in solution stacked in flexible columns are systems reminiscent of polydisperse polymer solutions.These supramolecular polymers have an equilibrium…
We show that in experimental atomic force microscopy studies of the lifetime distribution of mechanically stressed folded proteins the effects of externally applied fluctuations can not be distinguished from those of internally present…
Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…
Embryonic tissues deform across broad spatial and temporal scales and relax stress through active rearrangements. A quantitative link between cell-scale activity, spatial forcing, and emergent tissue-scale mechanics remains incomplete.…
In this work, it is demonstrated that the usual power system dynamic model exhibits a feedforward-feedback control structure. The distinct properties of the feedforward and feedback subsystems are identified and studied using respective…
We establish the long-time existence of large-data weak solutions to a system of nonlinear partial differential equations. The system of interest governs the motion of non-Newtonian fluids described by a simplified viscoelastic rate-type…
A simple way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions…
The elasto-inertial effects on particle focusing in a square-tube flow were investigated experimentally and numerically. Microscale experiments using spherical particles in dilute polymer solutions demonstrated that the particles are…
We investigate how the kinetic energy acquired by a dense granular system driven by an external vibration depends on the input energy. Our focus is on the dependence of the granular behavior on two main parameters: frequency and vibration…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…