Related papers: Funnels in Energy Landscapes
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…
We present a class of simple algorithms that allows to find the reaction path in systems with a complex potential energy landscape. The approach does not need any knowledge on the product state and does not require the calculation of any…
Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the presence of such topological obstacles is a debated question in…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound and unbound conformations of six proteins to explore their…
Oscillating foils in synchronized pitch/heave motions can be used to harvest hydrokinetic energy. By understanding the wake structure and its correlation with the foil kinematics, predictive models for how foils can operate in array…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
Cell motility in viscous fluids is ubiquitous and affects many biological processes, including reproduction, infection, and the marine life ecosystem. Here we review the biophysical and mechanical principles of locomotion at the small…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
By dividing potential energy landscapes into basins of attractions surrounding minima and linking those basins that are connected by transition state valleys, a network description of energy landscapes naturally arises. These networks are…
Recently, significant progress has been made in conceptually describing the dynamic aspects of coarse particle entrainment, which has been explored experimentally for open channel flows. The aim of this study is to extend the application of…
We show that certain free energy functionals that are not convex with respect to the usual convex structure on their domain of definition, are strictly convex in the sense of displacement convexity under a natural change of variables. We…
It is known from the wave-like motion of microtubules in motility assays that the piconewton forces that motors produce can be sufficient to bend the filaments. In cellular phenomena such as cytosplasmic streaming, molecular motors…
We study the activated motion of adsorbed polymers which are driven over a structured substrate by a localized point force.Our theory applies to experiments with single polymers using, for example, tips of scanning force microscopes to drag…
Energy landscapes are high-dimensional surfaces representing the dependence of system energy on variable configurations, which determine crucially the system's emergent behavior but are difficult to be analyzed due to their high-dimensional…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
This paper focuses on studying a model for molecular motors responsible for the bending of the axoneme in the flagella of microorganisms. The model is a coupled system of partial differential equations inspired by J\"ulicher et al. or…