相关论文: Proteins and polymers
We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the…
Tracer-diffusion of small molecules through dense systems of chain polymers is studied within an athermal lattice model, where hard core interactions are taken into account by means of the site exclusion principle. An approximate mapping of…
We review various simple analytical theories for homopolymers within a unified framework. The common guideline of our approach is the Flory theory, and its various avatars, with the attempt of being reasonably self-contained. We expect this…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of two monomer types. Although these chains…
For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…
A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from…
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…
We investigate interfacial properties between two highly incompatible polymers of different stiffness. The extensive Monte Carlo simulations of the binary polymer melt yield detailed interfacial profiles and the interfacial tension via an…
Unlike most synthetic materials, biological materials often stiffen as they are deformed. This nonlinear elastic response, critical for the physiological function of some tissues, has been documented since at least the 19th century, but the…
We make use of the previously developed formalism for a monomer ensemble and include angular dependence of the segments of the polymer chains thus described. In particular we show how to deal with stiffness when the polymer chain is…
Studies of how protein fold have shown that the way protein clumps form in the test tube is similar to how proteins form the so-called ``amyloid'' deposits that are the pathological signal of a variety of diseases, among them the memory…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
One of the most puzzling and unsolved challenges in molecular biology is understanding how proteins fold. Despite having advanced predictive tools that can accurately estimate the native structures of proteins, we still lack a comprehensive…
Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape.…
I develop a kinetic mechanism to explain chain folding in polymer crystallization which is based on the competition between the formation of stems, which is due to frequent occupations of trans states along the chains in the supercooled…
Pan, Vekilov and Lubchenko[\textit{J. Phys. Chem. B}, 2010, \textbf{114}, 7620] have proposed that dense stable protein clusters appearing in weak protein solutions above the solubility curve are composed of protein oligomers. The…
The competition between chain entropy and bending rigidity in compact polymers can be addressed within a lattice model introduced by P.J. Flory in 1956. It exhibits a transition between an entropy dominated disordered phase and an…
Polymer fibers consist of macromolecules oriented along the fiber axis. Better alignment of chains leads to an increased strength of the fiber. It is believed that the key factor preventing formation of a perfectly oriented fiber is…
We consider a lattice model of a semiflexible homopolymer chain in a bad solvent. Beside the temperature $T$, this model is described by (i) a curvature energy $\varepsilon_h$, representing the stiffness of the chain (ii) a…