Related papers: Medium effects on the selection of sequences foldi…
The effect of ambient disorders and sequence heterogeneities on the reptation of a long polymer is studied with the aid of a disordered tube model. The dynamics of a random heteropolymer is found to be much slower than that of a homopolymer…
We study surface effects in amorphous polymer systems by means of computer simulation. In the framework of molecular dynamics, we present two different methods to prepare such surfaces. {\em Free} surfaces are stabilized solely by…
Cotranslational folding depends on the folding speed and stability of the nascent protein. It remains difficult, however, to predict which proteins cotranslationally fold. Here, we simulate evolution of model proteins to investigate how…
Polymerization and formation of crosslinked polymer networks are important processes in manufacturing, materials fabrication, and in the case of hydrated polymer networks, synthesis of biomedical materials, drug delivery, and tissue…
Biological molecules can form hydrogen bonds between nearby residues, leading to helical secondary structures. The associated reduction of configurational entropy leads to a temperature dependence of this effect: the "helix-coil…
The folding characteristics of sequences reduced with a possibly simplified representation of five types of residues are shown to be similar to their original ones with the natural set of residues (20 types or 20 letters). The reduced…
The study of the noise induced effects on the dynamics of a chain molecule crossing a potential barrier, in the presence of a metastable state, is presented. A two-dimensional stochastic version of the Rouse model for a flexible polymer has…
In this article, we quantitatively study, through stochastic models, the efects of several intracellular phenomena, such as cell volume growth, cell division, gene replication as well as fuctuations of available RNA polymerases and…
A mean field rate theory description of the homo- and co-polymerization of $f$-functional molecules is developed, which contains the formation of short cyclic structures inside the network. The predictions of this model are compared with…
In this paper we present a method to study the folding structure of a simple model consisting of two kinds of monomers, hydrophobic and hydrophilic. This method has three main steps: an efficient simulation method to bring an open sequence…
The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the…
In this letter, the possible dynamic scaling properties of protein molecules in folding are investigated theoretically by assuming that the protein molecules are percolated networks. It is shown that the fractal character and the fractal…
Cells contain multiple condensates which spontaneously form due to the heterotypic interactions between their components. Although the proteins and disordered region sequences that are responsible for condensate formation have been…
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.…
Using path integral technique, we show exactly that for a semiflexible biopolymer in constant extension ensemble, no matter how long the polymer and how large the external force, the effects of short range correlations in the…
The effect of boundaries on the force distributions in granular media is illustrated by simulations of 2D packings of frictionless, Hertzian spheres. To elucidate discrepancies between experimental observations and theoretical predictions,…
Hydrostatic pressure is a common perturbation to probe the conformations of proteins. There are two common forms of pressure dependent potentials of mean force (PMFs) derived from hydrophobic molecules available for the coarse grained…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
We study the equilibrium properties of a single flexible homopolymers where consecutive monomers are represented by impenetrable hard spherical beads tangential to each other, and non-consecutive monomers interact via a square-well…
We present a detailed study of the static and dynamic behavior of long semiflexible polymer chains in a melt. Starting from previously obtained fully equilibrated high molecular weight polymer melts [{\it Zhang et al.} ACS Macro Lett. 3,…