Related papers: Long range correlations and folding angle in polym…
A kinetic model for the nucleation mechanism of protein folding is proposed. A protein is modeled as a heteropolymer consisting of hydrophobic and hydrophilic beads with equal constant bond lengths and bond angles. The total energy of the…
We study knotted polymers in equilibrium with an array of obstacles which models confinement in a gel or immersion in a melt. We find a crossover in both the geometrical and the topological behavior of the polymer. When the polymers' radius…
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…
The phase behavior of colloid-polymer mixtures, and of solutions of globular proteins, is often interpreted in terms of a simple model of hard spheres with short-ranged attraction. While such a model yields a qualitative understanding of…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
We introduce a simple geometric model for a double-stranded and double-helical polymer. We study the statistical mechanics of such polymers using both analytical techniques and simulation. Our model has a single energy-scale which…
While the structure of chromatin has been studied in great detail on length scales below 30 nm, amazingly little is known about the higher-order folding motifs of chromatin in interphase. Recent experiments give evidence that the folding…
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…
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…
Proteins are linear chain molecules that play a central role in life and health. Protein native state folds are modular assemblies of space-filling building blocks of {\alpha}-helices, \{beta}-sheets and tight turns. Here we deduce the…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
Kinetic barriers cause polymers to crystallize incompletely, into nanoscale lamellae interleaved with amorphous regions. As a result, crystalline polymers are full of crystal-melt interfaces, which dominate their physical properties. The…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
A single semiflexible polymer chain folds into a toroidal object under poor solvent conditions. In this study, we examined the morphological change in such a toroidal state as a function of the width and stiffness of the chain together with…
Molecular process of polymer collapse was reproduced by isothermal molecular dynamics simulation. The initial polymer chains were obtained by mean of random walks in continuum space. Two potential models were considered to represent short…
The properties of the interface in a phase-separated solution of polymers with different degrees of polymerization and Kuhn segment lengths are calculated. The starting point is the planar interface, the profile of which is calculated in…
We examine the phase transition of polymer adsorption as well as the underlying kinetics of polymer binding from dilute solutions on a structureless solid surface. The emphasis is put on the properties of regular multiblock copolymers,…
The hydrogen phase diagram has a number of unusual features which are generally well reproduced by density functional calculations. Unfortunately, these calculations fail to provide good physical insights into why those features occur. In…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…