Related papers: Multiple scales and phases in discrete chains with…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
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…
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…
By characterizing the phase dynamics in coupled oscillators, we gain insights into the fundamental phenomena of complex systems. The collective dynamics in oscillatory systems are often described by order parameters, which are insufficient…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
Interacting proteins coevolve at multiple but interconnected scales, from the residue-residue over the protein-protein up to the family-family level. The recent accumulation of enormous amounts of sequence data allows for the development of…
A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
Electrostatic interactions play a fundamental role in the structure and function of proteins. Due to ionizable amino acid residues present on the solvent-exposed surfaces of proteins, the protein charge is not constant but varies with the…
We review the development of thermodynamic protein hydropathic scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Darwinian evolution has organized each protein family…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…
Proteins form a very important class of polymers. In spite of major advances in the understanding of polymer science, the protein problem has remained largely unsolved. Here, we show that a polymer chain viewed as a tube not only captures…
Topologically ordered systems are characterized by topological invariants that are often calculated from the momentum space integration of a certain function that represents the curvature of the many-body state. The curvature function may…
The morphologies of phase separating systems have formal distinctions such as symmetry groups, but the analysis protocol for labeling a particular phase field with a morphology requires manual expertise, arbitrary thresholds, or established…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
We study the phase-ordering kinetics of the one-dimensional Heisenberg model with conserved order parameter, by means of scaling arguments and numerical simulations. We find a rich dynamical pattern with a regime characterized by two…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
Multiscale phenomena exhibit complex structure-function relationships, and predicting their macroscopic behavior requires deducing differential equations at different scales. The complexity of these equations and the number of essential…
The intrinsic property of proteins to form structural motifs such as alpha-helices and beta-sheets leads to a complex phase behavior in which proteins can assemble into various types of aggregates including crystals, liquidlike phases of…
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…