Related papers: Linking in domain-swapped protein dimers
We study statistical properties of interacting protein-like surfaces and predict two strong, related effects: (i) statistically enhanced self-attraction of proteins; (ii) statistically enhanced attraction of proteins with similar…
The statistical mechanics of polymers grafted on surfaces has been the subject of intense research activity because of many potential applications. In this paper, we analytically investigate the conformational changes caused by a single…
We discuss the entropy of a circular polymer under a topological constraint. We call it the {\it topological entropy} of the polymer, in short. A ring polymer does not change its topology (knot type) under any thermal fluctuations. Through…
We explored the Protein DataBank (PDB) to collect protein-ssDNA structures and create a multiconformational docking benchmark including both bound and unbound protein structures. Due to ssDNA high flexibility when not bound, no ssDNA…
We revisit the classical problem of a polymer confined in a slit in both of its static and dynamic aspects. We confirm a number of well known scaling predictions and analyse their range of validity by means of comprehensive Molecular…
We have investigated interlayer interactions in the bilayer PtTe$_{2}$ system, which influence the electronic energy bands near the Fermi levels. Our diffusion Monte Carlo (DMC) calculations for the high-symmetry bilayer stackings (AA, AB,…
Vitrimers are a relatively new class of polymeric materials containing associative covalent dynamic bonds that make them recyclable by design. However, the fundamental mechanisms controlling their viscoelastic properties remain poorly…
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…
Using numerical simulations we study the pinning and dynamics of interacting colloids on periodic one-dimensional substrates. As a function of colloid density, temperature, and substrate strength, we find a variety of pinned and dynamic…
We present an analysis of the role of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we compute the harmonic spectrum within the Gaussian…
By providing new insights into the distribution of a protein's torsion angles, recent statistical models for this data have pointed the way to more efficient methods for protein structure prediction. Most current approaches have…
This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size r of a protein bridge and/or the presence of a kink at half DNA…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy…
The entanglement properties in an antiferromagnetic dimerized Heisenberg spin-1/2 chain are investigated. The entanglement gap, which is the difference between the ground-state energy and the minimal energy that any separable state can…
We employed the random graph theory approach to analyze the protein-protein interaction database DIP (Feb. 2004), for seven species (S. cerevisiae, H. pylori, E. coli, C. elegans, H. sapiens, M. musculus and D. melanogaster). Several global…
We investigate the long-distance asymptotic behavior of the dimer correlations in the spin-1/2 alternating $XY$chain both at T=0 and at sufficiently low-temperatures. The correlations consist of the dimer long-range order part and the…
Protein-protein interactions can be properly modeled as scale-free complex networks, while the lethality of proteins has been correlated with the node degrees, therefore defining a lethality-centrality rule. In this work we revisit this…
A new theoretical survey of proteins' resistance to constant speed stretching is performed for a set of 17 134 proteins as described by a structure-based model. The proteins selected have no gaps in their structure determination and consist…
Integral membrane proteins deform the surrounding bilayer creating long-ranged forces that influence distant proteins. These forces can be attractive or repulsive, depending on the proteins' shape, height, contact angle with the bilayer, as…