Related papers: Sequence determines degree of knottedness in a coa…
We present a novel phenomenological theory describing how topological constraints in prime-knot ring polymers induce collective (cooperative) modes of motion. In low-complexity knots, chain segments can move quasi-independently. However, as…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
We consider a natural model of random knotting- choose a knot diagram at random from the finite set of diagrams with n crossings. We tabulate diagrams with 10 and fewer crossings and classify the diagrams by knot type, allowing us to…
After the recent ground-breaking advances in protein structure prediction, one of the remaining challenges in protein machine learning is to reliably predict distributions of structural states. Parametric models of fluctuations are…
Knots and links are fascinating and intricate topological objects. Their influence spans from DNA and molecular chemistry to vortices in superfluid helium, defects in liquid crystals and cosmic strings in the early universe. Here, we find…
The transport of DNA polymers through nanoscale pores is central to many biological processes, from bacterial gene exchange to viral infection. In single-molecule nanopore sensing, the detection of nucleic acid and protein analytes relies…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Given a (genus 2) cube-with-holes M, i.e. the complement in S^3 of a handlebody H, we relate intrinsic properties of M (like its cut number) with extrinsic features depending on the way the handlebody H is knotted in S^3. Starting from a…
We study random heteropolymer chain with gaussian distribution of kinds of monomers. The long-range correlations between kinds of monomers were introduce. The mean-field analysis of such heteropolymer indicates the existence of infinite…
Protein-protein binding enables orderly and lawful biological self-organization, and is therefore considered a miracle of nature. Protein-protein binding is steered by electrostatic forces, hydrogen bonding, van der Waals force, and…
With the help of lattice Monte Carlo modelling of heteropolymers, we show that the necessary condition for a protein to fold on short call is to proceed through partially folded intermediates. These elementary structures are formed at an…
Constraints can affect dramatically the behavior of diffusion processes. Recently, we analyzed a natural and a technological system and reported that they perform diffusion-like discrete steps displaying a peculiar constraint, whereby the…
Common experience tells us that a knot significantly weakens the polymer strand in which it is tied, which in turn leads to more facile chain rupture under tensile loading. Using first-principles molecular dynamics calculations we describe…
Topological entanglements are abundant, and often detrimental, in polymeric systems in biology and materials science. Here we theoretically investigate the topological simplification of knots by diffusing slip-links (SLs), which may…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…
The interplay of topological constraints and Coulomb interactions in static and dynamic properties of charged polymers is investigated by numerical simulations and scaling arguments. In the absence of screening, the long-range interaction…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
Topological constraints can affect both equilibrium and dynamic properties of polymer systems, and can play a role in the organization of chromosomes. Despite many theoretical studies, the effects of topological constraints on the…
We study the influence of some quenched disorder in the sequence of monomers on the entropic elasticity of long polymeric chains. Starting from the Kratky-Porod model, we show numerically that some randomness in the favoured angles between…