Related papers: Enumerating Designing Sequences in the HP Model
Hydrophobic polyelectrolytes have been predicted to adopt an unique pearl-necklace conformation in aqueous solvents. We present in this Letter an attempt to characterise quantitatively this conformation with a focus on $D_p$, the pearl…
In view of recent intense experimental and theoretical interests in the biophysics of liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs), heteropolymer models with chain molecules configured as self-avoiding…
Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher…
Dissipative Particle Dynamics (DPD) is becoming a popular particle based method to study flow through microchannels due to the ease with which the presence of biological cells or DNA chains can be modeled. Many Lab-On-Chip (LOC) devices…
An orientable sequence of order $n$ is a cyclic binary sequence such that each length-$n$ substring appears at most once \emph{in either direction}. Maximal length orientable sequences are known only for $n\leq 7$, and a trivial upper bound…
We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences…
Identifying the driving forces and the mechanism of association of huntingtin-exon1, a close marker for the progress of Huntington's disease, is an important prerequisite towards finding potential drug targets, and ultimately a cure. We…
Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length $N \sim {\cal O}(10^4)$. Based on the standard simple…
For graphs $H$, we study the extremal function $M_H(n)$ which is the maximum running time (until stabilisation) of an $H$-bootstrap percolation process on $n$ vertices. Building on previous work in the clique case $H=K_k$, we develop a…
In this paper, we study the abundance of self-avoiding paths of a given length on a supercritical percolation cluster on $\bbZ^d$. More precisely, we count $Z_N$ the number of self-avoiding paths of length $N$ on the infinite cluster,…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
Chain-like macromolecules in solution, whether biological or synthetic, transform from an extended conformation to a compact one when temperature or other system parameters change. This collapse transition is relevant in various phenomena,…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are…
Quantum annealing is a promising approach for obtaining good approximate solutions to difficult optimization problems. Folding a protein sequence into its minimum-energy structure represents such a problem. For testing new algorithms and…
An earlier one-dimensional lattice model of hydrophobic attraction is extended to two and three dimensions and studied by Monte Carlo simulation. The solvent-mediated contribution to the potential of mean force between hydrophobic solute…
We study a simple heteropolymer model containing sequence-independent local interactions on both square and triangular lattices. Sticking to a two-letter code, we investigate the model for varying strength $\kappa$ of the local…
Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure…
Under dehydration conditions, amphipathic Late Embryogenesis Abundant (LEA) proteins fold spontaneously from a random conformation into alpha-helical structures and this transition is promoted by the presence of membranes. To gain insight…
Approximately 1% of the known protein structures display knotted configurations in their native fold but their function is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport,…