Related papers: Are there Unfoldable Proteins in Dimension Three?
Soss proved that it is NP-hard to find the maximum 2D span of a fixed-angle polygonal chain: the largest distance achievable between the endpoints in a planar embedding. These fixed-angle chains can serve as models of protein backbones. The…
We study the folding of the regular triangular lattice in three dimensional embedding space, a model for the crumpling of polymerised membranes. We consider a discrete model, where folds are either planar or form the angles of a regular…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
The notion of multidimensional quadrilateral lattice is introduced. It is shown that such a lattice is characterized by a system of integrable discrete nonlinear equations. Different useful formulations of the system are given. The…
Film formation from solvent evaporation in polymer ternary solutions is relevant for several technological applications, such as the fabrication of organic solar cells. The performance of the final device will strongly depend on the…
Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…
The paper studies the modes of vibrations of a lattice with rod-like particles, in a continuum model where the sites of the lattice are the connections among strings and rigid rods. In these structures then, translational and rotational…
The computer artificial intelligence system AlphaFold has recently predicted previously unknown three-dimensional structures of thousands of proteins. Focusing on the subset with high-confidence scores, we algorithmically analyze these…
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…
In this article we construct many examples of properly convex irreducible domains divided by Zariski dense relatively hyperbolic groups in every dimension at least 3. This answers a question of Benoist. Relative hyperbolicity and non-strict…
The one-dimensional problem of selecting the triple helix with the highest volume fraction is solved and hence the condition for a helix to be close-packed is obtained. The close-packed triple helix is shown to have a pitch angle of $v_{CP}…
We provide the exact solution of several variants of simple models of the zipping transition of two bound polymers, such as occurs in DNA/RNA, in two and three dimensions using pairs of directed lattice paths. In three dimensions the…
The geometric dimensionality of a physical system significantly impacts its fundamental characteristics. While experiments are fundamentally limited to the maximum of three spatial dimensions, there is a growing interest in harnessing…
Kinetics of folding of a protein held in a force-clamp are compared to an unconstrained folding. The comparison is made within a simple topology-based dynamical model of ubiquitin. We demonstrate that the experimentally observed variations…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
Quantum (and classical) binding energy considerations in n-dimensional space indicate that atoms (and planets) can only exist in three-dimensional space. This is why observable space is solely 3-dimensional. Both a novel Virial theorem…
Protein design is the inverse approach of the three-dimensional (3D) structure prediction for elucidating the relationship between the 3D structures and amino acid sequences. In general, the computation of the protein design involves a…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
Scaling of folding properties of proteins is studied in a toy system -- the lattice Go model with various two- and three- dimensional geometries of the maximally compact native states. Characteristic folding times grow as power laws with…