Related papers: Are there Unfoldable Proteins in Dimension Three?
Motivation: Protein folding is a dynamic process during which a protein's amino acid sequence undergoes a series of 3-dimensional (3D) conformational changes en route to reaching a native 3D structure; the resulting 3D structural…
As a prelude to what might be expected as forthcoming breakthroughs in finding new approaches toward solving three-dimensional lattice models in the twenty-first century, we review the exact solutions of two lattice models in three…
Changes in lattice structure across sub-regions of protein crystals are challenging to assess when relying on whole crystal measurements. Because of this difficulty, macromolecular structure determination from protein micro and nano…
The realization of the Hofstadter model in a strongly anisotropic ladder geometry has now become possible in one-dimensional optical lattices with a synthetic dimension. In this work, we show how the Hofstadter Hamiltonian in such ladder…
We show that given $m$ proteins (or protein backbones, which are modeled as 3D polygonal chains each of length O(n)) the problem of protein local structure alignment under the discrete Fr\'{e}chet distance is as hard as Independent Set. So…
In suitable environments, proteins, nucleic acids and certain synthetic polymers fold into unique conformations. This work shows that it is possible to construct lattice models of foldable heteropolymers by expressing the energy only in…
In this review we summarize the ongoing effort to study extra-dimensional gauge theories with lattice simulations. In these models the Higgs field is identified with extra-dimensional components of the gauge field. The Higgs potential is…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
Model off-lattice sequences in two dimensions are constructed so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic interactions. The native states of these sequences are…
We analyse the conformational behaviour of a linear semiflexible homo-polymer chain confined by two geometrical constraints under a good solvent condition in two dimensions. The constraints are stair shaped impenetrable surfaces. The…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
There are plausibility arguments that QED in three dimensions has a critical number of flavors of massless two-component fermions, below which scale invariance is broken by the presence of bilinear condensate. We present numerical evidences…
Natively unfolded proteins exist as an ensemble of flexible conformations lacking a well defined tertiary structure along a large portion of their polypeptide chain. Despite the absence of a stable configuration, they are involved in…
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…
Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the presence of such topological obstacles is a debated question in…
This article is concerned with the rigidity properties of geometric realizations of incidence geometries of rank two as points and lines in the Euclidean plane; we care about the distance being preserved among collinear points. We discuss…
A recent paper on the large-scale structure of the Universe presented evidence for a rectangular three-dimensional lattice of galaxy superclusters and voids, with lattice spacing ~120 Mpc and called for some ``hitherto unknown process'' to…
A two-dimensional square-lattice model for the formation of secondary structures in proteins, the hydrogen-bonding model, is extended to include the effects of solvent quality. This is achieved by allowing configuration-dependent…
Multidimensional consistency has emerged as a key integrability property for partial difference equations (P$\Delta$Es) defined on the "space-time" lattice. It has led, among other major insights, to a classification of scalar affine-linear…
In this study, we investigate the lattice angle, which is defined as the angle between two vectors whose components are integers. We focus on the set of angles between a fixed integer vector and other integer vectors. For…