Related papers: Computational Complexity of Flattening Fixed-Angle…
We prove that any finite polyhedral manifold in 3D can be continuously flattened into 2D while preserving intrinsic distances and avoiding crossings, answering a 19-year-old open problem, if we extend standard folding models to allow for…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
Pattern matching is a fundamental tool for answering complex graph queries. Unfortunately, existing solutions have limited capabilities: they do not scale to process large graphs and/or support only a restricted set of search templates or…
Because the constant extension ensemble of single chain molecule is not always equivalent with constant force ensemble, a model of double-stranded conformations, as in RNA molecules and $\beta$-sheets in proteins, with fixed extension…
Analytical relations for the mechanical response of single polymer chains are valuable for modeling purposes, on both the molecular and the continuum scale. These relations can be obtained using statistical thermodynamics and an idealized…
Given a graph G and an integer k, the objective of the $\Pi$-Contraction problem is to check whether there exists at most k edges in G such that contracting them in G results in a graph satisfying the property $\Pi$. We investigate the…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
Given a graph $G(V,E)$, a vertex subset $S$ of $G$ is called an open packing in $G$ if no pair of distinct vertices in $S$ have a common neighbour in $G$. The size of a largest open packing in $G$ is called the open packing number,…
In this paper we study the phenomenon of kinetic partitioning when a polypeptide chain has two ground state conformations one of which is more kinetically reachable than the other. This question is relevant to understand the phenomenology…
Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing…
In 1985, Chv\'{a}tal introduced the concept of star cutsets as a means to investigate the properties of perfect graphs, which inspired many researchers to study cutsets with some specific structures, for example, star cutsets, clique…
We study the two-dimensional hierarchical rectangle packing problem, motivated by applications in analog integrated circuit layout, facility layout, and logistics. Unlike classical strip or bin packing, the dimensions of the container are…
Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…
Modeling folding surfaces with nonzero thickness is of practical interest for mechanical engineering. There are many existing approaches that account for material thickness in folding applications. We propose a new systematic and broadly…
By molecular dynamics simulation, discovered is a strange rigid-like nature for a hexagonally packed domain of short chain molecules. In spite of the non-bonded short-range interaction potential (Lennard-Jones potential) among chain…
We analyse the nature of the confinement of an infinitely long (and finite) linear semiflexible homo-polymer chain confined in between two geometrical constraints (A&B) under good solvent condition in two dimensions. The constraints are…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
The binding complexes formed by proteins and small molecule ligands are ubiquitous and critical to life. Despite recent advancements in protein structure prediction, existing algorithms are so far unable to systematically predict the…
A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…