Related papers: Computational Complexity of Flattening Fixed-Angle…
"Flat origami" refers to the folding of flat, zero-curvature paper such that the finished object lies in a plane. Mathematically, flat origami consists of a continuous, piecewise isometric map $f:P\subseteq\mathbb{R}^2\to\mathbb{R}^2$ along…
We consider a lattice model of a semiflexible homopolymer chain in a bad solvent. Beside the temperature $T$, this model is described by (i) a curvature energy $\varepsilon_h$, representing the stiffness of the chain (ii) a…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Coarse-grained (lattice-) models have a long tradition in aiding efforts to decipher the physical or biological complexity of proteins. Despite the simplicity of these models, however, numerical simulations are often computationally very…
When can a plane graph with prescribed edge lengths and prescribed angles (from among $\{0,180^\circ, 360^\circ$\}) be folded flat to lie in an infinitesimally thin line, without crossings? This problem generalizes the classic theory of…
The hydrophobic/polar HP model on the square lattice has been widely used to investigate basics of protein folding. In the cases where all designing sequences (sequences with unique ground states) were enumerated without restrictions on the…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
We study algorithmic aspects of bending wires and sheet metal into a specified structure. Problems of this type are closely related to the question of deciding whether a simple non-self-intersecting wire structure (a carpenter's ruler) can…
We study the problem of deciding whether a crease pattern can be folded by simple folds (folding along one line at a time) under the infinite all-layers model introduced by [Akitaya et al., 2017], in which each simple fold is defined by an…
A folded chain, with one end fixed at the ceiling and the other end released from the same elevation, is commonly modeled as an energy-conserving system in one-dimension. However, the analytical paradigms in previous literature is…
The (Perfect) Matching Cut problem is to decide if a connected graph has a (perfect) matching that is also an edge cut. The Disconnected Perfect Matching problem is to decide if a connected graph has a perfect matching that contains a…
The freely rotating chain is one of the classic discrete models of a polymer in dilute solution. It consists of a broken line of N straight segments of fixed length such that the angle between adjacent segments is constant and the N-1…
Optimal geometrical arrangements, such as the stacking of atoms, are of relevance in diverse disciplines. A classic problem is the determination of the optimal arrangement of spheres in three dimensions in order to achieve the highest…
Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the…
The NP-complete problem Matching Cut is to decide if a graph has a matching that is also an edge cut of the graph. We prove new complexity results for Matching Cut restricted to $H$-free graphs, that is, graphs that do not contain some…
Although rare, an increasing number of proteins have been observed to contain entanglements in their native structures. To gain more insight into the significance of protein knotting, researchers have been investigating protein knot…
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…
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…
This paper investigated the problem of embedding a simple Hamiltonian Cycle with n vertices on n points inside a simple polygon. This problem seeks to embed a straight-line cycle (without bends), which does not intersect either itself or…
To determine the 3D conformation of proteins is a necessity to understand their functions or interactions with other molecules. It is commonly admitted that, when proteins fold from their primary linear structures to their final 3D…