Related papers: Computational Complexity of Flattening Fixed-Angle…
Lattice models have been used extensively over the past thirty years to examine the principles of protein folding and design. These models can be used to determine the conformation of the lowest energy fold out of a large number of possible…
We consider a Hamiltonian decomposition problem of partitioning a regular graph into edge-disjoint Hamiltonian cycles. It is known that verifying vertex non-adjacency in the 1-skeleton of the symmetric and asymmetric traveling salesperson…
Deciding whether a family of disjoint line segments in the plane can be linked into a simple polygon (or a simple polygonal chain) by adding segments between their endpoints is NP-hard.
Computing planar orthogonal drawings with the minimum number of bends is one of the most relevant topics in Graph Drawing. The problem is known to be NP-hard, even when we want to test the existence of a rectilinear planar drawing, i.e., an…
Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of two monomer types. Although these chains…
We revisit several maximization problems for geometric networks design under the non-crossing constraint, first studied by Alon, Rajagopalan and Suri (ACM Symposium on Computational Geometry, 1993). Given a set of $n$ points in the plane in…
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…
We study the effect of edge contractions on simplicial homology because these contractions have turned to be useful in various applications involving topology. It was observed previously that contracting edges that satisfy the so called…
In this paper, we show that deciding rigid foldability of a given crease pattern using all creases is weakly NP-hard by a reduction from Partition, and that deciding rigid foldability with optional creases is strongly NP-hard by a reduction…
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…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
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}…
Given two $k$-graphs $H$ and $F$, a perfect $F$-packing in $H$ is a collection of vertex-disjoint copies of $F$ in $H$ which together cover all the vertices in $H$. In the case when $F$ is a single edge, a perfect $F$-packing is simply a…
We consider a two-letter self-avoiding (square) lattice heteropolymer model of N_H (out ofN) attracting sites. At zero temperature, permanent links are formed leading to collapse structures for any fraction rho_H=N_H/N. The average chain…
Complex molecules and mesoscopic structures are naturally described by general networks of elementary building blocks and tight-binding is one of the simplest quantum model suitable for studying the physical properties arising from the…
In this paper we investigate the discrete version of the classical hanging chain problem. We generalize the problem, by allowing for arbitrary mass and length of each link. We show that the shape of the chain can be obtained by solving a…
Despite the variety of protein sizes, shapes, and backbone configurations found in nature, the design of novel protein folds remains an open problem. Within simple lattice models it has been shown that all structures are not equally…
We give a counterexample to a conjecture of Poon [Poo06] that any orthogonal tree in two dimensions can always be flattened by a continuous motion that preserves edge lengths and avoids self-intersection. We show our example is locked by…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
Motivated by adjacency in perfect matching polytopes, we study the shortest reconfiguration problem of perfect matchings via alternating cycles. Namely, we want to find a shortest sequence of perfect matchings which transforms one given…