Related papers: Computational Complexity of Flattening Fixed-Angle…
Continuing results from JCDCGGG 2016 and 2017, we solve several new cases of the simple foldability problem -- deciding which crease patterns can be folded flat by a sequence of (some model of) simple folds. We give new efficient algorithms…
A foundational result in origami mathematics is Kawasaki and Justin's simple, efficient characterization of flat foldability for unassigned single-vertex crease patterns (where each crease can fold mountain or valley) on flat material. This…
Quantum annealing is a promising approach for obtaining good approximate solutions to difficult optimization problems. Folding a protein sequence into its minimum-energy structure represents such a problem. For testing new algorithms and…
Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure…
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 extend linkage unfolding results from the well-studied case of polygonal linkages to the more general case of linkages of polygons. More precisely, we consider chains of nonoverlapping rigid planar shapes (Jordan regions) that are hinged…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
A planar kinematic chain consists of $n$ links connected by joints. In this work we investigate the space of configurations, described in terms of joint angles, that guarantee that the kinematic chain is closed. We give explicit formulas…
We explore the following problem: given a collection of creases on a piece of paper, each assigned a folding direction of mountain or valley, is there a flat folding by a sequence of simple folds? There are several models of simple folds;…
In this paper, we study movements of simple polygonal chains in 3D. We say that an open, simple polygonal chain can be straightened if it can be continuously reconfigured to a straight sequence of segments in such a manner that both the…
Among the unsolved problems in computational biology, protein folding is one of the most interesting challenges. To study this folding, tools like neural networks and genetic algorithms have received a lot of attention, mainly due to the…
It has recently been shown that any simple (i.e. nonintersecting) polygonal chain in the plane can be reconfigured to lie on a straight line, and any simple polygon can be reconfigured to be convex. This result cannot be extended to tree…
In this paper, we study movements of simple polygonal chains in 3D. We say that an open, simple polygonal chain can be straightened if it can be continuously reconfigured to a straight sequence of segments in such a manner that both the…
It is widely accepted that (1) the natural or folded state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino acid sequence. The H-P (hydrophobic-hydrophilic) model is a…
The hydrophobic-polar (HP) model represents proteins as binary strings embedded in lattices, with fold quality measured by an energy score. We prove that the optimal fold energy is not monotonic under concatenation for several standard…
Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that…
A linkage $\mathcal{L}$ consists of a graph $G=(V,E)$ and an edge-length function $\ell$. Deciding whether $\mathcal{L}$ can be realized as a planar straight-line embedding in $\mathbb{R}^2$ with edge length $\ell(e)$ for all $e \in E$ is…
We have exactly enumerated all sequences and conformations of HP proteins with chains of up to 19 monomers on the simple cubic lattice. For two variants of the hydrophobic-polar (HP) model, where only two types of monomers are…