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The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…

We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…

In a book embedding of a graph G, the vertices of G are placed in order along a straight-line called spine of the book, and the edges of G are drawn on a set of half-planes, called the pages of the book, such that two edges drawn on a page…

We study the problem of embedding graphs in the plane as good geometric spanners. That is, for a graph $G$, the goal is to construct a straight-line drawing $\Gamma$ of $G$ in the plane such that, for any two vertices $u$ and $v$ of $G$,…

The conformational complexity of linear polymers far exceeds that of point-like atoms and molecules. Polymers can bend, twist, even become knotted. Thus they may also display a much richer phase structure than point particles. But it is not…

The evolution of occupied volume under progressive fragmentation of granular matter is studied using a purely geometric model. Rather than modelling disorder directly, properties are investigated by analysing highly ordered reference…

Pancake Flipping is the problem of sorting a stack of pancakes of different sizes (that is, a permutation), when the only allowed operation is to insert a spatula anywhere in the stack and to flip the pancakes above it (that is, to perform…

We describe a randomized algorithm that, given a set $P$ of points in the plane, computes the best location to insert a new point $p$, such that the Delaunay triangulation of $P\cup\{p\}$ has the largest possible minimum angle. The expected…

This paper examines the relationship between the knotting of an embedded surface in $\R^3$ and the knotting of its fold curves, formed by the singular set of projection to a plane. The first result shows that every surface, no matter how…

The problem that we consider is the following: given an $n \times n$ array $A$ of positive numbers, find a tiling using at most $p$ rectangles (which means that each array element must be covered by some rectangle and no two rectangles must…

Nucleation and growth is the dominant relaxation mechanism driving first order phase transitions. In two-dimensional at systems nucleation has been applied to a wide range of problems in physics, chemistry and biology. Here we study…

A map is a partition of the sphere into regions that are labeled as countries or holes. The vertices of a map graph are the countries of a map. There is an edge if and only if the countries are adjacent and meet in at least one point. For a…

Folding can transform mundane objects such as napkins into stunning works of art. However, finding new folding transformations for sheet materials is a challenging problem that requires expertise and real-world experimentation. In this…

Optimization problems consist of either maximizing or minimizing an objective function. Instead of looking for a maximum solution (resp. minimum solution), one can find a minimum maximal solution (resp. maximum minimal solution). Such…

Bundling crossings is a strategy which can enhance the readability of drawings. In this paper we consider good drawings, i.e., we require that any two edges have at most one common point which can be a common vertex or a crossing. Our main…

When folding a 3D object from a 2D material like paper, typically only an approximation of the original surface geometry is needed. Such an approximation can effectively be created by a (progressive) mesh simplification approach, e.g. using…

A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…

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…

The flip graph is the graph whose nodes correspond to non-isomorphic combinatorial triangulations and whose edges connect pairs of triangulations that can be obtained one from the other by flipping a single edge. In this note we show that…

Flexible network design deals with building a network that guarantees some connectivity requirements between its vertices, even when some of its elements (like vertices or edges) fail. In particular, the set of edges (resp. vertices) of a…