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An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
Successful scientific applications of large-scale molecular dynamics often rely on automated methods for identifying the local crystalline structure of condensed phases. Many existing methods for structural identification, such as Common…
Structured optimization uses a prescribed set of atoms to assemble a solution that fits a model to data. Polarity, which extends the familiar notion of orthogonality from linear sets to general convex sets, plays a special role in a simple…
A typical computational geometry problem begins: Consider a set P of n points in R^d. However, many applications today work with input that is not precisely known, for example when the data is sensed and has some known error model. What if…
Single Particle Imaging techniques at X-ray lasers have made significant strides, yet the challenge of determining the orientation of freely rotating molecules during delivery remains. In this study, we propose a novel method to partially…
We discuss whether the diffractive structure functions defined by current experiments at HERA are indeed probing the partonic structure function of the pomeron. We observe that the {\it pseudorapidity} cuts commonly employed require that…
Accurately predicting the three-dimensional structures of protein-ligand complexes remains a fundamental challenge in computational drug discovery that limits the pace and success of therapeutic design. Deep learning methods have recently…
This paper presents a data structure that summarizes distances between configurations across a robot configuration space, using a binary space partition whose cells contain parameters used for a locally linear approximation of the distance…
Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge.…
The partition problem is a well-known basic NP-complete problem. We mainly consider the optimization version of it in this paper. The problem has been investigated from various perspectives for a long time and can be solved efficiently in…
The local arrangement of atoms is one of the most important predictors of mechanical and functional properties of materials. However, algorithms for identifying the geometrical arrangements of atoms in complex materials systems are lacking.…
Faults and geological barriers can drastically affect the flow patterns in porous media. Such fractures can be modeled as interfaces that interact with the surrounding matrix. We propose a new technique for the estimation of the location…
We give compact extended formulations for the packing and partitioning orbitopes (with respect to the full symmetric group) described and analyzed in (Kaibel and Pfetsch, 2008). These polytopes are the convex hulls of all 0/1-matrices with…
In this paper we study the problem of shape part retrieval in the point cloud domain. Shape retrieval methods in the literature rely on the presence of an existing query object, but what if the part we are looking for is not available? We…
We present conjectured candidates for the least perimeter partition of a disc into $N \le 10$ regions which take one of two possible areas. We assume that the optimal partition is connected, and therefore enumerate all three-connected…
Many man-made objects are characterised by a shape that is symmetric along one or more planar directions. Estimating the location and orientation of such symmetry planes can aid many tasks such as estimating the overall orientation of an…
In current simulations of fission, the number of protons and neutrons in a given fission fragment is almost always obtained by integrating the total density of particles in the sector of space that contains the fragment. Because of the…
The partial oracles framework is a quantum search algorithm that has the potential to exceed the quadratic speedup of Grover's algorithm, up to a theoretical maximum of an exponential speedup. Until now, however, the framework has lacked an…
Nuclear Magnetic Resonance (NMR) spectroscopy is particularly well-suited to determine the structure of molecules and materials in powdered form. Structure determination usually proceeds by finding the best match between experimentally…
The geometric optimization of crystal structures is a procedure widely used in Chemistry that changes the geometrical placement of the particles inside a structure. It is called structural relaxation and constitutes a local minimization…