Related papers: A central partition of molecular conformational sp…
Molecular representation learning has attracted much attention recently. A molecule can be viewed as a 2D graph with nodes/atoms connected by edges/bonds, and can also be represented by a 3D conformation with 3-dimensional coordinates of…
We investigate the structure of two-dimensional partial cubes, i.e., of isometric subgraphs of hypercubes whose vertex set defines a set family of VC-dimension at most 2. Equivalently, those are the partial cubes which are not contractible…
The complexity of condensed matter arises from emergent behaviors that cannot be understood by analyzing individual constituents in isolation. While traditional condensed-matter approaches-developed primarily for ideal crystalline…
A classification of discrete integrable systems on quad-graphs, i.e. on surface cell decompositions with quadrilateral faces, is given. The notion of integrability laid in the basis of the classification is the three-dimensional…
Much scientific enquiry across disciplines is founded upon a mechanistic treatment of dynamic systems that ties form to function. A highly visible instance of this is in molecular biology, where an important goal is to determine…
We propose a method to recover the structure of a compound object from multiple silhouettes. Structure is expressed as a collection of 3D primitives chosen from a pre-defined library, each with an associated pose. This has several…
This paper describes in detail how (discrete) quaternions - ie. the abstract structure of 3-D space - emerge from, first, the Void, and thence from primitive combinatorial structures, using only the exclusion and co-occurrence of otherwise…
Deep generative models have achieved tremendous success in designing novel drug molecules in recent years. A new thread of works have shown the great potential in advancing the specificity and success rate of in silico drug design by…
This paper introduces a new shape-matching methodology, combinative matching, to combine interlocking parts for geometric shape assembly. Previous methods for geometric assembly typically rely on aligning parts by finding identical surfaces…
With the consolidation of deep learning in drug discovery, several novel algorithms for learning molecular representations have been proposed. Despite the interest of the community in developing new methods for learning molecular embeddings…
This article proposes a mortar type finite element formulation for consistently embedding curved, slender beams, i.e. 1D Cosserat continua, into 3D solid volumes. A consistent 1D-3D coupling scheme for this problem type is proposed, which…
Two line arrangements in $\mathbb{CP}^2$ can have different topological properties even if they are combinatorially isomorphic. Results by Dan Cohen and Suciu and by Randell show that a reducible moduli space under complex conjugation is a…
Using computed x-ray tomography we determine the three dimensional (3d) structure of binary hard sphere mixtures as a function of composition and size ratio of the particles, q. Using a recently introduced four-point correlation function we…
Configuration space integrals are powerful tools for studying the homotopy type of the space of long embeddings in terms of a combinatorial object called a graph complex. It is unknown whether these integrals give a cochain map due to…
Relational representation learning transforms relational data into continuous and low-dimensional vector representations. However, vector-based representations fall short in capturing crucial properties of relational data that are complex…
We extend our generic rigidity theory for periodic frameworks in the plane to frameworks with a broader class of crystallographic symmetry. Along the way we introduce a new class of combinatorial matroids and associated linear…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
We construct a series of finitely presented semigroups. The centers of these semigroups encode uniquely up to rigid ambient isotopy in 3-space all non-oriented spatial graphs. This encoding is obtained by using three-page embeddings of…
The motivation of this work is to define cohomology classes in the space of knots that are both easy to find and to evaluate, by reducing the problem to simple linear algebra. We achieve this goal by defining a combinatorial graded cochain…
The embedding of a given point set with non-crystallographic symmetry into higher-dimensional space is reviewed, with special emphasis on the Minkowski embedding known from number theory. This is a natural choice that does not require an a…