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Spatial heterogeneity can have dramatic effects on the biochemical networks that drive cell regulation and decision-making. For this reason, a number of methods have been developed to model spatial heterogeneity and incorporated into widely…
This paper considers the learning of Boolean rules in either disjunctive normal form (DNF, OR-of-ANDs, equivalent to decision rule sets) or conjunctive normal form (CNF, AND-of-ORs) as an interpretable model for classification. An integer…
We seek to automate the design of molecules based on specific chemical properties. Our primary contributions are a simpler method for generating SMILES strings guaranteed to be chemically valid, using a combination of a new context-free…
Algorithms to generate various combinatorial structures find tremendous importance in computer science. In this paper, we begin by reviewing an algorithm proposed by Rohl that generates all unique permutations of a list of elements which…
The present work deals with the formulation of a Virtual Element Method (VEM) for two dimensional structural problems. The contribution is split in two parts: in part I, the elastic problem is discussed, while in part II [3] the method is…
Discrete structure rules for validating molecular structures are usually limited to fulfillment of the octet rule or similar simple deterministic heuristics. We propose a model, inspired by language modeling from natural language…
The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the…
In recent years, the interest in interpretable classification models has grown. One of the proposed ways to improve the interpretability of a rule-based classification model is to use sets (unordered collections) of rules, instead of lists…
This paper introduces the concept of a generating set for stochastic matrices -- a subset of matrices whose repeated composition generates the entire set. Understanding such generating sets requires specifying the "indivisible elements" and…
High-order harmonic generation by a bicircular field, which consists of two coplanar counter-rotating circularly polarized fields of frequency $r\omega$ and $s\omega$ ($r$ and $s$ are integers), is investigated for a polyatomic molecule.…
A proof-of-concept framework for identifying molecules of unknown elemental composition and structure using experimental rotational data and probabilistic deep learning is presented. Using a minimal set of input data determined…
Astrochemistry lies at the nexus of astronomy, chemistry, and molecular physics. On the basis of precise laboratory data, a rich collection of more than 200 familiar and exotic molecules have been identified in the interstellar medium, the…
A novel approach is presented for the solution of instantaneous chemical equilibrium problems. The chemical equilibrium can be considered, due to its intrinsically local character, as a mapping of the three-dimensional parameter space…
We introduce an algorithm that conjectures the structure of a permutation class in the form of a disjoint cover of "rules"; similar to generalized grid classes. The cover is usually easily verified by a human and translated into an…
Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we…
Designing a new drug is a lengthy and expensive process. As the space of potential molecules is very large (10^23-10^60), a common technique during drug discovery is to start from a molecule which already has some of the desired properties.…
Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their…
Soliton molecules, bound states composed of interacting fundamental solitons, exhibit remarkable resemblance with chemical compounds and phenomena in quantum mechanics. Whereas optical molecules composed of two or more temporally locked…
Engineered quantum systems allow us to observe phenomena that are not easily accessible naturally. The LEGO-like nature of superconducting circuits makes them particularly suited for building and coupling artificial atoms. Here, we…
Odd electrons of benzenoid units and correlation of these electrons having different spins are the main concepts of the molecular theory of graphene. In contrast to the theory of aromaticity, the molecular theory is based on the fact that…