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We introduce a mixed-integer linear programming (MILP) framework capable of determining whether a chemical reaction network possesses the property of being endotactic or strongly endotactic. The network property of being strongly endotactic…
Graph mining applications analyze the structural properties of large graphs, and they do so by finding subgraph isomorphisms, which makes them computationally intensive. Existing graph mining techniques including both custom graph mining…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
An algorithm is developed for structure identification of amorphous carbonaceous nanomaterials with a joint x-ray and neutron diffraction data analysis, using the data on the chemical composition of the sample from other diagnostics. The…
Changes in the extent of local concavity along with changes in surface roughness of binding sites of proteins have long been considered as useful markers to identify functional sites of proteins. However, an algorithm that describes the…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
Machine learning methods have shown promise in predicting molecular properties, and given sufficient training data machine learning approaches can enable rapid high-throughput virtual screening of large libraries of compounds. Graph-based…
Mapper, a topological algorithm, is frequently used as an exploratory tool to build a graphical representation of data. This representation can help to gain a better understanding of the intrinsic shape of high-dimensional genomic data and…
This paper introduces a new representation method that is mainly based on chemical bonds among atoms in materials. Each chemical bond and its surrounded atoms are considered as a unified unit or a local structure that is expected to reflect…
We call change-point problem (CPP) the identification of changes in the probabilistic behavior of a sequence of observations. Solving the CPP involves detecting the number and position of such changes. In genetics the study of how and what…
In graph learning, maps between graphs and their subgraphs frequently arise. For instance, when coarsening or rewiring operations are present along the pipeline, one needs to keep track of the corresponding nodes between the original and…
Atomic-resolution imaging with scanning transmission electron microscopy is a powerful tool for characterizing the nanoscale structure of materials, in particular features such as defects, local strains, and symmetry-breaking distortions.…
There is increasing interest in using high-energy collisions to probe the structure of nuclei, in particular with the high-precision data made possible by collisions performed with pairs of isobaric species. A systematic study requires a…
Determining protein structures at an atomic level remains a significant challenge in structural biology. We introduce $\texttt{RecCrysFormer}$, a hybrid model that exploits the strengths of transformers with the aim of integrating…
Open problems in the study of the nucleon structure using electromagnetic probes are discussed. The focus is on experimental aspects in the regime of strong interaction QCD. Significant progress in our understanding of the nucleon structure…
In this paper, we propose a novel concept for engineered molecular communication (MC) systems inspired by animal olfaction. We focus on a multi-user scenario where several transmitters wish to communicate with a central receiver. We assume…
Motivation: Assessing the match between two biomolecular structures is at the heart of structural analyses such as superposition, alignment and docking. These tasks are typically solved with specialized structure-matching techniques…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
We demonstrate a method to optically map multiple modes of mechanical structures simultaneously. The fast and robust method, based on a modified phase-lock-loop, is demonstrated on a silicon nitride membrane and compared with three…
One-dimensional NMR spectroscopy is one of the most widely used techniques for the characterization of organic compounds and natural products. For molecules with up to 36 non-hydrogen atoms, the number of possible structures has been…