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Discovering the underlying dynamics of complex systems from data is an important practical topic. Constrained optimization algorithms are widely utilized and lead to many successes. Yet, such purely data-driven methods may bring about…
The dynamics of ecological as well as chemical systems may depend on heterogeneous configurations. Heterogeneity in reaction-diffusion systems often increase modelling and simulating difficulties when non-linear effects are present. One…
In this paper, we propose a data-driven method to discover multiscale chemical reactions governed by the law of mass action. First, we use a single matrix to represent the stoichiometric coefficients for both the reactants and products in a…
Searching for potential active compounds in large databases is a necessary step to reduce time and costs in modern drug discovery pipelines. Such virtual screening methods seek to provide predictions that allow the search space to be…
Drug discovery is a complex process that involves sequentially screening and examining a vast array of molecules to identify those with the target properties. This process, also referred to as sequential experimentation, faces challenges…
Coarse-grained modeling in molecular simulations serves not only to extend accessible time and length scales beyond atomistic limits, but also to reduce high-dimensional chemical data to low-dimensional representations that expose the…
Multivariate Hawkes process provides a powerful framework for modeling temporal dependencies and event-driven interactions in complex systems. While existing methods primarily focus on uncovering causal structures among observed…
Linear conjugacy offers a new perspective to broaden the scope of stable biochemical reaction networks to the systems linearly conjugated to the well-established complex balanced mass action systems ($\ell$cCBMASs). This paper addresses the…
In machine learning one of the strategic tasks is the selection of only significant variables as predictors for the response(s). In this paper an approach is proposed which consists in the application of permutation tests on the candidate…
Cataloging the complex behaviors of dynamical systems can be challenging, even when they are well-described by a simple mechanistic model. If such a system is of limited analytical tractability, brute force simulation is often the only…
Designing synthetic routes for novel molecules is pivotal in various fields like medicine and chemistry. In this process, researchers need to explore a set of synthetic reactions to transform starting molecules into intermediates step by…
Mathematical models are crucial for optimizing and controlling chemical processes, yet they often face significant limitations in terms of computational time, algorithm complexity, and development costs. Hybrid models, which combine…
Entanglement is a crucial resource for achieving quantum advantages in quantum computation, quantum sensing, and quantum communication. As shown in this Letter, entanglement is also a valuable resource for the coherent control of the large…
An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic,…
Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…
In chemical reaction network theory, ordinary differential equations are used to model the temporal change of chemical species concentration. As the functional form of these ordinary differential equations systems is derived from an…
Chemotaxis is the process by which cells behave in a way that follows the chemical gradient. Applications to bacteria growth, tissue inflammation, and vascular tumors provide a focus on optimization strategies. Experiments can characterize…
The sustainable production of many bulk chemicals relies on heterogeneous catalysis. The rational design or improvement of the required catalysts critically depends on insights into the underlying mechanisms at the atomic scale. In recent…
Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the natural reaction coordinate, suitable for condensed phase and biomolecular systems,…
High energy e$^+$e$^-$ colliders offer unique possibility for the most general dark matter search based on the mono-photon signature. Analysis of the energy spectrum and angular distributions of photons from the initial state radiation can…