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Recent advances in microscopy and 3D reconstruction methods have allowed for characterization of cellular morphology in unprecedented detail, including the irregular geometries of intracellular subcompartments such as membrane-bound…
Establishing viable solid-state synthesis pathways for novel inorganic materials remains a major challenge in materials science. Previous pathway design methods using pair-wise reaction approaches have navigated the thermodynamic landscape…
Computational chemistry has become an indispensable tool for generating data and insights, pervading all branches of experimental chemistry. Its most central concept is the potential energy hypersurface, key to all chemistry and materials…
Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and post-reaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that…
Chemical plants are complex and dynamical systems consisting of many components for manipulation and sensing, whose state transitions depend on various factors such as time, disturbance, and operation procedures. For the purpose of…
Chemical reactions are a prominent feature of molecular communication (MC) systems, with no direct parallels in wireless communications. While chemical reactions may be used inside the transmitter nodes, receiver nodes or the communication…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
The study of rare events in molecular and atomic systems such as conformal changes and cluster rearrangements has been one of the most important research themes in chemical physics. Key challenges are associated with long waiting times…
Computing long-timescale kinetics of biomolecular processes remains a major challenge for atomistic simulations. A way out is to exploit local kinetic information to construct the global stationary flux across the reaction space. The…
The path integral approach offers not only an exact expression for the non- equilibrium dynamics of dissipative quantum systems, but is also a convenient starting point for perturbative treatments. An alternative way to explore the…
The chemistry of an astrophysical environment is closely coupled to its dynamics, the latter often found to be complex. Hence, to properly model these environments a 3D context is necessary. However, solving chemical kinetics within a 3D…
Temporal causal representation learning methods assume that causal mechanisms switch instantaneously between discrete domains, yet real-world systems often exhibit continuous mechanism transitions. For example, a vehicle's dynamics evolve…
In a dynamical system, the transition between reactants and products is typically mediated by an energy barrier whose properties determine the corresponding pathways and rates. The latter is the flux through a dividing surface (DS) between…
Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity (e.g. a protein) in all its states (free, bound, degraded, etc.). In…
The need for clear, trustworthy explanations of deep learning model predictions is essential for high-criticality fields, such as medicine and biometric identification. Class Activation Maps (CAMs) are an increasingly popular category of…
Machine-learned interatomic potentials (MLPs) provide near density functional theory (DFT) accuracy at reduced computational cost, but their reliability depends on representative training data and often deteriorates in transition-state…
Ultrafast charge transfer (CT) processes redistribute electronic charge within and between molecular units and play a central role in many physical, chemical, and biological phenomena. However, the microscopic pathways of multiple CT…
Chemical potential of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot satisfy a constant chemical potential…
We introduce a new method for transforming chemical systems into desired logical operators (e.g. NAND-gates) or similar signal-manipulation components. The method is based upon open-loop dynamic regulation, where external conditions such as…
We present a general approach to isolate chemical reaction mechanism as an independently controllable variable across chemically distinct systems. Modern approaches to reduce the computational expense of molecular dynamics simulations often…