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The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…
Various biological system models have been proposed in systems biology, which are based on the complex biological reactions kinetic of various components. These models are not practical because we lack of kinetic information. In this paper,…
Subsystem Density-Functional Theory (DFT) is an emerging technique for calculating the electronic structure of complex molecular and condensed phase systems. In this topical review, we focus on some recent advances in this field related to…
Many scientific and engineering systems exhibit intrinsically multimodal behavior arising from latent regime switching and non-unique physical mechanisms. In such settings, learning the full conditional distribution of admissible outcomes…
Surfaces serve as highly efficient catalysts for a vast variety of chemical reactions. Typically, such surface reactions involve billions of molecules which diffuse and react over macroscopic areas. Therefore, stochastic fluctuations are…
Molecular modeling of thermally activated chemistry in condensed phases is essential to understand polymerization, depolymerization, and other processing steps of molecular materials. Current methods typically combine molecular dynamics…
Which reaction networks, when taken with mass-action kinetics, have the capacity for multiple steady states? There is no complete answer to this question, but over the last 40 years various criteria have been developed that can answer this…
Quantum embedding methods enable the study of large, strongly correlated quantum systems by (usually self-consistent) decomposition into computationally manageable subproblems, in the spirit of divide-and-conquer methods. Among these,…
Temperature gradients represent energy sources that can be harvested to generate steady reaction or transport fluxes. Technological developments could lead to the transfer of free energy from heat sources and sinks to chemical systems for…
We formulate a continuum electro-chemo-mechanical gradient theory which couples electrochemical reactions with mechanical deformation and damage in solids. The framework models species transport across the host due to diffusion/migration…
Phase separation is the thermodynamic process that explains how droplets form in multicomponent fluids. These droplets can provide controlled compartments to localize chemical reactions, and reactions can also affect the droplets' dynamics.…
In this paper, we propose an optimization-based sparse learning approach to identify the set of most influential reactions in a chemical reaction network. This reduced set of reactions is then employed to construct a reduced chemical…
The theory of patterns formation for a reaction-diffusion system defined on a multiplex is developed by means of a perturbative approach. The intra-layer diffusion constants act as small parameter in the expansion and the unperturbed state…
Site density functional theory (SDFT) provides a rigorous framework for statistical mechanics analysis of inhomogeneous molecular liquids. The key defining feature of these systems is the presence of two very distinct interactions scales…
We present a general computational protocol for the evaluation of extensive molecular response properties in complex environments within a polarizable quantum embedding framework. The approach extends multilevel density functional theory…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
Processes involving multi-input multi-step reaction cascades are used in developing novel biosensing, biocomputing, and decision making systems. In various applications different changes in responses of the constituent processing steps…
Quantum embedding methods have recently developed significantly to model large molecular structures. This work proposes a novel wave function theory in density functional theory (WTF-in-DFT) embedding scheme based on pair-coupled cluster…
This article provides the first mathematical analysis of the Density Matrix Embedding Theory (DMET) method. We prove that, under certain assumptions, (i) the exact ground-state density matrix is a fixed-point of the DMET map for…
Chemical reaction network theory is a field of applied mathematics concerned with modeling chemical systems, and can be used in other contexts such as in systems biology to study cellular signaling pathways or epidemiology to study the…