Related papers: Multi-site Reaction Dynamics Through Multi-fragmen…
A nonperturbative electron transfer rate theory is developed based on the reduced density matrix dynamics, which can be evaluated readily for the Debye solvent model without further approximation. Not only does it recover for reaction rates…
Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…
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…
To determine the electron heat flux density on macroscopic scales, the most widely used approach is to solve a diffusion equation through a multi-group technique. This method is however restricted to transport induced by temperature…
We present a mathematical study for the development of Multiple Sclerosis in which a spatio-temporal kinetic { theory} model describes, at the mesoscopic level, the dynamics of a high number of interacting agents. We consider both…
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…
Nanostructures with open shell transition metal or molecular constituents host often strong electronic correlations and are highly sensitive to atomistic material details. This tutorial review discusses method developments and applications…
Matter at extreme temperatures and pressures -- commonly known as warm dense matter (WDM) in the literature -- is ubiquitous throughout our Universe and occurs in a number of astrophysical objects such as giant planet interiors and brown…
Non-uniform product (color) distribution in colorimetric paper-based sensors affects the accuracy and reliability of measurements. The underlying mechanisms responsible for this are still unclear. The coffee ring effect explains the…
The self consistent version of the density functional theory (DFT) is presented, which allows to calculate the ground state and dynamic properties of finite multi-electron systems such as atoms, molecules and clusters. The exact functional…
Large Genomic Foundation Models have recently achieved remarkable results and in-vivo translation capabilities. However these models quickly grow to over a few Billion of parameters and are expensive to run when compute is limited. To…
We describe a formulation of the density matrix embedding theory at finite temperature. We present a generalization of the ground-state bath orbital construction that embeds a mean-field finite-temperature density matrix up to a given order…
Theoretical work has shed light on the phase behavior of idealized mixtures of many components with random interactions. But typical mixtures interact through particular physical features, leading to a structured, non-random interaction…
This dissertation explores how deep generative models can advance the analysis of challenging biological problems by integrating domain knowledge with deep learning. It focuses on two areas: DNA reaction kinetics and cryogenic electron…
We present the advantages of a multiscale modelling strategy for the understanding of systems with charged interfaces. On the one hand, one can simulate a complex system at different levels, depending on the relevant length and time scales…
A combination of reaction-diffusion models with moving-boundary problems yields a system in which the diffusion (spreading and penetration) and reaction (transformation) evolve the system's state and geometry over time. These systems can be…
Machine learning has recently emerged as a powerful tool for generating new molecular and material structures. The success of state-of-the-art models stems from their ability to incorporate physical symmetries, such as translation,…
A subsystem approach for obtaining electron binding energies in the valence region and apply it to the case of halide ions (X$^-$, X = F-At) in water. This approach is based on electronic structure calculations combining the relativistic…
The accurate electronic structure calculation for strongly correlated chemical systems requires an adequate description for both static and dynamic electron correlation, and is a persistent challenge for quantum chemistry. In order to…
The tight binding model is a minimal electronic structure model for molecular modelling and simulation. We show that the total energy in this model can be decomposed into site energies, that is, into contributions from each atomic site…