Related papers: Electronic Collective Variables for Chemical React…
The bottleneck in enhanced sampling lies in finding collective variables (CVs) that can effectively accelerate protein conformational changes. True reaction coordinates (tRCs) that can predict the committor are considered the optimal CVs,…
Enhanced sampling methods are indispensable in computational physics and chemistry, where atomistic simulations cannot exhaustively sample the high-dimensional configuration space of dynamical systems due to the sampling problem. A class of…
We propose a novel measure valued process which models the behaviour of chemical reaction networks in spatially heterogeneous systems. It models reaction dynamics between different molecular species and continuous movement of molecules in…
In modern day simulations of many-body systems much of the computational complexity is shifted to the identification of slowly changing molecular order parameters called collective variables (CV) or reaction coordinates. A vast array of…
Computing accurate reaction rates is a central challenge in computational chemistry and biology because of the high cost of free energy estimation with unbiased molecular dynamics. In this work, a data-driven machine learning algorithm is…
We introduce EChemDID, a model to describe electrochemical driving force in reactive molecular dynamics simulations. The method describes the equilibration of external electrochemical potentials (voltage) within metallic structures and…
Understanding the evolution of electrified solid-liquid interfaces during electrochemical reactions is crucial. However, capturing the dynamic behavior of the interfaces with high temporal resolution and accuracy over long timescales…
Accurately predicting chemical reaction outcomes and potential byproducts is a fundamental task of modern chemistry, enabling the efficient design of synthetic pathways and driving progress in chemical science. Reaction mechanism, which…
Collective variable (CV) or order parameter based enhanced sampling algorithms have achieved great success due to their ability to efficiently explore the rough potential energy landscapes of complex systems. However, the degeneracy of…
A mathematical model for chemical reactions in electrolytes is developed using an Energy variational method consistent with classical thermodynamics. Electrostatics and chemical reactions are included in properly defined energetic and…
Quantum-mechanically-driven charge polarization and charge transfer are ubiquitous in biomolecular systems, controlling reaction rates, allosteric interactions, ligand-protein binding, membrane transport, and dynamically-driven structural…
We lay the foundation of a circuit theory for chemical reaction networks. Chemical reactions are grouped into chemical modules solely characterized by their current-concentration characteristic, as electrical devices by their…
Quantum Molecular Dynamics (QMD) calculations of central collisions between heavy nuclei are used to study fragment production and the creation of collective flow. It is shown that the final phase space distributions are compatible with the…
Electronic coherences are key to understanding and controlling photo-induced molecular transformations. We identify a crucial quantum-mechanical feature of electron-nuclear correlation, the projected nuclear quantum momenta, essential to…
The study of electronic transitions within a molecule connected to the absorption or emission of light is a common task in the process of the design of new materials. The transitions are complex quantum mechanical processes and a detailed…
Classical theories of chemical kinetics assume independent reactions in dilute solutions, whose rates are determined by mean concentrations. In condensed matter, strong interactions alter chemical activities and create inhomogeneities that…
Chemical bonding is the stabilization of a composite molecular system caused by different interactions in and between the subsystems, among the strong kinds of bonding is covalent bonding especially important. Characteristic for covalent…
Investigating processes in complex molecular systems, which are characterized by many variables, is a crucial problem in computational physics. These systems can be reduced to a few meaningful degrees of freedom known as collective…
We propose a new and general formalism for elementary chemical reactions where quantum electronic variables are used as reaction coordinates. This formalism is in principle applicable to all kinds of chemical reactions ionic or covalent.…
In this second paper we complete the classical description of an isolated system of "charged positive-energy particles, with Grassmann-valued electric charges and mutual Coulomb interaction, plus a transverse electro-magnetic field" in the…