Related papers: Two-dimensional RMSD projections for reaction path…
In the construction of reduced-order models for dynamical systems, linear projection methods, such as proper orthogonal decompositions, are commonly employed. However, for many dynamical systems, the lower dimensional representation of the…
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…
Ring-polymer molecular dynamics (RPMD) has become a popular method for describing chemical reactions due to its ability to simultaneously capture tunneling, zero-point energy, anharmonicity and recrossing. Here we highlight that despite its…
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…
Given a multidimensional free-energy or potential-energy landscape, finding reaction paths that connect an initial (or reactant) state and a final (or product) state is important for biophysics and materials science. The likelihood of a…
Transition path sampling (TPS) is a powerful technique for investigating rare transitions, especially when the mechanism is unknown and one does not have access to the reaction coordinate. Straightforward application of TPS does not…
The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…
In solar physics, a severe numerical challenge for modern simulations is properly representing a transition region between the million-degree hot corona and a much cooler plasma of about 10000 K (e.g., the upper chromosphere or a…
We derive new equations using the mixed-frame approach for one- and two-dimensional (axisymmetric) time-dependent radiation transport and the associated couplings with matter. Our formulation is multi-group and multi-angle and includes…
This study develops an algorithm to reproduce reaction route maps (RRMs) in shape space from the outputs of potential search algorithms. To demonstrate this, GRRM is utilized as a potential search algorithm but the proposed algorithm should…
Projection-based model reduction is among the most widely adopted methods for constructing parametric Reduced-Order Models (ROM). Utilizing the snapshot data from solving full-order governing equations, the Proper Orthogonal Decomposition…
Geophysical inversion should ideally produce geologically realistic subsurface models that explain the available data. Multiple-point statistics is a geostatistical approach to construct subsurface models that are consistent with…
Dynamical reweighting methods permit to estimate kinetic observables of a stochastic process governed by a target potential $\tilde{V}(x)$ from trajectories that have been generated at a different potential $V(x)$. In this article, we…
Synthetic molecular dynamics (synMD) trajectories from learned generative models have been proposed as a useful addition to the biomolecular simulation toolbox. The computational expense of explicitly integrating the equations of motion in…
Retrosynthetic planning aims to devise a complete multi-step synthetic route from starting materials to a target molecule. Current strategies use a decoupled approach of single-step retrosynthesis models and search algorithms, taking only…
Magnetic reconnection is an explosive process that accelerates particles to high energies in Earth's magnetosphere, offering a unique natural laboratory to study this phenomenon. This study investigates how well data-driven fully kinetic…
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…
The identification of trajectories that contribute to the reaction rate is the crucial dynamical ingredient in any classical chemical reactivity calculation. This problem often requires a full scale numerical simulation of the dynamics, in…
Microstructure reconstruction and compression techniques are designed to find a microstructure with desired properties. While the microstructure reconstruction searches for a microstructure with prescribed statistical properties, the…
The extension of mixed quantum/classical theory (MQCT) to describe collisional energy transfer is developed for symmetric-top-rotor + linear-rotor system type and is applied to $ \rm ND_3 + \rm D_2 $. State-to-state transition cross…