Related papers: Finding reaction pathways with optimal atomic inde…
Determining transition states (TSs) of surface reactions is central to understanding and designing heterogeneous catalysts but remains computationally prohibitive with density functional theory (DFT). While machine learning potentials…
We compare Evolutionary Algorithms with Minima Hopping for global optimization in the field of cluster structure prediction. We introduce a new {\em average offspring} recombination operator and compare it with previously used operators.…
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…
To obtain an electron-density map from a macromolecular crystal the phase-problem needs to be solved, which often involves the use of heavy-atom derivative crystals and concomitantly the determination of the heavy atom substructure. This is…
Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and…
Model reduction methods are relevant when the computation time of a full convection-diffusion-reaction simulation based on detailed chemical reaction mechanisms is too large. In this article, we review a model reduction approach based on…
The minimum energy path (MEP) describes the mechanism of reaction, and the energy barrier along the path can be used to calculate the reaction rate in thermal systems. The nudged elastic band (NEB) method is one of the most commonly used…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
Geometry optimization is an important part of both computational materials and surface science because it is the path to finding ground state atomic structures and reaction pathways. These properties are used in the estimation of…
This paper proposes a learning-based approach to accelerate the interior-point method (IPM) for solving optimal power flow (OPF) problems by learning the structure of the IPM central path from its early stable iterations. Unlike traditional…
Understanding kinetics including reaction pathways and associated transition rates is an important yet difficult problem in numerous chemical and biological systems especially in situations with multiple competing pathways. When these…
We present a novel method, which we call dual minima hopping method (DMHM), that allows us to find the global minimum of the potential energy surface (PES) within density functional theory for systems where a fast but less accurate…
In recent years, deep learning has made remarkable strides, surpassing human capabilities in tasks like strategy games, and it has found applications in complex domains, including protein folding. In the realm of quantum chemistry, machine…
We extend the non-parametric framework of reaction coordinate optimization to non-equilibrium ensembles of (short) trajectories. For example, we show how, starting from such an ensemble, one can obtain an equilibrium free energy profile…
For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive…
The computational efficiency of stochastic simulation algorithms is notoriously limited by the kinetic trapping of the simulated trajectories within low energy basins. Here we present a new method that overcomes kinetic trapping while still…
A model Hamiltonian for the reaction CH$_4^+ \rightarrow$ CH$_3^+$ + H, parametrized to exhibit either early or late inner transition states, is employed to investigate the dynamical characteristics of the roaming mechanism. Tight/loose…
Atom tunneling in the hydrogen atom transfer reaction of the 2,4,6-tri-tert-butylphenyl radical to 3,5-di-tert-butylneophyl, which has a short but strongly curved reaction path, was investigated using instanton theory. We found the…
Nonequilibrium phase transitions are notably difficult to analyze because their mechanisms depend on the system's dynamics in a complex way due to the lack of time-reversal symmetry. To complicate matters, the system's steady-state…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…