Related papers: PASTA: Python Algorithms for Searching Transition …
Shortcuts to adiabaticity (STA) are fast routes to the final results of slow, adiabatic changes of the controlling parameters of a system. The shortcuts are designed by a set of analytical and numerical methods suitable for different…
Instanton theory is an established method to calculate rate constants of chemical reactions including atom tunneling. Technical and methodological improvements increased its applicability. Still, a large number of energy and gradient…
Aims. Chemical databases such as the UMIST Database for Astrochemistry (UDFA) are indispensable in the numerical modeling of astrochemical networks. Several of the listed reactions in the UDFA have properties that are problematic in…
The cross sections for the $p p \to p p \eta$ reaction are evaluated at energies relevant for the HADES, PANDA, and SIS100 experiments at GSI-FAIR. Consideration includes the $\eta$-bremsstrahlung mechanism involving intermediate proton…
CONQUEST is a DFT code which was designed from the beginning to enable extremely large-scale calculations on massively parallel platforms, implementing both exact and linear scaling solvers for the ground state. It uses local basis sets…
Zeolites are important for industrial catalytic processes involving organic molecules. Understanding molecular reaction mechanisms within the confined nanoporous environment can guide the selection of pore topologies, material compositions,…
Transition interface sampling (TIS) and replica exchange TIS (RETIS) are powerful methods for computing rates of rare events inaccessible to straightforward molecular dynamics (MD) simulations. Path reweighting extends their output,…
Identifying transition states (TSs), the high-energy configurations that molecules pass through during chemical reactions, is essential for understanding and designing chemical processes. However, accurately and efficiently identifying…
In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance nucleation, protein folding, and chemical reactions. For these…
Simulated tempering (ST) has attracted a great deal of attention in the last years, due to its capability to allow systems with complex dynamics to escape from regions separated by large entropic barriers. However its performance is…
We present a state-space-based path integral method to calculate the rate of electron transfer (ET) in multi-state, multi-electron condensed-phase processes. We employ an exact path integral in discrete electronic states and continuous…
One of the most important and difficult parts of constructing a multidimensional numerical simulation of flame acceleration and deflagration-to-detonation transition (DDT) in a reacting flow is finding a reliable and affordable model of the…
By transforming identification and control for nonlinear system into optimization problems, a novel optimization method named state transition algorithm (STA) is introduced to solve the problems. In the proposed STA, a solution to a…
Drawing on theoretical insights, we advocate an error-based thresholding (EBT) mechanism for learned ISTA (LISTA), which utilizes a function of the layer-wise reconstruction error to suggest a specific threshold for each observation in the…
This paper provides a new way of developing the fast iterative shrinkage/thresholding algorithm (FISTA) that is widely used for minimizing composite convex functions with a nonsmooth term such as the $\ell_1$ regularizer. In particular,…
Disentangling the mechanistic details of a chemical reaction pathway is a hard problem that often requires a considerable amount of chemical intuition and a component of luck. Experiments struggle in observing short-life metastable…
The prediction of reaction pathways for solid-solid transformations remains a key challenge. Here, we develop a pathway sampling method via swarm intelligence and graph theory, and demonstrate that our PALLAS method is an effective tool to…
Global optimization of crystal compositions is a significant yet computationally intensive method to identify stable structures within chemical space. The specific physical properties linked to a three-dimensional atomic arrangement make…
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…
"Leaping" methods show great promise for significantly accelerating stochastic simulations of complex biochemical reaction networks. However, few practical applications of leaping have appeared in the literature to date. Here, we address…