Related papers: PASTA: Python Algorithms for Searching Transition …
In this article, we review the analytical and numerical approaches for computing the phase space structures in two degrees-of-freedom Hamiltonian systems that arise in chemical reactions. In particular, these phase space structures are the…
The bandgap constitutes a challenging problem in density functional theory (DFT) methodologies. It is known that the energy gap values calculated by common DFT approaches are underestimated. The bandgap was also found to be related to the…
Real-time time-dependent density functional theory (rt-TDDFT) is a well-established method for studying the dynamic response of matter in the femtosecond or optical range. In this method, the Kohn-Sham (KS) wave functions are propagated…
We show that neural networks can be optimized to represent minimum energy paths as continuous functions, offering a flexible alternative to discrete path-search methods such as Nudged Elastic Band (NEB). Our approach parameterizes reaction…
The MechElastic Python package evaluates the mechanical and elastic properties of bulk and 2D materials using the elastic coefficient matrix ($C_{ij}$) obtained from any ab-initio density-functional theory (DFT) code. The current version of…
Significant progress has been made recently in the automation and standardization of ab initio point defect calculations. However, the task of developing, implementing, and benchmarking charge corrections for density functional theory (DFT)…
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…
In this paper we present an algorithm which allows single-stage direct Langevin dynamics simulations of transitions over arbitrary high energy barriers employing the concept of the energy-dependent temperature (EDT). In our algorithm,…
We present a new density-functional method of the self-consistent electronic-structure calculation which does not exploit any local density approximations (LDA). We use the exchange-correlation energy which consists of the exact exchange…
We present an efficient method to compute transition rates between states for a two-state system. The method utilizes the equivalence between steady-state flux and mean first passage rate for such systems. More specifically, the procedure…
Context: We present COSTA (COld STream finder Algorithm), a novel algorithm to search for cold kinematical substructures in the phase space of planetary nebulae (PNe) and globular clusters (GCs) in the halo of massive galaxies and…
The interpretation of the intensity and polarization of the spectral line radiation produced in the atmosphere of the Sun and of other stars requires solving a radiative transfer problem that can be very complex, especially when the main…
Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three…
The prompt online detection of abrupt changes in image data is essential for timely decision-making in broad applications, from video surveillance to manufacturing quality control. Existing methods, however, face three key challenges.…
Up to now, it is not possible to obtain analytical solutions for complex molecular association processes (e.g. Molecule recognition in Signaling or catalysis). Instead Brownian Dynamics (BD) simulations are commonly used to estimate the…
In a physical system, changing parameters such as temperature can induce a phase transition: an abrupt change from one state of matter to another. Analogous phenomena have recently been observed in large language models. Typically, the task…
Contemporary materials science research is heavily conducted in silico, involving massive simulations of the atomic-scale evolution of materials. Cataloging basic patterns in the atomic displacements is key to understanding and predicting…
The reliability of atomistic simulations depends on the quality of the underlying energy models providing the source of physical information, for instance for the calculation of migration barriers in atomistic Kinetic Monte Carlo…
The kinetics of collective rearrangements in solution, such as protein folding and nanocrystal phase transitions, often involve free energy barriers that are both long and rough. Applying methods of transition path sampling to harvest…
Bio-orthogonal click chemistry has become an indispensable part of the biochemist's toolbox. Despite the wide variety of applications that have been developed in recent years, only a limited number of bio-orthogonal click reactions have…