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Conceiving a molecule as composed of smaller molecular fragments, or subunits, is one of the pillars of the chemical and physical sciences, and leads to productive methods in quantum chemistry. Using a fragmentation scheme, efficient…
StructOpt, an open-source structure optimization suite, applies genetic algorithm and particle swarm methods to obtain atomic structures that minimize an objective function. The objective function typically consists of the energy and the…
ESPResSo 4.0 is an extensible simulation package for research on soft matter. This versatile molecular dynamics program was originally developed for coarse-grained simulations of charged systems Limbach et al., Comput. Phys. Commun. 174,…
We present TopoTB, a software package written in the Mathematica language, designed to compute electronic structures, topological properties, and phase diagrams based on tight-binding models. TopoTB is user-friendly, with an interactive…
The computational pipelines of single-particle cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) include an early particle-picking stage, in which a micrograph or tomogram is scanned to extract candidate particles,…
The Mixture-of-Experts (MoE) paradigm has emerged as a promising solution to scale up model capacity while maintaining inference efficiency. However, deploying MoE models across heterogeneous end-cloud environments poses new challenges in…
The interplay of electronic and nuclear degrees of freedom presents an outstanding problem in condensed matter physics and chemistry. Computational challenges arise especially for large systems, long time scales, in nonequilibrium, or in…
Cryo-electron tomography (cryo-ET) is an imaging technique that allows three-dimensional visualization of macro-molecular assemblies under near-native conditions. Cryo-ET comes with a number of challenges, mainly low signal-to-noise and…
Electronic structure calculations of molecular systems are among the most promising applications for fault-tolerant quantum computing (FTQC) in quantum chemistry and drug design. However, while recent algorithmic advancements such as…
Density matrix embedding theory (DMET) [Phys. Rev. Lett., 109, 186404 (2012)], introduced a new approach to quantum cluster embedding methods, whereby the mapping of strongly correlated bulk problems to an impurity with finite set of bath…
Quantum computational chemistry has emerged as an important application of quantum computing. Hybrid quantum-classical computing methods, such as variational quantum eigensolvers (VQE), have been designed as promising solutions to quantum…
Electromagnetically Induced Transparency (EIT) and Autler-Townes (AT) are two phenomena that could be featured by a variety of three-level atomic systems. The considered phenomena, EIT and AT, are similar "looking" in the sense that they…
The newly developed machine learning (ML) empirical pseudopotential (EP) method overcomes the poor transferability of the traditional EP method with the help of ML techniques while preserving its formal simplicity and computational…
Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current…
Measurement and analysis of high energetic particles for scientific, medical or industrial applications is a complex procedure, requiring the design of sophisticated detector and data processing systems. The development of adaptive and…
Quantum engineering requires controllable artificial systems with quantum coherence exceeding the device size and operation time. This can be achieved with geometrically confined low-dimensional electronic structures embedded within…
Electronic transitions involving core-level orbitals offer a localized, atomic-site and element specific peek window into statistical systems such as molecular liquids. Although formally understood, the complex relation between structure…
A review of the present status, recent enhancements, and applicability of the SIESTA program is presented. Since its debut in the mid-nineties, SIESTA's flexibility, efficiency and free distribution has given advanced materials simulation…
Existing text-driven infrared and visible image fusion approaches often rely on textual information at the sentence level, which can lead to semantic noise from redundant text and fail to fully exploit the deeper semantic value of textual…
The modulation and engineering of the free-electron wave function bring new ingredients to the electron-matter interaction. We study the dynamics of a free-electron passing by a two-level system fully quantum mechanically and emphasize the…