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\texttt{aurel} is an open-source Python package designed to \emph{au}tomatically calculate \emph{rel}ativistic quantities. It uses an efficient, flexible and user-friendly caching and dependency-tracking system, ideal for managing the…

Instrumentation and Methods for Astrophysics · Physics 2026-02-13 Robyn L. Munoz , Christian T. Byrnes , Will J. Roper

The Poynting effect generically manifests itself as the extension of the material in the direction perpendicular to an applied shear deformation (torsion) and is a material parameter hard to design. Unlike isotropic solids, in designed…

Soft Condensed Matter · Physics 2022-07-12 Aref Ghorbani , David Dykstra , Corentin Coulais , Daniel Bonn , Erik van der Linden , Mehdi Habibi

We present KITE, a general purpose open-source tight-binding software for accurate real-space simulations of electronic structure and quantum transport properties of large-scale molecular and condensed systems with tens of billions of…

Mesoscale and Nanoscale Physics · Physics 2020-03-16 Simão M. João , Miša Anđelković , Lucian Covaci , Tatiana Rappoport , João M. V. P. Lopes , Aires Ferreira

We present assembly-theory, a Rust package for computing assembly indices of covalently bonded molecular structures. This is a key complexity measure of assembly theory, a recent theoretical framework quantifying selection across diverse…

The minimum spanning tree (MST), a graph constructed from a distribution of points, draws lines between pairs of points so that all points are linked in a single skeletal structure that contains no loops and has minimal total edge length.…

Instrumentation and Methods for Astrophysics · Physics 2019-10-22 Krishna Naidoo

The MIRS software for the modeling of ro-vibrational spectra of polyatomic molecules was considerably extended and improved. The original version (Nikitin, et al. JQSRT, 2003, pp. 239--249) was especially designed for separate or…

Atmospheric and Oceanic Physics · Physics 2012-05-15 Andrei Nikitin , Michaël Rey , Jean Paul Champion , Vladimir Tyuterev

Moir\'e structures formed by twisting three layers of graphene with two independent twist angles present an ideal platform for studying correlated quantum phenomena, as an infinite set of angle pairs is predicted to exhibit flat bands.…

relentless is an open-source Python package that enables the optimization of objective functions computed using molecular dynamics simulations. It has a high-level, extensible interface for model parametrization; setting up, running, and…

Soft Condensed Matter · Physics 2024-08-07 Adithya N Sreenivasan , C. Levi Petix , Zachary M. Sherman , Michael P. Howard

Quantum transport has far-reaching applications in modern electronics as it enables the control of currents in nanoscale systems such as quantum dots. In this paper we introduce tinie: a state-of-the-art quantum transport simulation…

Mesoscale and Nanoscale Physics · Physics 2021-09-23 R. Duda , J. Keski-Rahkonen , J. Solanpää , E. Räsänen

This thesis details a Python-based software designed to calculate the Jones polynomial, a vital mathematical tool from Knot Theory used for characterizing the topological and geometrical complexity of curves in \( \mathbb{R}^3 \), which is…

Mathematical Software · Computer Science 2024-10-31 Caleb Musfeldt

Processing of medical images such as MRI or CT presents unique challenges compared to RGB images typically used in computer vision. These include a lack of labels for large datasets, high computational costs, and metadata to describe the…

Image and Video Processing · Electrical Eng. & Systems 2021-08-06 Fernando Pérez-García , Rachel Sparks , Sébastien Ourselin

The interplay of twist and strain in bilayer graphene enables the formation of moir\'e patterns and narrow bands that host correlated and topological phases. While magic-angle twisted bilayer graphene has been widely studied, strain…

Mesoscale and Nanoscale Physics · Physics 2026-03-10 Federico Escudero , Dong Wang , Pierre A. Pantaleón , Shengjun Yuan , Francisco Guinea , Zhen Zhan

Mooney images are high-contrast, two-tone visual stimuli, created by thresholding photographic images. They allow researchers to separate image content from image understanding, making them valuable for studying visual perception. An ideal…

Neurons and Cognition · Quantitative Biology 2026-01-21 Lars C. Reining , Thabo Matthies , Luisa Haussner , Rabea Turon , Thomas S. A. Wallis

We present an open-source software for the simulation of observables in magnetic resonance experiments, including nuclear magnetic/quadrupole resonance NMR/NQR and electron spin resonance (ESR), developed to assist experimental research in…

Structure-informed materials informatics is a rapidly evolving discipline of materials science relying on the featurization of atomic structures or configurations to construct vector, voxel, graph, graphlet, and other representations useful…

Materials Science · Physics 2024-12-17 Adam M. Krajewski , Jonathan W. Siegel , Zi-Kui Liu

The exotic internal structure of polar topologies in multi-ferroic materials offers a rich landscape for materials science research. As the spatial scale of these entities are often sub-atomic in nature, aberration corrected transmission…

Tensor decompositions have become essential tools for feature extraction and compression of multiway data. Recent advances in tensor operators have enabled desirable properties of standard matrix algebra to be retained for multilinear…

Numerical Analysis · Mathematics 2024-10-01 Katherine Keegan , Elizabeth Newman

Quantitative understanding of the spatial distribution of magnetic fields and Meissner screening currents in two-dimensional (2D) superconductors and mesoscopic thin film superconducting devices is critical to interpreting the results of…

Superconductivity · Physics 2022-07-28 Logan Bishop-Van Horn , Kathryn A. Moler

Recent advances in the manipulation of complex oxide layers, particularly the fabrication of atomically thin cuprate superconducting films via molecular beam epitaxy, have revealed new ways in which nanoscale engineering can govern…

We present the design of a flexible quantum-chemical method development framework, which supports employing any type of basis function. This design has been implemented in the light-weight program package molsturm, yielding a…

Chemical Physics · Physics 2018-11-15 Michael F. Herbst , Andreas Dreuw , James Emil Avery