Statistical physics
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Power-law distributions in empirical data Open
Power-law distributions occur in many situations of scientific interest and have significant consequences for our understanding of natural and man-made phenomena. Unfortunately, the empirical detection and characterization of power laws is…
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Joint effect of ageing and multilayer structure prevents ordering in the voter model Open
The voter model rules are simple, with agents copying the state of a random neighbor, but they lead to non-trivial dynamics. Besides opinion processes, the model has also applications for catalysis and species competition. Inspired by the …
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DiffuCpG Open
DiffuCpG 1. Introduction In this study, we used a generative AI diffusion model to address missing methylation data. We trained the model with Whole-Genome Bisulfite Sequencing data from 26 acute myeloid leukemia samples and validated it w…
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The ORCA quantum chemistry program package Open
In this contribution to the special software-centered issue, the ORCA program package is described. We start with a short historical perspective of how the project began and go on to discuss its current feature set. ORCA has grown into a r…
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GFN2-xTB—An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions Open
An extended semiempirical tight-binding model is presented, which is primarily designed for the fast calculation of structures and noncovalent interaction energies for molecular systems with roughly 1000 atoms. The essential novelty in thi…
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CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations Open
CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling…
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LOBSTER: A tool to extract chemical bonding from plane‐wave based DFT Open
The computer program LOBSTER (Local Orbital Basis Suite Towards Electronic‐Structure Reconstruction) enables chemical‐bonding analysis based on periodic plane‐wave (PAW) density‐functional theory (DFT) output and is applicable to a wide ra…
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Active Particles in Complex and Crowded Environments Open
Differently from passive Brownian particles, active particles, also known as self-propelled Brownian particles or microswimmers and nanoswimmers, are capable of taking up energy from their environment and converting it into directed motion…
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The coefficient of determination <i>R</i> <sup>2</sup> and intra-class correlation coefficient from generalized linear mixed-effects models revisited and expanded Open
The coefficient of determination R 2 quantifies the proportion of variance explained by a statistical model and is an important summary statistic of biological interest. However, estimating R 2 for generalized linear mixed models (GLMMs) r…
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Improvements to the <span>APBS</span> biomolecular solvation software suite Open
The Adaptive Poisson–Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and …
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Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals Open
In the past 30 years, Kohn–Sham density functional theory has emerged as the most popular electronic structure method in computational chemistry. To assess the ever-increasing number of approximate exchange-correlation functionals, this re…
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Solving the quantum many-body problem with artificial neural networks Open
Machine learning and quantum physics Elucidating the behavior of quantum interacting systems of many particles remains one of the biggest challenges in physics. Traditional numerical methods often work well, but some of the most interestin…
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ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution Open
Molecular dynamics (MD) simulations have become increasingly popular in studying the motions and functions of biomolecules. The accuracy of the simulation, however, is highly determined by the molecular mechanics (MM) force field (FF), a s…
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Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics Open
We introduce a scheme for molecular simulations, the deep potential molecular dynamics (DPMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data. T…
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Simulating galaxy formation with the IllustrisTNG model Open
We introduce an updated physical model to simulate the formation and\nevolution of galaxies in cosmological, large-scale\ngravity+magnetohydrodynamical simulations with the moving mesh code AREPO. The\noverall framework builds upon the suc…
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A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions Open
We present the updated and extended GMTKN55 benchmark database for more accurate and extensive energetic evaluation of density functionals and other electronic structure methods with detailed guidelines for method users.
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Remarks on the Sachdev-Ye-Kitaev model Open
We study a quantum mechanical model proposed by Sachdev, Ye and Kitaev. The model consists of N Majorana fermions with random interactions of a few fermions at a time. It it tractable in the large N limit, where the classical variable is a…
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<i>Colloquium</i>: Many-body localization, thermalization, and entanglement Open
Thermalizing quantum systems are conventionally described by statistical\nmechanics at equilibrium. However, not all systems fall into this category,\nwith many body localization providing a generic mechanism for thermalization to\nfail in…
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QuantumATK: an integrated platform of electronic and atomic-scale modelling tools Open
QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been pr…
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<i>Colloquium</i>: Quantum coherence as a resource Open
The coherent superposition of states, in combination with the quantization of observables, represents one of the most fundamental features that mark the departure of quantum mechanics from the classical realm. Quantum coherence in many-bod…
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Reynolds averaged turbulence modelling using deep neural networks with embedded invariance Open
There exists significant demand for improved Reynolds-averaged Navier–Stokes (RANS) turbulence models that are informed by and can represent a richer set of turbulence physics. This paper presents a method of using deep neural networks to …
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Scaling Laws for Neural Language Models Open
We study empirical scaling laws for language model performance on the cross-entropy loss. The loss scales as a power-law with model size, dataset size, and the amount of compute used for training, with some trends spanning more than seven …
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First results from the IllustrisTNG simulations: the galaxy colour bimodality Open
We introduce the first two simulations of the IllustrisTNG project, a next generation of cosmological magnetohydrodynamical simulations, focusing on the optical colours of galaxies. We explore TNG100, a rerun of the original Illustris box,…
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Adiabatic quantum computation Open
Adiabatic quantum computing (AQC) started as an approach to solving optimization problems, and has evolved into an important universal alternative to the standard circuit model of quantum computing, with deep connections to both classical …
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Perspective: Machine learning potentials for atomistic simulations Open
Nowadays, computer simulations have become a standard tool in essentially all fields of chemistry, condensed matter physics, and materials science. In order to keep up with state-of-the-art experiments and the ever growing complexity of th…
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Extended <span>tight‐binding</span> quantum chemistry methods Open
This review covers a family of atomistic, mostly quantum chemistry (QC) based semiempirical methods for the fast and reasonably accurate description of large molecules in gas and condensed phase. The theory is derived from a density functi…
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Moment Tensor Potentials: A Class of Systematically Improvable Interatomic Potentials Open
Density functional theory offers a very accurate way of computing materials\nproperties from first principles. However, it is too expensive for modelling\nlarge-scale molecular systems whose properties are, in contrast, computed using\nint…
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Secure quantum key distribution with realistic devices Open
In principle, quantum key distribution (QKD) offers information-theoretic security based on the laws of physics. In practice, however, the imperfections of realistic devices might introduce deviations from the idealized models used in secu…
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Turbulence Modeling in the Age of Data Open
Data from experiments and direct simulations of turbulence have historically been used to calibrate simple engineering models such as those based on the Reynolds-averaged Navier–Stokes (RANS) equations. In the past few years, with the avai…
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First-principles Phonon Calculations with Phonopy and Phono3py Open
Harmonic, quasi-harmonic, and anharmonic phonon properties of crystals are getting to be better predicted using first-principles phonon calculations by virtue of the progress of the calculation methods and increasing computer power. In thi…