wfl Python Toolkit for Creating Machine Learning Interatomic Potentials and Related Atomistic Simulation WorkflowsPredictive atomistic simulations are increasingly employed for data intensive high throughput studies that take advantage of constantly growing computational resources. To handle the sheer number of…Elena Gelžinytė, Simon Wengert, Tamás K. Stenczel et al.·Jun 20, 2023SaveLearn
Automatic Generation of Accurate and Cost-efficient Auxiliary Basis SetsWe have recently discussed an algorithm to automatically generate auxiliary basis sets (ABSs) of the standard form for density fitting (DF) or resolution-of-the-identity (RI) calculations in a given…Susi Lehtola·Jun 19, 2023SaveLearn
Physics Constrained Unsupervised Deep Learning for Rapid, High Resolution Scanning Coherent Diffraction ReconstructionBy circumventing the resolution limitations of optics, coherent diffractive imaging (CDI) and ptychography are making their way into scientific fields ranging from X-ray imaging to astronomy. Yet,…Oliver Hoidn, Aashwin Ananda Mishra, Apurva Mehta·Jun 19, 2023SaveLearn
General Local Reactive Boundary Condition for Dissolution and Precipitation Using the Lattice Boltzmann MethodA general and local reactive boundary condition (RBC) for studying first-order equilibrium reactions using the lattice Boltzmann method (LBM) is presented. Its main characteristics are accurate…Julius Weinmiller, Martin P. Lautenschlaeger, Benjamin Kellers et al.·Jun 19, 2023SaveLearn
Machine learning of hidden variables in multiscale fluid simulationSolving fluid dynamics equations often requires the use of closure relations that account for missing microphysics. For example, when solving equations related to fluid dynamics for systems with a…Archis S. Joglekar, Alexander G. R. Thomas·Jun 19, 2023SaveLearn
A filtered embedded weighted compact nonlinear scheme for hyperbolic conservation lawIn situations where a wide range of flow scales are involved, the nonlinear scheme used should be capable of both shock capturing and low-dissipation.Most of the existing WCNS schemes are too…Xuan Liu, Yaobing Min, Jinsheng Cai et al.·Jun 16, 2023SaveLearn
Why solvent response contributions to solvation free energies are compatible with Ben-Naim's theoremWe resolve a seeming paradox arising from a common misinterpretation of Ben-Naim's theorem, which rests on a pairwise decomposition of the Hamiltonian of a molecular solute/solvent system into…Leonard P. Heinz, Helmut Grubmüller·Jun 15, 2023SaveLearn
Adjusting the numerical viscosity in the Godunov-like SPH method at modeling compressible flowsThe paper proposes a way to control the viscosity of numerical approximation in the contact SPH method. This variant of SPH contains momentum and energy fluxes in the right-hand sides of the…A. N. Parshikov, S. A. Medin, G. D. Rublev et al.·Jun 14, 2023SaveLearn
Reduced-order Modeling on a Near-term Quantum ComputerQuantum computing is an advancing area of research in which computer hardware and algorithms are developed to take advantage of quantum mechanical phenomena. In recent studies, quantum algorithms…Katherine Asztalos, René Steijl, Romit Maulik·Jun 13, 2023SaveLearn
Hybrid-Delta Tracking on a Structured Mesh in MCATKMonte Carlo Application Toolkit (MCATK) commonly uses surface tracking on a structured mesh to compute scalar fluxes. In this mode, higher fidelity requires more mesh cells and isotopes and thus more…J. P. Morgan, Travis J. Trahan, Timothy P. Burke et al.·Jun 13, 2023SaveLearn
Transferable Machine Learning Approach for Predicting Electronic Structures of Charged DefectsThe study of the electronic properties of charged defects is crucial for our understanding of various electrical properties of materials. However, the high computational cost of density functional…Yuxing Ma, Yang Zhong, Yu Hongyu et al.·Jun 13, 2023SaveLearn
Towards a Machine-Learned Poisson Solver for Low-Temperature Plasma Simulations in Complex GeometriesPoisson's equation plays an important role in modeling many physical systems. In electrostatic self-consistent low-temperature plasma (LTP) simulations, Poisson's equation is solved at each…Ihda Chaerony Siffa, Markus M. Becker, Klaus-Dieter Weltmann et al.·Jun 13, 2023SaveLearn
Nanomechanical behavior of pentagraphyne-based single-layer and nanotubes through reactive classical molecular dynamicsIn a recent theoretical study, a new 2D carbon allotrope called pentagraphyne (PG-yne) was proposed. This allotrope is derived from pentagraphene by introducing acetylenic linkages between sp3 and…J. M. De Sousa, W. H. S. Brandão, W. L. A. P. Silva et al.·Jun 12, 2023SaveLearn
Reliable machine learning potentials based on artificial neural network for grapheneGraphene is one of the most researched two dimensional (2D) material due to its unique combination of mechanical, thermal and electrical properties. Special 2D structure of graphene enables it to…Akash Singh, Yumeng Li·Jun 12, 2023SaveLearn
Numerically stable neural network for simulating Kardar-Parisi-Zhang growth in the presence of uncorrelated and correlated noisesNumerical simulations are essential tools for exploring the dynamic scaling properties of the nonlinear Kadar-Parisi-Zhang (KPZ) equation. Yet the inherent nonlinearity frequently causes numerical…Tianshu Song, Hui Xia·Jun 12, 2023SaveLearn
Spin-flip dynamics in core-excited states in the basis of irreducible spherical tensor operatorsRecent experimental advances in ultrafast science put different processes occurring on the electronic timescale below a few femtoseconds in focus. In the present theoretical work, we demonstrate how…Thies Romig, Vladislav Kochetov, Sergey I. Bokarev·Jun 11, 2023SaveLearn
On the unimportance of memory for the time non-local components of the Kadanoff-Baym equationsThe generalized Kadanoff-Baym ansatz (GKBA) is an approximation to the Kadanoff-Baym equations (KBE), that neglects certain memory effects that contribute to the Green's function at non-equal times.…Cian C. Reeves, Yuanran Zhu, Chao Yang et al.·Jun 9, 2023SaveLearn
Bridging Scales: a Hybrid Model to Simulate Vascular Tumor Growth and Treatment ResponseCancer is a disease driven by random DNA mutations and the interaction of many complex phenomena. To improve the understanding and ultimately find more effective treatments, researchers leverage…Tobias Duswald, Ernesto A. B. F. Lima, J. Tinsley Oden et al.·Jun 9, 2023SaveLearn
Laser-induced alignment of nanoparticles and macromolecules for single-particle-imaging applicationsLaser-induced alignment of particles and molecules was long envisioned to support three-dimensional structure determination using "single-molecule diffraction" with x-ray free-electron lasers [PRL…Muhamed Amin, Jean-Michel Hartmann, Amit K. Samanta et al.·Jun 9, 2023SaveLearn
Bayesian model calibration for diblock copolymer thin film self-assembly using power spectrum of microscopy data and machine learning surrogateIdentifying parameters of computational models from experimental data, or model calibration, is fundamental for assessing and improving the predictability and reliability of computer simulations. In…Lianghao Cao, Keyi Wu, J. Tinsley Oden et al.·Jun 8, 2023SaveLearn
Numerical coupling of aerosol emissions, dry removal, and turbulent mixing in the E3SM Atmosphere Model version 1 (EAMv1), part I: dust budget analyses and the impacts of a revised coupling schemeAn earlier study evaluating the dust life cycle in the Energy Exascale Earth System Model (E3SM) Atmosphere Model version 1 (EAMv1) has revealed that the simulated global mean dust lifetime is…Hui Wan, Kai Zhang, Christopher J. Vogl et al.·Jun 8, 2023SaveLearn
Octree-based hierarchical sampling optimization for the volumetric super-resolution of scientific dataWhen introducing physics-constrained deep learning solutions to the volumetric super-resolution of scientific data, the training is challenging to converge and always time-consuming. We propose a new…Xinjie Wang, Maoquan Sun, Yundong Guo et al.·Jun 8, 2023SaveLearn
A Quantum Kinetic Monte Carlo Method For Lindblad EquationIn this paper, we generalize the Quantum Kinetic Monte Carlo (QKMC) method of the Schrodinger equation, which was first proposed by [Z. Cai and J. Lu. SIAM J. Sci. Comput., 40(3):B706-B722, 2018] to…Limin Xu·Jun 8, 2023SaveLearn
Physics-informed reinforcement learning for sample-efficient optimization of freeform nanophotonic devicesIn the field of optics, precise control of light with arbitrary spatial resolution has long been a sought-after goal. Freeform nanophotonic devices are critical building blocks for achieving this…Chaejin Park, Sanmun Kim, Anthony W. Jung et al.·Jun 7, 2023SaveLearn
Autoencoders for dimensionality reduction in molecular dynamics: collective variable dimension, biasing and transition statesThe heat shock protein 90 (Hsp90) is a molecular chaperone that controls the folding and activation of client proteins using the free energy of ATP hydrolysis. The Hsp90 active site is in its…Zineb Belkacemi, Marc Bianciotto, Herve Minoux et al.·Jun 5, 2023SaveLearn