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The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large-scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…

Artificial Intelligence · Computer Science 2016-09-01 Bassam AlKindy , Bashar Al-Nuaimi , Christophe Guyeux , Jean-François Couchot , Michel Salomon , Reem Alsrraj , Laurent Philippe

Evolutionary crystal structure prediction proved to be a powerful approach for studying a wide range of materials. Here, we present a specifically designed algorithm for the prediction of the structure of complex crystals consisting of…

Materials Science · Physics 2012-05-21 Qiang Zhu , Artem R. Oganov , Colin W. Glass , Harold T. Stokes

We provide a description of the SNSPH code--a parallel 3-dimensional radiation hydrodynamics code implementing treecode gravity, smooth particle hydrodynamics, and flux-limited diffusion transport schemes. We provide descriptions of the…

Astrophysics · Physics 2009-11-13 C. L. Fryer , G. Rockefeller , M. S. Warren

We introduce SPHRAY, a Smoothed Particle Hydrodynamics (SPH) ray tracer designed to solve the 3D, time dependent, radiative transfer (RT) equations for arbitrary density fields. The SPH nature of SPHRAY makes the incorporation of separate…

Astrophysics · Physics 2009-11-13 Gabriel Altay , Rupert A. C. Croft , Inti Pelupessy

We present a novel distributed evolutionary algorithm, KaFFPaE, to solve the Graph Partitioning Problem, which makes use of KaFFPa (Karlsruhe Fast Flow Partitioner). The use of our multilevel graph partitioner KaFFPa provides new effective…

Neural and Evolutionary Computing · Computer Science 2011-10-05 Peter Sanders , Christian Schulz

We present a series of colour evolution models for Luminous Red Galaxies (LRGs) in the 7th spectroscopic data release of the Sloan Digital Sky Survey (SDSS), computed using the full-spectrum fitting code VESPA on high signal-to-noise…

Cosmology and Nongalactic Astrophysics · Physics 2015-05-20 Rita Tojeiro , Will J. Percival , Alan F. Heavens , Raul Jimenez

Simultaneous perturbation stochastic approximation (SPSA) is widely used in stochastic optimization due to its high efficiency, asymptotic stability, and reduced number of required loss function measurements. However, the standard SPSA…

Optimization and Control · Mathematics 2023-02-07 Zhichao Jia , Ziyi Wei , James C. Spall

We report on progress applying the stochastic LapH method to estimate all-to-all propagators required in correlation functions of multi-hadron operators relevant for pion-pion scattering. Large-volume results for $I=2$ and $I=1$ pion-pion…

High Energy Physics - Lattice · Physics 2015-11-19 John Bulava , Ben Hörz , Brendan Fahy , K. J. Juge , Colin Morningstar , Chik Him Wong

We present the smoothed-particle hydrodynamics simulation code, Bonsai-SPH, which is a continuation of our previously developed gravity-only hierarchical $N$-body code (called Bonsai). The code is optimized for Graphics Processing Unit…

Instrumentation and Methods for Astrophysics · Physics 2020-02-17 Jeroen Bédorf , Simon Portegies Zwart

The Shcramm-Loewner evolution (SLE) is a correlated exploration process, in which for the chordal set up, the tip of the trace evolves in a self-avoiding manner towards the infinity. The resulting curves are named SLE$_{\kappa}$,…

Statistical Mechanics · Physics 2019-06-26 M. N. Najafi , S. Tizdast , J. Cheraghalizadeh

Production of open and hidden charm hadrons in heavy ion collisions is considered within the statistical coalescence model. The charmed quark-antiquark pairs are assumed to be created at the initial stage of the reaction in hard parton…

High Energy Physics - Phenomenology · Physics 2009-11-07 A. P. Kostyuk

Evolutionary Algorithms are naturally inspired approximation optimisation algorithms that usually interfere with science problems when common mathematical methods are unable to provide a good solution or finding the exact solution requires…

Artificial Intelligence · Computer Science 2021-02-03 Mohammed ElKomy

Existing multi-strategy adaptive differential evolution (DE) commonly involves trials of multiple strategies and then rewards better-performing ones with more resources. However, the trials of an exploitative or explorative strategy may…

Neural and Evolutionary Computing · Computer Science 2021-12-03 Sheng Xin Zhang , Wing Shing Chan , Kit Sang Tang , Shao Yong Zheng

Chemical algorithms are statistical algorithms described and represented as chemical reaction networks. They are particularly attractive for traffic shaping and general control of network dynamics; they are analytically tractable, they…

Emerging Technologies · Computer Science 2016-01-21 Massimo Monti , Manolis Sifalakis , Christian F. Tschudin , Marco Luise

Abundances of N, Si, S, and Fe for 45 damped Lyman alpha systems (DLAs) have been compiled and detailed one-zone chemical evolution models have been constructed for 30 of them. Assuming continuous star formation, we found that final…

Astrophysics · Physics 2009-11-13 R. B. C. Henry , Jason X. Prochaska

Hash codes are a very efficient data representation needed to be able to cope with the ever growing amounts of data. We introduce a random forest semantic hashing scheme with information-theoretic code aggregation, showing for the first…

Computer Vision and Pattern Recognition · Computer Science 2015-04-20 Qiang Qiu , Guillermo Sapiro , Alex Bronstein

Recent applications of machine learning and statistical inference provide case studies demonstrating how such approaches can accelerate the discovery process in physical chemistry and related fields. Examples discussed in this review…

Chemical Physics · Physics 2017-06-20 Ryan B. Jadrich , Beth A. Lindquist , Thomas M. Truskett

We present the updated version of the code used to compute stellar evolutionary tracks in Padova. It is the result of a thorough revision of the major input physics, together with the inclusion of the pre-main sequence phase, not present in…

Solar and Stellar Astrophysics · Physics 2015-03-20 A. Bressan , P. Marigo , L. Girardi , B. Salasnich , C. Dal Cero , S. Rubele , A. Nanni

Recovering a tree that represents the evolutionary history of a group of species is a key task in phylogenetics. Performing this task using sequence data from multiple genetic markers poses two key challenges. The first is the discordance…

Populations and Evolution · Quantitative Biology 2026-03-12 Ortal Reshef , Ofer Glassman , Or Zuk , Yariv Aizenbud , Boaz Nadler , Ariel Jaffe

Scalar field comparison is a fundamental task in scientific visualization. In topological data analysis, we compare topological descriptors of scalar fields -- such as persistence diagrams and merge trees -- because they provide succinct…

Computational Geometry · Computer Science 2024-09-18 Weiran Lyu , Raghavendra Sridharamurthy , Jeff M. Phillips , Bei Wang