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Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

Populations and Evolution · Quantitative Biology 2025-11-11 Jonathan D. Mitchell , Barbara R. Holland

We present $\texttt{Abacus}$, a fast and accurate cosmological $N$-body code based on a new method for calculating the gravitational potential from a static multipole mesh. The method analytically separates the near- and far-field forces,…

Cosmology and Nongalactic Astrophysics · Physics 2021-10-25 Lehman H. Garrison , Daniel J. Eisenstein , Douglas Ferrer , Nina A. Maksimova , Philip A. Pinto

We review recent progress in computational methods for studying the dynamical evolution of large star clusters. After describing some highlights of a new comparison of different models, including N-body models, we mention in detail recent…

Astrophysics · Physics 2007-05-23 D. C. Heggie , M. Giersz , R. Spurzem , K. Takahashi

We introduce an object-oriented framework for parallel programming, which is based on the observation that programming objects can be naturally interpreted as processes. A parallel program consists of a collection of persistent processes…

Programming Languages · Computer Science 2014-04-21 Edward Givelberg

A novel code for the approximate computation of long-range forces between N mutually interacting bodies is presented. The code is based on a hierarchical tree of cubic cells and features mutual cell-cell interactions which are calculated…

Astrophysics · Physics 2009-11-07 Walter Dehnen

Cosmological fluctuations retain a memory of the physics that generated them in their spatial correlations. The strength of correlations varies smoothly as a function of external kinematics, which is encoded in differential equations…

High Energy Physics - Theory · Physics 2024-07-04 Nima Arkani-Hamed , Daniel Baumann , Aaron Hillman , Austin Joyce , Hayden Lee , Guilherme L. Pimentel

We present a numerical code to simulate maps of Galactic emission in intensity and polarization at microwave frequencies, aiding in the design of Cosmic Microwave Background experiments. This Python code builds on existing efforts to…

Cosmology and Nongalactic Astrophysics · Physics 2017-06-21 Ben Thorne , Jo Dunkley , David Alonso , Sigurd Naess

We present the multi-GPU realization of the StePS (Stereographically Projected Cosmological Simulations) algorithm with MPI-OpenMP-CUDA hybrid parallelization and nearly ideal scale-out to multiple compute nodes. Our new zoom-in…

Cosmology and Nongalactic Astrophysics · Physics 2019-03-22 Gábor Rácz , István Szapudi , László Dobos , István Csabai , Alexander S. Szalay

We compare the performance of two very different parallel gravitational $N$-body codes for astrophysical simulations on large GPU clusters, both pioneer in their own fields as well as in certain mutual scales - NBODY6++ and Bonsai. We carry…

Instrumentation and Methods for Astrophysics · Physics 2016-01-20 Siyi Huang , Rainer Spurzem , Peter Berczik

We present a general parallelized and easy-to-use code to perform numerical simulations of structure formation using the COLA (COmoving Lagrangian Acceleration) method for cosmological models that exhibit scale-dependent growth at the level…

Cosmology and Nongalactic Astrophysics · Physics 2017-08-09 Hans A. Winther , Kazuya Koyama , Marc Manera , Bill S. Wright , Gong-Bo Zhao

Quantum simulations constructing probability tensors of biological multi-taxa in phylogenetic trees are proposed, in terms of positive trace preserving maps, describing evolving systems of quantum walks with multiple walkers. Basic…

Quantum Physics · Physics 2011-05-10 Demosthenes Ellinas , Peter Jarvis

We present a new open-source cosmological code, called SWIFT, designed to solve the equations of hydrodynamics using a particle-based approach (Smooth Particle Hydrodynamics) on hybrid shared/distributed-memory architectures. SWIFT was…

Distributed, Parallel, and Cluster Computing · Computer Science 2022-08-03 Matthieu Schaller , Pedro Gonnet , Aidan B. G. Chalk , Peter W. Draper

We present CosFly, a box-structured planning and multimodal simulation pipeline for aerial tracking, together with CosFly-Track, a large-scale UAV dataset for dynamic target tracking across diverse environments including urban centers,…

We present a new N-body code, gevolution, for the evolution of large scale structure in the Universe. Our code is based on a weak field expansion of General Relativity and calculates all six metric degrees of freedom in Poisson gauge.…

Cosmology and Nongalactic Astrophysics · Physics 2016-08-05 Julian Adamek , David Daverio , Ruth Durrer , Martin Kunz

We present a field-level emulator for large-scale structure, capturing the cosmology dependence and the time evolution of cosmic structure formation. The emulator maps linear displacement fields to their corresponding nonlinear…

Cosmology and Nongalactic Astrophysics · Physics 2024-08-15 Drew Jamieson , Yin Li , Francisco Villaescusa-Navarro , Shirley Ho , David N. Spergel

GYOTO, a general relativistic ray-tracing code, is presented. It aims at computing images of astronomical bodies in the vicinity of compact objects, as well as trajectories of massive bodies in relativistic environments. This code is…

General Relativity and Quantum Cosmology · Physics 2012-03-15 Frederic H. Vincent , Thibaut Paumard , Eric Gourgoulhon , Guy Perrin

Many processes and models --in biological, physical, social, and other contexts-- produce trees whose depth scales logarithmically with the number of leaves. Phylogenetic trees, describing the evolutionary relationships between biological…

Quantitative Methods · Quantitative Biology 2010-05-11 Emilio Hernandez-Garcia , Murat Tugrul , E. Alejandro Herrada , Victor M. Eguiluz , Konstantin Klemm

Based on the cosmological principle only, the method of describing the evolution of the Universe, called cosmography, is in fact a kinematics of cosmological expansion. The effectiveness of cosmography lies in the fact that it allows, based…

General Relativity and Quantum Cosmology · Physics 2018-12-07 Yu. L. Bolotin , V. A. Cherkaskiy , O. Yu. Ivashtenko , M. I. Konchatnyi , L. G. Zazunov

An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…

Quantitative Methods · Quantitative Biology 2013-08-26 Paulo Murilo Castro de Oliveira

Numerical modeling of a mathematical model of the cosmological evolution of an asymmetric scalar doublet with kinetic interaction between the components was carried out. A wide range of values of fundamental parameters and initial…

General Relativity and Quantum Cosmology · Physics 2024-11-26 Yu. G. Ignsat'ev , I. A. Kokh
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