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Computational Physics

New submissions

[ total of 10 entries: 1-10 ]
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New submissions for Tue, 20 Mar 18

[1]  arXiv:1803.06714 [pdf, other]
Title: Mathematics for cryo-electron microscopy
Authors: Amit Singer
Comments: Proceedings of the International Congress of Mathematicians 2018
Subjects: Computational Physics (physics.comp-ph); History and Overview (math.HO)

Single-particle cryo-electron microscopy (cryo-EM) has recently joined X-ray crystallography and NMR spectroscopy as a high-resolution structural method for biological macromolecules. Cryo-EM was selected by Nature Methods as Method of the Year 2015, large scale investments in cryo-EM facilities are being made all over the world, and the Nobel Prize in Chemistry 2017 was awarded to Jacques Dubochet, Joachim Frank and Richard Henderson "for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution". This paper focuses on the mathematical principles underlying existing algorithms for structure determination using single particle cryo-EM.

[2]  arXiv:1803.07030 [pdf, other]
Title: Vegas: Software package for the atomistic simulation of magnetic materials
Subjects: Computational Physics (physics.comp-ph)

We present an open-source software package, Vegas, for the atomistic simulation of magnetic materials. Using the classical Heisenberg model and the Monte Carlo Metropolis algorithm, Vegas provides the required tools to simulate and analyze magnetic phenomena of a great variety of systems. Vegas stores the history of the simulation, i.e. the magnetization and energy of the system at every time step, allowing to analyze static and dynamic magnetic phenomena from results obtained in a single simulation. Also, standardized input and output file formats are employed to facilitate the simulation process and the exchange and archiving of data. We include results from simulations performed using Vegas, showing its applicability to study different magnetic phenomena.

Cross-lists for Tue, 20 Mar 18

[3]  arXiv:1803.06880 (cross-list from physics.flu-dyn) [pdf, other]
Title: Scaling of energy amplification in viscoelastic channel and Couette flow
Comments: 40 pages, 10 figures, the material was partially presented at 2015 APS-DFD meeting, this manuscript was never submitted to a journal
Subjects: Fluid Dynamics (physics.flu-dyn); Computational Physics (physics.comp-ph)

The linear amplification of disturbances is critical in setting up transition scenarios in viscoelastic channel and Couette flow, and may also play an important role when such flows are fully turbulent. As such, it is of interest to assess how this amplification, defined as the steady-state variance maintained under Gaussian white noise forcing, scales with the main nondimensional parameters: the Reynolds ($Re$) and Weissenberg ($Wi$) numbers. This scaling is derived analytically in the two limits of strong and weak elasticity for when the forcing is streamwise-constant. The latter is the relevant forcing for capturing the overall behaviour because it was previously shown to have the dominant contribution to amplification. The final expressions show that for weak elasticity the scaling retains a form similar to the well-known O($Re^3$) relationship with an added elastic correction. For strong elasticity, however, the scaling is O($Wi^3$) with a viscous correction. The key factor leading to such a mirroring in the scaling is the introduction of forcing in the polymer stress. The results demonstrate that energy amplification in a viscoelastic flow can be very sensitive to the model parameters even at low $Re$. They also suggest that energy amplification can be significantly increased by forcing the polymer stress, thereby opening up possibilities such as flow control using systematically designed polymer stress perturbations.

[4]  arXiv:1803.06893 (cross-list from math.NA) [pdf, other]
Title: On reference solutions and the sensitivity of the 2d Kelvin-Helmholtz instability problem
Comments: 20 pages, 11 figures, 1 table
Subjects: Numerical Analysis (math.NA); Computational Physics (physics.comp-ph); Fluid Dynamics (physics.flu-dyn)

Two-dimensional Kelvin-Helmholtz instability problems are popular examples for assessing discretizations or turbulence models for incompressible flows. Unfortunately, the results in the literature differ considerably. This paper presents computational studies of a Kelvin-Helmholtz instability problem with high order divergence-free finite element methods. Reference results in several quantities of interest are obtained for three different Reynolds numbers up to the beginning of the final vortex pairing. A mesh-independent prediction of the final pairing is not achieved due to the sensitivity of the considered problem with respect to small perturbations. A theoretical explanation of this sensitivity to small perturbations is provided based on the theory of self-organization of 2d turbulence. Possible sources of perturbations that arise in almost any numerical simulation are discussed.

[5]  arXiv:1803.06976 (cross-list from physics.flu-dyn) [pdf, other]
Title: Slope limiting the velocity field in a discontinuous Galerkin divergence free two-phase flow solver
Subjects: Fluid Dynamics (physics.flu-dyn); Computational Physics (physics.comp-ph)

Solving the Navier-Stokes equations when the density field contains a large sharp discontinuity---such as a water/air free surface---is numerically challenging. Convective instabilities cause Gibbs oscillations which quickly destroy the solution. We investigate the use of slope limiters for the velocity field to overcome this problem in a way that does not compromise on the mass conservation properties. The equations are discretised using the interior penalty discontinuous Galerkin finite element method that is divergence free to machine precision.
A slope limiter made specifically for exactly divergence free (solenoidal) fields is presented and used to illustrated the difficulties in obtaining convectively stable fields that are also exactly solenoidal. The lessons learned from this are applied in constructing a simpler method based on the use of an existing scalar slope limiter applied to each velocity component.
We show by numerical examples how both presented slope limiting methods are vastly superior to the naive non-limited method. The methods can solve difficult two-phase problems with high density ratios and high Reynolds numbers---typical for marine and offshore water/air simulations---in a way that conserves mass and stops unbounded energy growth caused by the Gibbs phenomenon.

[6]  arXiv:1803.07016 (cross-list from cs.CE) [pdf, ps, other]
Title: Solving coupled problems of lumped parameter models in a platform for severe accidents in nuclear reactors
Subjects: Computational Engineering, Finance, and Science (cs.CE); Computational Physics (physics.comp-ph)

This paper focuses on solving coupled problems of lumped parameter models. Such problems are of interest for the simulation of severe accidents in nuclear reactors~: these coarse-grained models allow for fast calculations for statistical analysis used for risk assessment and solutions of large problems when considering the whole severe accident scenario. However, this modeling approach has several numerical flaws. Besides, in this industrial context, computational efficiency is of great importance leading to various numerical constraints. The objective of this research is to analyze the applicability of explicit coupling strategies to solve such coupled problems and to design implicit coupling schemes allowing stable and accurate computations. The proposed schemes are theoretically analyzed and tested within CEA's procor platform on a problem of heat conduction solved with coupled lumped parameter models and coupled 1D models. Numerical results are discussed and allow us to emphasize the benefits of using the designed coupling schemes instead of the usual explicit coupling schemes.

Replacements for Tue, 20 Mar 18

[7]  arXiv:1803.03259 (replaced) [pdf, other]
Title: A reciprocal formulation of non-exponential radiative transfer. 1: Sketch and motivation
Authors: Eugene d'Eon
Comments: 14 pages, fixed typos, more clarity, notation summary table, tweaked abstract and title
Subjects: Computational Physics (physics.comp-ph); Graphics (cs.GR); Nuclear Theory (nucl-th)
[8]  arXiv:1703.05371 (replaced) [pdf, other]
Title: Directional Sensitivity In Light-Mass Dark Matter Searches With Single-Electron Resolution Ionization Detectors
Comments: Most recent version
Subjects: Instrumentation and Detectors (physics.ins-det); Cosmology and Nongalactic Astrophysics (astro-ph.CO); Materials Science (cond-mat.mtrl-sci); High Energy Physics - Experiment (hep-ex); Computational Physics (physics.comp-ph)
[9]  arXiv:1801.07337 (replaced) [pdf]
Title: Machine Learning and Finite Element Method for Physical Systems Modeling
Subjects: Computational Engineering, Finance, and Science (cs.CE); Computational Physics (physics.comp-ph)
[10]  arXiv:1803.03490 (replaced) [pdf, ps, other]
Title: Computing Transition Rates for Rare Event: When Kramers Theory meets Free Energy Landscape
Authors: François Sicard
Comments: 5 pages, 1 figure, Supplemental Material (6 pages, 3 figures)
Subjects: Statistical Mechanics (cond-mat.stat-mech); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph); Computational Physics (physics.comp-ph)
[ total of 10 entries: 1-10 ]
[ showing up to 2000 entries per page: fewer | more ]

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