Computational science & discovery最新文献

{"title":"Accuracy of momentum transport calculations in full-f gyrokinetic simulations","authors":"Y. Idomura","doi":"10.1088/1749-4699/5/1/014018","DOIUrl":"https://doi.org/10.1088/1749-4699/5/1/014018","url":null,"abstract":"Accuracy of momentum transport calculations in gyrokinetic simulations are studied using the full-f gyrokinetic Eulerian code GT5D. Toroidal angular momentum conservation is examined both in the axisymmetric limit without turbulent fluctuations and in turbulent tokamaks. As shown by Scott and Smirnov (2010 Phys. Plasmas 17 112302), the toroidal angular momentum is conserved when the simulation is based on modern gyrokinetic theory with an energetic consistency. The convergence of turbulent heat and momentum fluxes is examined by implementing higher-order drift and polarization terms. The results support the correctness of the turbulent momentum transport computed using conventional first-order gyrokinetics.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"5 1","pages":"014018"},"PeriodicalIF":0.0,"publicationDate":"2012-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/5/1/014018","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60597090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biomolecular electrostatics—I want your solvation (model)*","authors":"J. Bardhan","doi":"10.1088/1749-4699/5/1/013001","DOIUrl":"https://doi.org/10.1088/1749-4699/5/1/013001","url":null,"abstract":"We review the mathematical and computational foundations for implicit-solvent models in theoretical chemistry and molecular biophysics. These models are valuable theoretical tools for studying the influence of a solvent, often water or an aqueous electrolyte, on a molecular solute such as a protein. Detailed chemical and physical aspects of implicit-solvent models have been addressed in numerous exhaustive reviews, as have numerical algorithms for simulating the most popular models. This work highlights several important conceptual developments, focusing on selected works that spotlight the need for research at the intersections between chemical, biological, mathematical, and computational physics. To introduce the field to computational scientists, we begin by describing the basic theoretical ideas of implicit-solvent models and numerical implementations. We then address practical and philosophical challenges in parameterization, and major advances that speed up calculations (covering continuum theories based on Poisson as well as faster approximate theories such as generalized Born). We briefly describe the main shortcomings of existing models, and survey promising developments that deliver improved realism in a computationally tractable way, i.e. without increasing simulation time significantly. The review concludes with a discussion of ongoing modeling challenges and relevant trends in high-performance computing and computational science.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"5 1","pages":"013001"},"PeriodicalIF":0.0,"publicationDate":"2012-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/5/1/013001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Finite Element Estimation of Protein-Ligand Association Rates with Post-Encounter Effects: Applications to Calcium binding in Troponin C and SERCA.","authors":"P M Kekenes-Huskey,&nbsp;A Gillette,&nbsp;J Hake,&nbsp;J A McCammon","doi":"10.1088/1749-4699/5/1/014015","DOIUrl":"https://doi.org/10.1088/1749-4699/5/1/014015","url":null,"abstract":"<p><p>We introduce a computational pipeline and suite of software tools for the approximation of diffusion-limited binding based on a recently developed theoretical framework. Our approach handles molecular geometries generated from high-resolution structural data and can account for active sites buried within the protein or behind gating mechanisms. Using tools from the FEniCS library and the APBS solver, we implement a numerical code for our method and study two Ca(2+)-binding proteins: Troponin C and the Sarcoplasmic Reticulum Ca(2+) ATPase (SERCA). We find that a combination of diffusional encounter and internal 'buried channel' descriptions provide superior descriptions of association rates, improving estimates by orders of magnitude.</p>","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"5 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2012-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/5/1/014015","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40215906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Overdetermined shooting methods for computing standing water waves with spectral accuracy","authors":"J. Wilkening, Jia Yu","doi":"10.1088/1749-4699/5/1/014017","DOIUrl":"https://doi.org/10.1088/1749-4699/5/1/014017","url":null,"abstract":"A high-performance shooting algorithm is developed to compute time-periodic solutions of the free-surface Euler equations with spectral accuracy in double and quadruple precision. The method is used to study resonance and its effect on standing water waves. We identify new nucleation mechanisms in which isolated large-amplitude solutions, and closed loops of such solutions, suddenly exist for depths below a critical threshold. We also study degenerate and secondary bifurcations related to Wilton's ripples in the traveling case, and explore the breakdown of self-similarity at the crests of extreme standing waves. In shallow water, we find that standing waves take the form of counter-propagating solitary waves that repeatedly collide quasi-elastically. In deep water with surface tension, we find that standing waves resemble counter-propagating depression waves. We also discuss the existence and non-uniqueness of solutions, and smooth versus erratic dependence of Fourier modes on wave amplitude and fluid depth. In the numerical method, robustness is achieved by posing the problem as an overdetermined nonlinear system and using either adjoint-based minimization techniques or a quadratically convergent trust-region method to minimize the objective function. Efficiency is achieved in the trust-region approach by parallelizing the Jacobian computation, so the setup cost of computing the Dirichlet-to-Neumann operator in the variational equation is not repeated for each column. Updates of the Jacobian are also delayed until the previous Jacobian ceases to be useful. Accuracy is maintained using spectral collocation with optional mesh refinement in space, a high-order Runge–Kutta or spectral deferred correction method in time and quadruple precision for improved navigation of delicate regions of parameter space as well as validation of double-precision results. Implementation issues for transferring much of the computation to a graphic processing units are briefly discussed, and the performance of the algorithm is tested for a number of hardware configurations.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"1 1","pages":"014017"},"PeriodicalIF":0.0,"publicationDate":"2012-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/5/1/014017","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60597042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Particle-in-cell simulations of shock-driven reconnection in relativistic striped winds","authors":"L. Sironi, A. Spitkovsky","doi":"10.1088/1749-4699/5/1/014014","DOIUrl":"https://doi.org/10.1088/1749-4699/5/1/014014","url":null,"abstract":"By means of two- and three-dimensional particle-in-cell simulations, we investigate the process of driven magnetic reconnection at the termination shock of relativistic striped flows. In pulsar winds and in magnetar-powered relativistic jets, the flow consists of stripes of alternating magnetic field polarity, separated by current sheets of hot plasma. At the wind termination shock, the flow compresses and the alternating fields annihilate by driven magnetic reconnection. Irrespective of the stripe wavelength ? or the wind magnetization ? (in the regime ????1 of magnetically dominated flows), shock-driven reconnection transfers all the magnetic energy of alternating fields to the particles, whose average Lorentz factor increases by a factor of ? with respect to the pre-shock value. In the limit ?/(rL?)???1, where rL is the relativistic Larmor radius in the wind, the post-shock particle spectrum approaches a flat power-law tail with slope around ?1.5, populated by particles accelerated by the reconnection electric field. The presence of a current-aligned ?guide? magnetic field suppresses the acceleration of particles only when the guide field is stronger than the alternating component. Our findings place important constraints on the models of non-thermal radiation from Pulsar Wind Nebulae and relativistic jets.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"5 1","pages":"014014"},"PeriodicalIF":0.0,"publicationDate":"2012-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/5/1/014014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver (APBS).","authors":"Robert Konecny, Nathan A Baker, J Andrew McCammon","doi":"10.1088/1749-4699/5/1/015005","DOIUrl":"10.1088/1749-4699/5/1/015005","url":null,"abstract":"<p><p>The Adaptive Poisson-Boltzmann Solver (APBS) is a state-of-the-art suite for performing Poisson-Boltzmann electrostatic calculations on biomolecules. The iAPBS package provides a modular programmatic interface to the APBS library of electrostatic calculation routines. The iAPBS interface library can be linked with a FORTRAN or C/C++ program thus making all of the APBS functionality available from within the application. Several application modules for popular molecular dynamics simulation packages - Amber, NAMD and CHARMM are distributed with iAPBS allowing users of these packages to perform implicit solvent electrostatic calculations with APBS.</p>","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2012-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419494/pdf/nihms397126.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30842990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isogeometric analysis in reduced magnetohydrodynamics","authors":"A. Ratnani, E. Sonnendrücker","doi":"10.1088/1749-4699/5/1/014007","DOIUrl":"https://doi.org/10.1088/1749-4699/5/1/014007","url":null,"abstract":"Isogeometric analysis (IGA) consists of using computer-aided design (CAD) models defining the geometry of the computational domain using both B-splines and non- uniform rational B-splines (NURBS) to represent the unknowns that are the solution of a partial differential equation using a finite element principle. In this paper, we review the main ideas of IGA and apply it to a reduced magnetohydrodynamic (MHD) model that is used in tokamak simulations. This is a first step towards arbitrary high-order and smooth approximations of reduced MHD generalizing the Bezier splines approach of Czarny and Huysmans( 2008 J.Comput.Phys. 227 7423-45).","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"5 1","pages":"014007"},"PeriodicalIF":0.0,"publicationDate":"2012-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/5/1/014007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction.","authors":"Y Cheng,&nbsp;P Kekenes-Huskey,&nbsp;Je Hake,&nbsp;Mj Holst,&nbsp;Ja McCammon,&nbsp;Ap Michailova","doi":"10.1088/1749-4699/5/1/015002","DOIUrl":"https://doi.org/10.1088/1749-4699/5/1/015002","url":null,"abstract":"<p><p>This article provides a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally-validated estimates of the diffusion-limited association rates for the binding of acetylcholine to mouse acetylcholinesterase using crystallographic structural data. The predicted rate constants exhibit increasingly delayed steady-state times with increasing ionic strength and demonstrate the role of an enzyme's electrostatic potential in influencing ligand binding. At the sub-cellular scale, an extension of SMOL solves a non-linear, reaction-diffusion system describing Ca²⁺ ligand buffering and diffusion in experimentally-derived rodent ventricular myocyte geometries. Results reveal the important role for mobile and stationary Ca²⁺ buffers, including Ca²⁺ indicator dye. We found that the alterations in Ca²⁺-binding and dissociation rates of troponin C (TnC) and total TnC concentration modulate subcellular Ca²⁺ signals. Model predicts that reduced off-rate in whole troponin complex (TnC, TnI, TnT) versus reconstructed thin filaments (Tn, Tm, actin) alters cytosolic Ca²⁺ dynamics under control conditions or in disease-linked TnC mutations. The ultimate goal of these studies is to develop scalable methods and theories for integration of molecular-scale information into simulations of cellular-scale systems.</p>","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2012-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/5/1/015002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31316525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An arbitrary curvilinear-coordinate method for particle-in-cell modeling","authors":"C. Fichtl, J. Finn, K. Cartwright","doi":"10.1088/1749-4699/5/1/014011","DOIUrl":"https://doi.org/10.1088/1749-4699/5/1/014011","url":null,"abstract":"A new approach to kinetic simulation of plasmas in complex geometries, based on the particle-in-cell (PIC) simulation method, is explored. In the two-dimensional (2D) electrostatic version of our method, called the arbitrary curvilinear-coordinate PIC method, all essential PIC operations are carried out in 2D on a uniform grid on the unit square logical domain, and mapped to a nonuniform boundary-fitted grid on the physical domain. As the resulting logical grid equations of motion are not separable, we have developed an extension of the semi-implicit modified leapfrog integration technique to preserve the symplectic nature of the logical grid particle mover. A generalized, curvilinear-coordinate formulation of Poisson's equations to solve for the electrostatic fields on the uniform logical grid is also developed. By our formulation, we compute the plasma charge density on the logical grid based on the particles' positions on the logical domain. That is, the plasma particles are weighted to the uniform logical grid and the self-consistent mean electrostatic fields obtained from the solution of the logical grid Poisson equation are interpolated to the particle positions on the logical grid. This process eliminates the complexity associated with the weighting and interpolation processes on the nonuniform physical grid and allows us to run the PIC method on arbitrary boundary-fitted meshes.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"5 1","pages":"014011"},"PeriodicalIF":0.0,"publicationDate":"2012-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/5/1/014011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An efficient, block-by-block algorithm for inverting a block tridiagonal, nearly block Toeplitz matrix","authors":"M. Reuter, Judith C. Hill","doi":"10.1088/1749-4699/5/1/014009","DOIUrl":"https://doi.org/10.1088/1749-4699/5/1/014009","url":null,"abstract":"We present an algorithm for computing any block of the inverse of a block tridiagonal, nearly block Toeplitz matrix (defined as a block tridiagonal matrix with a small number of deviations from the purely block Toeplitz structure). By exploiting both the block tridiagonal and the nearly block Toeplitz structures, this method scales independently of the total number of blocks in the matrix and linearly with the number of deviations. Numerical studies demonstrate this scaling and the advantages of our method over alternatives.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"5 1","pages":"014009"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/5/1/014009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}