Computational science & discovery最新文献

{"title":"Cross-language Babel structs—making scientific interfaces more efficient","authors":"A. Prantl, D. Ebner, T. Epperly","doi":"10.1088/1749-4699/6/1/014004","DOIUrl":"https://doi.org/10.1088/1749-4699/6/1/014004","url":null,"abstract":"Babel is an open-source language interoperability framework tailored to the needs of high-performance scientific computing. As an integral element of the Common Component Architecture, it is employed in a wide range of scientific applications where it is used to connect components written in different programming languages. In this paper we describe how we extended Babel to support interoperable tuple data types (structs). Structs are a common idiom in (mono-lingual) scientific application programming interfaces (APIs); they are an efficient way to pass tuples of nonuniform data between functions, and are supported natively by most programming languages. Using our extended version of Babel, developers of scientific codes can now pass structs as arguments between functions implemented in any of the supported languages. In C, C++, Fortran 2003/2008 and Chapel, structs can be passed without the overhead of data marshaling or copying, providing language interoperability at minimal cost. Other supported languages are Fortran 77, Fortran 90/95, Java and Python. We will show how we designed a struct implementation that is interoperable with all of the supported languages and present benchmark data to compare the performance of all language bindings, highlighting the differences between languages that offer native struct support and an object-oriented interface with getter/setter methods. A case study shows how structs can help simplify the interfaces of scientific codes significantly.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"6 1","pages":"014004"},"PeriodicalIF":0.0,"publicationDate":"2013-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/6/1/014004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596846","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":"Application of PDSLin to the magnetic reconnection problem","authors":"Xuefei Yuan, X. Li, I. Yamazaki, S. Jardin, A. Koniges, D. Keyes","doi":"10.1088/1749-4699/6/1/014002","DOIUrl":"https://doi.org/10.1088/1749-4699/6/1/014002","url":null,"abstract":"Magnetic reconnection is a fundamental process in a magnetized plasma at both low and high magnetic Lundquist numbers (the ratio of the resistive diffusion time to the Alfven wave transit time), which occurs in a wide variety of laboratory and space plasmas, e.g. magnetic fusion experiments, the solar corona and the Earth's magnetotail. An implicit time advance for the two-fluid magnetic reconnection problem is known to be difficult because of the large condition number of the associated matrix. This is especially troublesome when the collisionless ion skin depth is large so that the Whistler waves, which cause the fast reconnection, dominate the physics (Yuan et al 2012 J. Comput. Phys. 231 5822–53). For small system sizes, a direct solver such as SuperLU can be employed to obtain an accurate solution as long as the condition number is bounded by the reciprocal of the floating-point machine precision. However, SuperLU scales effectively only to hundreds of processors or less. For larger system sizes, it has been shown that physics-based (Chacon and Knoll 2003 J. Comput. Phys. 188 573–92) or other preconditioners can be applied to provide adequate solver performance. In recent years, we have been developing a new algebraic hybrid linear solver, PDSLin (Parallel Domain decomposition Schur complement-based Linear solver) (Yamazaki and Li 2010 Proc. VECPAR pp 421–34 and Yamazaki et al 2011 Technical Report). In this work, we compare numerical results from a direct solver and the proposed hybrid solver for the magnetic reconnection problem and demonstrate that the new hybrid solver is scalable to thousands of processors while maintaining the same robustness as a direct solver.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"6 1","pages":"014002"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/6/1/014002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596835","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":"A new model for approximating RNA folding trajectories and population kinetics","authors":"Bonnie Kirkpatrick, Monir Hajiaghayi, A. Condon","doi":"10.1088/1749-4699/6/1/014003","DOIUrl":"https://doi.org/10.1088/1749-4699/6/1/014003","url":null,"abstract":"RNA participates both in functional aspects of the cell and in gene regulation. The interactions of these molecules are mediated by their secondary structure which can be viewed as a planar circle graph with arcs for all the chemical bonds between pairs of bases in the RNA sequence. The problem of predicting RNA secondary structure, specifically the chemically most probable structure, has many useful and efficient algorithms. This leaves RNA folding, the problem of predicting the dynamic behavior of RNA structure over time, as the main open problem. RNA folding is important for functional understanding because some RNA molecules change secondary structure in response to interactions with the environment. The full RNA folding model on at most O(3n) secondary structures is the gold standard. We present a new subset approximation model for the full model, give methods to analyze its accuracy and discuss the relative merits of our model as compared with a pre-existing subset approximation. The main advantage of our model is that it generates Monte Carlo folding pathways with the same probabilities with which they are generated under the full model. The pre-existing subset approximation does not have this property.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"6 1","pages":"014003"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/6/1/014003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596841","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":"Utilization of efficient gradient and Hessian computations in the force field optimization process of molecular simulations","authors":"M. Hülsmann, Sonja Kopp, M. Huber, D. Reith","doi":"10.1088/1749-4699/6/1/015005","DOIUrl":"https://doi.org/10.1088/1749-4699/6/1/015005","url":null,"abstract":"Computer simulations of chemical systems, especially systems of condensed matter, are highly important for both scientific and industrial applications. Thereby, molecular interactions are modeled on a microscopic level in order to study their impact on macroscopic phenomena. To be capable of predicting physical properties quantitatively, accurate molecular models are indispensable. Molecular interactions are described mathematically by force fields, which have to be parameterized. Recently, an automated gradient-based optimization procedure was published by the authors based on the minimization of a loss function between simulated and experimental physical properties. The applicability of gradient-based procedures is not trivial at all because of two reasons: firstly, simulation data are affected by statistical noise, and secondly, the molecular simulations required for the loss function evaluations are extremely time-consuming. Within the optimization process, gradients and Hessians were approximated by finite differences so that additional simulations for the respective modified parameter sets were required. Hence, a more efficient approach to computing gradients and Hessians is presented in this work. The method developed here is based on directional instead of partial derivatives. It is compared with the classical computations with respect to computation time. Firstly, molecular simulations are replaced by fit functions that define a functional dependence between specific physical observables and force field parameters. The goal of these simulated simulations is to assess the new methodology without much computational effort. Secondly, it is applied to real molecular simulations of the three chemical substances phosgene, methanol and ethylene oxide. It is shown that up to 75% of the simulations can be avoided using the new algorithm.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"6 1","pages":"015005"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/6/1/015005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596997","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":"Parallel geometric classification of stem cells by their three-dimensional morphology","authors":"D. Juba, Antonio Cardone, C. Y. Ip, C. Simon, Christopher K. Tison, Girish Kumar, M. Brady, A. Varshney","doi":"10.1088/1749-4699/6/1/015007","DOIUrl":"https://doi.org/10.1088/1749-4699/6/1/015007","url":null,"abstract":"There is a need for tools to classify cells based on their three-dimensional (3D) shape. Cells exist in vivo in 3D, cells are frequently cultured within 3D scaffolds in vitro and 3D scaffolds are used for cell delivery in tissue engineering therapies. Recent work indicates that the physical structure of a tissue engineering scaffold can direct stem cell function by driving stem cells into morphologies that induce their differentiation. Thus, we have developed a rapid method for classifying cells based on their 3D shape. First, random lines are intersected with 3D Z-stacks of confocal images of stem cells. The intersection lengths are stored in histograms, which are then used to train a support vector machine (SVM) learning algorithm to distinguish between stem cells cultured on differentiation-inducing 3D scaffolds and those cultured on non-differentiating flat substrates. The trained SVM is able to properly classify the ?new? query cells over 80% of the time. The algorithm is easily parallelizable and we demonstrate its implementation on a commodity graphics processing unit (GPU). Use of a GPU to run the algorithm increases throughput by over 100-fold as compared to use of a CPU. The algorithm is also progressive, providing an approximate answer quickly and refining the answer over time. This allows further increase in the throughput of the algorithm by allowing the SVM classification scheme to terminate early if it becomes confident enough of the class of the cell being analyzed. These results demonstrate a rapid method for classifying stem cells based on their 3D shape that can be used by tissue engineers for identifying 3D tissue scaffold structures that drive stem cells into shapes that correlate with differentiation.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"6 1","pages":"015007"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/6/1/015007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60597123","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":"Nanoinformatics workshop report: Current resources, community needs, and the proposal of a collaborative framework for data sharing and information integration.","authors":"Stacey L Harper, James E Hutchison, Nathan Baker, Michele Ostraat, Sally Tinkle, Jeffrey Steevens, Mark D Hoover, Jessica Adamick, Krishna Rajan, Sharon Gaheen, Yoram Cohen, Andre Nel, Raul E Cachau, Mark Tuominen","doi":"10.1088/1749-4699/6/1/014008","DOIUrl":"10.1088/1749-4699/6/1/014008","url":null,"abstract":"<p><p>The quantity of information on nanomaterial properties and behavior continues to grow rapidly. Without a concerted effort to collect, organize and mine disparate information coming out of current research efforts, the value and effective use of this information will be limited at best. Data will not be translated to knowledge. At worst, erroneous conclusions will be drawn and future research may be misdirected. Nanoinformatics can be a powerful approach to enhance the value of global information in nanoscience and nanotechnology. Much progress has been made through grassroots efforts in nanoinformatics resulting in a multitude of resources and tools for nanoscience researchers. In 2012, the nanoinformatics community believed it was important to critically evaluate and refine currently available nanoinformatics approaches in order to best inform the science and support the future of predictive nanotechnology. The Greener Nano 2012: Nanoinformatics Tools and Resources Workshop brought together informatics groups with materials scientists active in nanoscience research to evaluate and reflect on the tools and resources that have recently emerged in support of predictive nanotechnology. The workshop goals were to establish a better understanding of current nanoinformatics approaches and to clearly define immediate and projected informatics infrastructure needs of the nanotechnology community. The theme of nanotechnology environmental health and safety (nanoEHS) was used to provide real-world, concrete examples on how informatics can be utilized to advance our knowledge and guide nanoscience. The benefit here is that the same properties that impact the performance of products could also be the properties that inform EHS. From a decision management standpoint, the dual use of such data should be considered a priority. Key outcomes include a proposed collaborative framework for data collection, data sharing and information integration.</p>","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"6 1","pages":"14008"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3895330/pdf/nihms543503.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32053797","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":"HDAT: web-based high-throughput screening data analysis tools","authors":"Rong Liu, Taimur Hassan, R. Rallo, Y. Cohen","doi":"10.1088/1749-4699/6/1/014006","DOIUrl":"https://doi.org/10.1088/1749-4699/6/1/014006","url":null,"abstract":"The increasing utilization of high-throughput screening (HTS) in toxicity studies of engineered nano-materials (ENMs) requires tools for rapid and reliable processing and analyses of large HTS datasets. In order to meet this need, a web-based platform for HTS data analyses tools (HDAT) was developed that provides statistical methods suitable for ENM toxicity data. As a publicly available computational nanoinformatics infrastructure, HDAT provides different plate normalization methods, various HTS summarization statistics, self-organizing map (SOM)-based clustering analysis, and visualization of raw and processed data using both heat map and SOM. HDAT has been successfully used in a number of HTS studies of ENM toxicity, thereby enabling analysis of toxicity mechanisms and development of structure?activity relationships for ENM toxicity. The online approach afforded by HDAT should encourage standardization of and future advances in HTS as well as facilitate convenient inter-laboratory comparisons of HTS datasets.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"6 1","pages":"014006"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/6/1/014006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596910","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":"Numerical simulations and experimental measurements of dense-core vortex rings in a sharply stratified environment","authors":"R. Camassa, S. Khatri, R. McLaughlin, K. Mertens, D. Nenon, C. Smith, C. Viotti","doi":"10.1088/1749-4699/6/1/014001","DOIUrl":"https://doi.org/10.1088/1749-4699/6/1/014001","url":null,"abstract":"We present three-dimensional direct numerical simulations of a vortex ring settling in sharply stratified miscible ambient fluids for near two-layer configurations, and comparisons of these simulations with the results from laboratory experiments. The core fluid of the vortex rings has density higher than both the top and the bottom layers of the ambient fluid, and is fully miscible in both layers. This setup ensures a rich parameter space that we partially explore in this study. In particular, a critical (bifurcation) phenomenon is identified that distinguishes the long-time behavior of the settling vortex ring as either being fully trapped at the ambient density layer or continuing through the layer in its downward motion. This critical behavior is determined by the initial conditions (e.g. the size and speed of the vortex ring, the initial distance to the layer, etc). The numerical simulations are able to provide evidence for this in qualitative agreement with an experimental phase diagram. Our setup isolates essential elements of mixing, trapping and escape through stratified fluids in a variety of situations, such as the mixing and dispersion of pollutants and plankton in the ocean.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"6 1","pages":"014001"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/6/1/014001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596794","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":"Understanding the mechanisms of sickle cell disease by simulations with a discrete particle model","authors":"Katrina Hui, G. Lin, Wenxiao Pan","doi":"10.1088/1749-4699/6/1/015004","DOIUrl":"https://doi.org/10.1088/1749-4699/6/1/015004","url":null,"abstract":"Sickle cell disease (SCD) is an inherited blood disorder characterized by rigid, sickle-shaped red blood cells (RBCs). Because of their rigidity and shape, sickle cells can get stuck in smaller blood vessels, causing blockages and depriving oxygen to tissues. This study develops and applies mathematical models to better understand the mechanism of SCD. Two-dimensional models of RBCs and blood vessels have been constructed by representing them as discrete particles interacting with different forces. The nonlinear, elastic property of healthy RBCs could be adequately reproduced using a cosine angle bending force and a worm-like chain spring force. With the ability to deform, RBCs can squeeze through narrow blood vessels. In modeling sickle cells as rigid bodies and applying repelling and friction forces from the blood vessel, this study shows that geometrical factors (dimensions of the sickle cell and blood vessels) as well as rigidity and adhesiveness of the sickle cell all play an important role in determining how, and if, sickle cells become trapped within narrow blood capillaries. With lack of data to validate the model, this study primarily provides a sensitivity analysis of factors influencing sickle cell occlusion and identified critical data to support future modeling.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"6 1","pages":"015004"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/6/1/015004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596988","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":"Novel methods in the Particle-In-Cell accelerator Code-Framework Warp","authors":"J. Vay, D. Grote, R. Cohen, A. Friedman","doi":"10.1088/1749-4699/5/1/014019","DOIUrl":"https://doi.org/10.1088/1749-4699/5/1/014019","url":null,"abstract":"The Particle-In-Cell (PIC) Code-Framework Warp is being developed by the Heavy Ion Fusion Science Virtual National Laboratory (HIFS-VNL) to guide the development of accelerators that can deliver beams suitable for high-energy density experiments and implosion of inertial fusion capsules. It is also applied in various areas outside the Heavy Ion Fusion program to the study and design of existing and next-generation high-energy accelerators, including the study of electron cloud effects and laser wakefield acceleration for example. This paper presents an overview of Warp's capabilities, summarizing recent original numerical methods that were developed by the HIFS-VNL (including PIC with adaptive mesh refinement, a large-timestep ?drift-Lorentz? mover for arbitrarily magnetized species, a relativistic Lorentz invariant leapfrog particle pusher, simulations in Lorentz-boosted frames, an electromagnetic solver with tunable numerical dispersion and efficient stride-based digital filtering), with special emphasis on the description of the mesh refinement capability. Selected examples of the applications of the methods to the abovementioned fields are given.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"5 1","pages":"014019"},"PeriodicalIF":0.0,"publicationDate":"2012-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/5/1/014019","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60597108","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}