Computational science & discovery最新文献_第3页

Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research. 纳米信息学知识基础设施：为纳米医学研究带来高效的信息管理。

Computational science & discovery Pub Date : 2013-11-27 DOI: 10.1088/1749-4699/6/1/014011

D de la Iglesia, R E Cachau, M García-Remesal, V Maojo

{"title":"Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research.","authors":"D de la Iglesia, R E Cachau, M García-Remesal, V Maojo","doi":"10.1088/1749-4699/6/1/014011","DOIUrl":"10.1088/1749-4699/6/1/014011","url":null,"abstract":"Nanotechnology represents an area of particular promise and significant opportunity across multiple scientific disciplines. Ongoing nanotechnology research ranges from the characterization of nanoparticles and nanomaterials to the analysis and processing of experimental data seeking correlations between nanoparticles and their functionalities and side effects. Due to their special properties, nanoparticles are suitable for cellular-level diagnostics and therapy, offering numerous applications in medicine, e.g. development of biomedical devices, tissue repair, drug delivery systems and biosensors. In nanomedicine, recent studies are producing large amounts of structural and property data, highlighting the role for computational approaches in information management. While in vitro and in vivo assays are expensive, the cost of computing is falling. Furthermore, improvements in the accuracy of computational methods (e.g. data mining, knowledge discovery, modeling and simulation) have enabled effective tools to automate the extraction, management and storage of these vast data volumes. Since this information is widely distributed, one major issue is how to locate and access data where it resides (which also poses data-sharing limitations). The novel discipline of nanoinformatics addresses the information challenges related to nanotechnology research. In this paper, we summarize the needs and challenges in the field and present an overview of extant initiatives and efforts.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"6 1","pages":"014011"},"PeriodicalIF":0.0,"publicationDate":"2013-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053539/pdf/nihms581421.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32427093","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}

引用次数: 0

caNanoLab: data sharing to expedite the use of nanotechnology in biomedicine. caNanoLab:数据共享以加速纳米技术在生物医学中的应用。

Computational science & discovery Pub Date : 2013-11-21 DOI: 10.1088/1749-4699/6/1/014010

Sharon Gaheen, George W Hinkal, Stephanie A Morris, Michal Lijowski, Mervi Heiskanen, Juli D Klemm

引用次数: 32

What makes computational open source software libraries successful 是什么让计算开源软件库成功

Computational science & discovery Pub Date : 2013-11-19 DOI: 10.1088/1749-4699/6/1/015010

W. Bangerth, T. Heister

引用次数: 36

Particle refining and coarsening method for smoothed particle hydrodynamics simulations 光滑颗粒流体动力学模拟的颗粒细化和粗化方法

Computational science & discovery Pub Date : 2013-11-19 DOI: 10.1088/1749-4699/6/1/015009

Y. Huang, O. Nydal, B. Yao, Z. Tian

引用次数: 2

Profiling the biological activity of oxide nanomaterials with mechanistic models 用机制模型分析氧化纳米材料的生物活性

Computational science & discovery Pub Date : 2013-11-19 DOI: 10.1088/1749-4699/6/1/014009

E. Burello

引用次数: 8

Integration of data: the Nanomaterial Registry project and data curation 数据整合:纳米材料注册项目和数据管理

Computational science & discovery Pub Date : 2013-11-05 DOI: 10.1088/1749-4699/6/1/014007

K. Guzan, K. Mills, Vijay Gupta, D. Murry, C. Scheier, Daphne Willis, M. Ostraat

引用次数: 11

Massively parallel conjugate heat transfer methods relying on large eddy simulation applied to an aeronautical combustor 基于大涡模拟的大规模平行共轭换热方法在航空燃烧室中的应用

Computational science & discovery Pub Date : 2013-10-31 DOI: 10.1088/1749-4699/6/1/015008

S. Jaure, F. Duchaine, G. Staffelbach, L. Gicquel

{"title":"Massively parallel conjugate heat transfer methods relying on large eddy simulation applied to an aeronautical combustor","authors":"S. Jaure, F. Duchaine, G. Staffelbach, L. Gicquel","doi":"10.1088/1749-4699/6/1/015008","DOIUrl":"https://doi.org/10.1088/1749-4699/6/1/015008","url":null,"abstract":"Optimizing gas turbines is a complex multi-physical and multi-component problem that has long been based on expensive experiments. Today, computer simulation can reduce design process costs and is acknowledged as a promising path for optimization. However, performing such computations using high-fidelity methods such as a large eddy simulation (LES) on gas turbines is challenging. Nevertheless, such simulations become accessible for specific components of gas turbines. These stand-alone simulations face a new challenge: to improve the quality of the results, new physics must be introduced. Therefore, an efficient massively parallel coupling methodology is investigated. The flow solver modeling relies on the LES code AVBP which has already been ported on massively parallel architectures. The conduction solver is based on the same data structure and thus shares its scalability. Accurately coupling these solvers while maintaining their scalability is challenging and is the actual objective of this work. To obtain such goals, a methodology is proposed and different key issues to code the coupling are addressed: convergence, stability, parallel geometry mapping, transfers and interpolation. This methodology is then applied to a real burner configuration, hence demonstrating the possibilities and limitations of the solution.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"6 1","pages":"015008"},"PeriodicalIF":0.0,"publicationDate":"2013-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/6/1/015008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60597137","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}

引用次数: 40

Computational approaches and metrics required for formulating biologically realistic nanomaterial pharmacokinetic models 计算方法和指标需要制定生物现实的纳米材料药代动力学模型

Computational science & discovery Pub Date : 2013-10-03 DOI: 10.1088/1749-4699/6/1/014005

J. Riviere, C. Scoglio, F. Sahneh, N. Monteiro-Riviere

{"title":"Computational approaches and metrics required for formulating biologically realistic nanomaterial pharmacokinetic models","authors":"J. Riviere, C. Scoglio, F. Sahneh, N. Monteiro-Riviere","doi":"10.1088/1749-4699/6/1/014005","DOIUrl":"https://doi.org/10.1088/1749-4699/6/1/014005","url":null,"abstract":"The field of nanomaterial pharmacokinetics is in its infancy, with major advances largely restricted by a lack of biologically relevant metrics, fundamental differences between particles and small molecules of organic chemicals and drugs relative to biological processes involved in disposition, a scarcity of sufficiently rich and characterized in vivo data and a lack of computational approaches to integrating nanomaterial properties to biological endpoints. A central concept that links nanomaterial properties to biological disposition, in addition to their colloidal properties, is the tendency to form a biocorona which modulates biological interactions including cellular uptake and biodistribution. Pharmacokinetic models must take this crucial process into consideration to accurately predict in vivo disposition, especially when extrapolating from laboratory animals to humans since allometric principles may not be applicable. The dynamics of corona formation, which modulates biological interactions including cellular uptake and biodistribution, is thereby a crucial process involved in the rate and extent of biodisposition. The challenge will be to develop a quantitative metric that characterizes a nanoparticle's surface adsorption forces that are important for predicting biocorona dynamics. These types of integrative quantitative approaches discussed in this paper for the dynamics of corona formation must be developed before realistic engineered nanomaterial risk assessment can be accomplished.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"6 1","pages":"014005"},"PeriodicalIF":0.0,"publicationDate":"2013-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4699/6/1/014005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60596904","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}

引用次数: 19

An integrated programming and development environment for adiabatic quantum optimization 绝热量子优化的集成编程和开发环境

Computational science & discovery Pub Date : 2013-09-13 DOI: 10.1088/1749-4680/7/1/015006

T. Humble, A. McCaskey, R. Bennink, J. Billings, E. D'Azevedo, Blair D. Sullivan, Christine Klymko, H. Seddiqi

{"title":"An integrated programming and development environment for adiabatic quantum optimization","authors":"T. Humble, A. McCaskey, R. Bennink, J. Billings, E. D'Azevedo, Blair D. Sullivan, Christine Klymko, H. Seddiqi","doi":"10.1088/1749-4680/7/1/015006","DOIUrl":"https://doi.org/10.1088/1749-4680/7/1/015006","url":null,"abstract":"Adiabatic quantum computing is a promising route to the computational power afforded by quantum information processing. The recent availability of adiabatic hardware has raised challenging questions about how to evaluate adiabatic quantum optimization (AQO) programs. Processor behavior depends on multiple steps to synthesize an adiabatic quantum program, which are each highly tunable. We present an integrated programming and development environment for AQO called Jade Adiabatic Development Environment (JADE) that provides control over all the steps taken during program synthesis. JADE captures the workflow needed to rigorously specify the AQO algorithm while allowing a variety of problem types, programming techniques, and processor configurations. We have also integrated JADE with a quantum simulation engine that enables program profiling using numerical calculation. The computational engine supports plug-ins for simulation methodologies tailored to various metrics and computing resources. We present the design, integration, and deployment of JADE and discuss its potential use for benchmarking AQO programs by the quantum computer science community.","PeriodicalId":89345,"journal":{"name":"Computational science & discovery","volume":"25 1","pages":"015006"},"PeriodicalIF":0.0,"publicationDate":"2013-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1088/1749-4680/7/1/015006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60595743","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}

引用次数: 26

Energy conservation tests of a coupled kinetic plasma–kinetic neutral transport code 耦合动力学等离子体-动力学中性输运码的能量守恒试验

Computational science & discovery Pub Date : 2013-05-20 DOI: 10.1088/1749-4699/6/1/015006

D. Stotler, C. Chang, G. Park, S. Ku

引用次数: 11