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Parallel Computing, Multiscale Modeling
United States

Biography

Yuefan Deng received his BA (1983) in Physics from Nankai University in China and his Ph. D. (1989) in Theoretical Physics from Columbia University in New York City. After his postdoctoral training in the Courant Institute of Mathematical Sciences at NYU, he joined the faculty of Stony Brook University, where he was promoted to full professor of Applied Mathematics in 1998.

Deng’s research covers parallel computing, molecular dynamics, Monte Carlo methods, and biomedical engineering. The latest focus is on the multi-scale modeling of platelet activations and aggregations (funded by US NIH, New York State, and IBM) on supercomputers, parallel optimization algorithms, and supercomputer network topologies. He publishes widely in diverse fields of physics, computational mathematics, and biomedical engineering. He has supervised nearly 30 doctoral theses in applied mathematics and Physics.

Deng taught more than 17,000 students ordinary differential equations and numerical analysis. He is the recipient (2016) of the State University of New York Chancellor’s Award for Excellence in Teaching.

Activities

Employment (12)

Stony Brook University: Stony Brook, NY, US

1999 to present | Professor (Applied Mathematics)
Employment
Source: Self-asserted source
Yuefan Deng

New York University - Abu Dhabi Campus: Abu Dhabi, Abu Dhabi, AE

2021-09-01 to 2022-05-31 | Visiting Professor (Mathematics)
Employment
Source: Self-asserted source
Yuefan Deng

Stony Brook University: Stony Brook, New York, US

2019 to 2022 | Associate Director (Institute for Engineering-Driven Medicine)
Employment
Source: Self-asserted source
Yuefan Deng

Brookhaven National Laboratory: Upton, NY, US

1999 to 2015 | Lab Associate
Employment
Source: Self-asserted source
Yuefan Deng

National University of Singapore: Singapore, SG

2013 to 2014 | Visiting Professor (Computer Science)
Employment
Source: Self-asserted source
Yuefan Deng

Columbia University: New York, NY, US

2010 to 2011 | Adjunct Professor (Applied Mathematics)
Employment
Source: Self-asserted source
Yuefan Deng

IBM Research - Thomas J. Watson Research Center: Yorktown Heights, New York, US

1999 to 2000 | Researcher
Employment
Source: Self-asserted source
Yuefan Deng

Los Alamos National Laboratory: Los Alamos, NM, US

1998 to 1998 | Faculty Visitor
Employment
Source: Self-asserted source
Yuefan Deng

Stony Brook University: Stony Brook, New York, US

1994 to 1998 | Associate Professor (Applied Mathematics)
Employment
Source: Self-asserted source
Yuefan Deng

Stony Brook University: Stony Brook, New York, US

1991 to 1994 | Assistant Professor (Applied Mathematics)
Employment
Source: Self-asserted source
Yuefan Deng

Stony Brook University: Stony Brook, New York, US

1989 to 1990 | Visiting Assistant Professor
Employment
Source: Self-asserted source
Yuefan Deng

New York University: New York, NY, US

1989-05-01 to 1989-08-31 | Research Associate (Courant Institute of Mathematical Sciences)
Employment
Source: Self-asserted source
Yuefan Deng

Education and qualifications (3)

Columbia University: New York, NY, US

1985-09-01 to 1989-05-01 | Ph.D. (Physics)
Education
Source: Self-asserted source
Yuefan Deng

Columbia University: New York, NY, US

1983-09-01 to 1985-05-20 | MA (Physics)
Education
Source: Self-asserted source
Yuefan Deng

Nankai University: Tianjin, CN

1979-09-01 to 1983-06-30 | BS (Physics)
Education
Source: Self-asserted source
Yuefan Deng

Funding (4)

MRI: Acquisition of SeaWulf - A Reconfigurable Computer System for Research and Education

2015-10-01 to 2018-09-30 | Grant
National Science Foundation - Directorate for Computer & Information Science & Engineering (Arlington, US)
GRANT_NUMBER: 1531492
Source: Self-asserted source
Yuefan Deng via DimensionsWizard

Collaborative Project: Analysis of Pattern Formation in Drosophila by Importance Sampling on Parallel Processors

1997-08-01 to 2000-07-31 | Grant
National Science Foundation - Directorate for Mathematical & Physical Sciences (Arlington, US)
GRANT_NUMBER: 9727177
Source: Self-asserted source
Yuefan Deng via DimensionsWizard

University - Industry Cooperative Research Programs in the Mathematical Sciences: Novel Parallel Molecular Dynamics Algorithms for Simulating Thin-film Depositions

Source: Self-asserted source
Yuefan Deng via DimensionsWizard

Postdoc: Parallel Multizone Adaptive Scheme for Multiphase Systems with Free and Moving Boundaries

1995-06-01 to 1997-11-30 | Grant
National Science Foundation - Directorate for Computer & Information Science & Engineering (Arlington, US)
GRANT_NUMBER: 9503988
Source: Self-asserted source
Yuefan Deng via DimensionsWizard

Works (50 of 91)

Items per page:
Page 1 of 2

Structural and Dynamical Analyses of Apo and Cap-binding eIF4E: Anin silicoStudy

2024-05-19 | Preprint
Contributors: Karin Hasegawa; Justin Burzachiello; Liam Connolly; Georgios Kementzidis; Ziyuan Niu; Evangelos Papadopoulos; Bertal Huseyin Aktas; Yuefan Deng
Source: check_circle
Crossref

An AI-Driven Framework for Discovery of BACE1 Inhibitors for Alzheimer’s Disease

2024-05-15 | Preprint
Contributors: Evan Xie; Karin Hasegawa; Georgios Kementzidis; Evangelos Papadopoulos; Bertal Huseyin Aktas; Yuefan Deng
Source: check_circle
Crossref

Platelet Biorheology and Mechanobiology in Thrombosis and Hemostasis: Perspectives from Multiscale Computation

International Journal of Molecular Sciences
2024-04 | Journal article | Author
Contributors: Rukiye Tuna; Wenjuan Yi; Esmeralda Crespo Cruz; JP Romero; Yi Ren; Jingjiao Guan; Yan Li; Yuefan Deng; Danny Bluestein; Zixiang Leonardo Liu et al.
Source: check_circle
Multidisciplinary Digital Publishing Institute
grade
Preferred source (of 2)‎

Platelet Biorheology and Mechanobiology in Thrombosis and Hemostasis: Perspectives from Multiscale Computation

2024-04-23 | Preprint
Contributors: Rukiye Tuna; Wenjuan Yi; Esmeralda Crespo Cruz; JP Romero; Yi Ren; Jingjiao Guan; Yan Li; Yuefan Deng; Danny Bluestein; Z. Leonardo Liu et al.
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Platelet Biorheology and Mechanobiology in Thrombosis: In Silico Perspectives

2024-02-14 | Preprint
Contributors: Rukiye Tuna; Wenjuan Yi; Esmeralda Crespo Cruz; JP Romero; Yi Ren; Jingjiao Guan; Yan Li; Yuefan Deng; Danny Bluestein; Z. Leonardo Liu et al.
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

AI-aided multiscale modeling of physiologically-significant blood clots

Computer Physics Communications
2023-06 | Journal article
Part of ISSN: 0010-4655
Contributors: Yicong Zhu; Changnian Han; Peng Zhang; Guojing Cong; James R. Kozloski; Chih-Chieh Yang; Leili Zhang; Yuefan Deng
Source: Self-asserted source
Yuefan Deng

A Multiscale Model for Shear-Mediated Platelet Adhesion Dynamics: Correlating In Silico with In Vitro Results

Annals of Biomedical Engineering
2023-05 | Journal article
Part of ISSN: 0090-6964
Part of ISSN: 1573-9686
Contributors: Peineng Wang; Jawaad Sheriff; Peng Zhang; Yuefan Deng; Danny Bluestein
Source: Self-asserted source
Yuefan Deng

Coarse-Grained Modeling of the SARS-CoV-2 Spike Glycoprotein by Physics-Informed Machine Learning

Computation
2023-02-02 | Journal article
Contributors: David Liang; Ziji Zhang; Miriam Rafailovich; Marcia Simon; Yuefan Deng; Peng Zhang
Source: check_circle
Crossref

Scalable multiscale modeling of platelets with 100 million particles

The Journal of Supercomputing
2022-12 | Journal article
Contributors: Changnian Han; Peng Zhang; Yicong Zhu; Guojing Cong; James R. Kozloski; Chih Chieh Yang; Leili Zhang; Yuefan Deng
Source: check_circle
Crossref

Optimal circulant graphs as low-latency network topologies

The Journal of Supercomputing
2022-07 | Journal article
Contributors: Xiaolong Huang; Alexandre F. Ramos; Yuefan Deng
Source: check_circle
Crossref

Online Machine Learning for Accelerating Molecular Dynamics Modeling of Cells

Frontiers in Molecular Biosciences
2022-01-27 | Journal article
Part of ISSN: 2296-889X
Contributors: Ziji Zhang; Peng Zhang; Changnian Han; Guojing Cong; Chih-Chieh Yang; Yuefan Deng
Source: Self-asserted source
Yuefan Deng

In Vitro Measurements of Shear-Mediated Platelet Adhesion Kinematics as Analyzed through Machine Learning

Annals of Biomedical Engineering
2021-12 | Journal article
Part of ISSN: 0090-6964
Part of ISSN: 1573-9686
Contributors: Jawaad Sheriff; Peineng Wang; Peng Zhang; Ziji Zhang; Yuefan Deng; Danny Bluestein
Source: Self-asserted source
Yuefan Deng

Molecular Dynamics Modeling of the SARS-CoV-2 Spike Protein at PH2 Through PH11.5

2021-07 | Preprint
Contributors: Niu Z; Zhang P; Rafailovich M; Simon M; Song M; Deng Y
Source: Self-asserted source
Yuefan Deng via Europe PubMed Central

A multiscale model for multiple platelet aggregation in shear flow

Biomechanics and Modeling in Mechanobiology
2021-06 | Journal article
Part of ISSN: 1617-7959
Part of ISSN: 1617-7940
Contributors: Prachi Gupta; Peng Zhang; Jawaad Sheriff; Danny Bluestein; Yuefan Deng
Source: Self-asserted source
Yuefan Deng

Rapid analysis of streaming platelet images by semi-unsupervised learning

Computerized Medical Imaging and Graphics
2021-04 | Journal article
Part of ISSN: 0895-6111
Contributors: Ziji Zhang; Peng Zhang; Peineng Wang; Jawaad Sheriff; Danny Bluestein; Yuefan Deng
Source: Self-asserted source
Yuefan Deng

A predictive multiscale model for simulating flow-induced platelet activation: Correlating in silico results with in vitro results

Journal of Biomechanics
2021-03 | Journal article
Part of ISSN: 0021-9290
Contributors: 0000-0001-9539-1136; Jawaad Sheriff; Shmuel Einav; MARVIN SLEPIAN; Yuefan Deng; Danny Bluestein
Source: Self-asserted source
Yuefan Deng

Artificial intelligence for accelerating time integrations in multiscale modeling

Journal of Computational Physics
2021-02 | Journal article
Contributors: Changnian Han; Peng Zhang; Danny Bluestein; Guojing Cong; Yuefan Deng
Source: check_circle
Crossref

Optimal low-latency network topologies for cluster performance enhancement

The Journal of Supercomputing
2020-12-02 | Journal article
Contributors: Yuefan Deng; Meng Guo; Alexandre F. Ramos; Xiaolong Huang; Zhipeng Xu; Weifeng Liu
Source: check_circle
Crossref

A Structured Table of Graphs with Symmetries and Other Special Properties

Symmetry
2019-12 | Journal article | Author
Contributors: Yidan Zhang; Xiaolong Huang; Zhipeng Xu; Yuefan Deng
Source: check_circle
Multidisciplinary Digital Publishing Institute
grade
Preferred source (of 2)‎

A New Record of Graph Enumeration Enabled by Parallel Processing

Mathematics
2019-12-10 | Journal article
Contributors: Zhipeng Xu; Xiaolong Huang; Fabian Jimenez; Yuefan Deng
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Applying Simulated Annealing and Parallel Computing to the Mobile Sequential Recommendation

IEEE Transactions on Knowledge and Data Engineering
2019-02-01 | Journal article
Contributors: Zeyang Ye; Keli Xiao; Yong Ge; Yuefan Deng
Source: check_circle
Crossref

A multiscale biomechanical model of platelets: Correlating with in-vitro results

Journal of Biomechanics
2017-01 | Journal article
Part of ISSN: 0021-9290
Contributors: 0000-0001-9539-1136; Li Zhang; Marvin J. Slepian; Yuefan Deng; Danny Bluestein
Source: Self-asserted source
Yuefan Deng

Scalability Test of multiscale fluid–platelet model for three top supercomputers

Computer Physics Communications
2016-07 | Journal article
Part of ISSN: 0010-4655
Contributors: 0000-0001-9539-1136; Na Zhang; Chao Gao; Li Zhang; yuxiang gao; Yuefan Deng; Danny Bluestein
Source: Self-asserted source
Yuefan Deng

A data-driven paradigm for mapping problems

Parallel Computing
2015 | Journal article
EID:

2-s2.0-84936100422

Contributors: Zhang, P.; Liu, L.; Deng, Y.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

A multiple time stepping algorithm for efficient multiscale modeling of platelets flowing in blood plasma

Journal of Computational Physics
2015 | Journal article
EID:

2-s2.0-84921502997

Contributors: Zhang, P.; Zhang, N.; Deng, Y.; Bluestein, D.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

A phenomenological particle-based platelet model for simulating filopodia formation during early activation

International Journal for Numerical Methods in Biomedical Engineering
2015 | Journal article
EID:

2-s2.0-84924870520

Contributors: Pothapragada, S.; Zhang, P.; Sheriff, J.; Livelli, M.; Slepian, M.J.; Deng, Y.; Bluestein, D.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Evaluation of various networks configurated by adding bypass or torus links

IEEE Transactions on Parallel and Distributed Systems
2015 | Journal article
EID:

2-s2.0-84925047665

Contributors: Zhang, P.; Deng, Y.; Feng, R.; Luo, X.; Wu, J.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Performance examinations of multiple time-stepping algorithms on stampede supercomputer

ACM International Conference Proceeding Series
2015 | Conference paper
EID:

2-s2.0-84942789829

Contributors: Zhang, N.; Zhang, P.; Zhang, L.; Zhu, X.; Huang, L.; Deng, Y.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Eigen analysis-based task mapping on parallel computers with cellular networks

Mathematics of Computation
2014 | Journal article
EID:

2-s2.0-84909993282

Contributors: Zhang, P.; Gao, Y.; Fierson, J.; Deng, Y.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Fairness of task scheduling in high performance computing environments

Scalable Computing
2014 | Journal article
EID:

2-s2.0-84910016670

Contributors: Sedighi, A.; Deng, Y.; Zhang, P.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Multiscale Particle-Based Modeling of Flowing Platelets in Blood Plasma Using Dissipative Particle Dynamics and Coarse Grained Molecular Dynamics

Cellular and Molecular Bioengineering
2014 | Journal article
EID:

2-s2.0-84906798168

Contributors: Zhang, P.; Gao, C.; Zhang, N.; Slepian, M.J.; Deng, Y.; Bluestein, D.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Parameterizing the Morse potential for coarse-grained modeling of blood plasma

Journal of Computational Physics
2014 | Journal article
EID:

2-s2.0-84887008406

Contributors: Zhang, N.; Zhang, P.; Kang, W.; Bluestein, D.; Deng, Y.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Supercomputer simulations of platelet activation in blood plasma at multiple scales

Proceedings of the 2014 International Conference on High Performance Computing and Simulation, HPCS 2014
2014 | Conference paper
EID:

2-s2.0-84908632087

Contributors: Pothapragada, S.; Deng, Y.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Lectures, Problems and Solutions for Ordinary Differential Equations

2014-10 | Book
Contributors: Yuefan Deng
Source: Self-asserted source
Yuefan Deng via Crossref Metadata Search

Analysis of Linpack and power efficiencies of the world's TOP500 supercomputers

Parallel Computing
2013 | Journal article
EID:

2-s2.0-84877773728

Contributors: Deng, Y.; Zhang, P.; Marques, C.; Powell, R.; Zhang, L.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Deadlock-free routing algorithms for 6D mesh/iBT interconnection networks

SNPD 2013 - 14th ACIS International Conference on Software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing
2013 | Conference paper
EID:

2-s2.0-84885986009

Contributors: Feng, R.; Zhang, P.; Deng, Y.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Multiscale modeling of flow induced thrombogenicity using dissipative particle dynamics and coarse grained molecular dynamics

ASME 2013 Summer Bioengineering Conference, SBC 2013
2013 | Conference paper
EID:

2-s2.0-84894682772

Contributors: Zhang, P.; Sheriff, J.; Soares, J.S.; Gao, C.; Pothapragada, S.; Zhang, N.; Deng, Y.; Bluestein, D.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Multiscale modeling of flow induced thrombogenicity using dissipative particle dynamics and molecular dynamics

ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology, NEMB 2013
2013 | Conference paper
EID:

2-s2.0-84890027382

Contributors: Bluestein, D.; Soares, J.S.; Zhang, P.; Gao, C.; Pothapragada, S.; Zhang, N.; Slepian, M.J.; Deng, Y.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Multiscale modeling of flow induced thrombogenicity with dissipative particle dynamics (DPD) and molecular dynamics (MD)

ASME 2013 Conference on Frontiers in Medical Devices: Applications of Computer Modeling and Simulation, FMD 2013
2013 | Conference paper
EID:

2-s2.0-84896331011

Contributors: Bluestein, D.; Soares, J.S.; Zhang, P.; Gao, C.; Pothapragada, S.; Zhang, N.; Slepian, M.J.; Deng, Y.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

An analysis of the topological properties of the interlaced bypass torus (iBT) networks

Applied Mathematics Letters
2012 | Journal article
EID:

2-s2.0-84865518529

Contributors: Zhang, P.; Deng, Y.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Design and analysis of pipelined broadcast algorithms for the all-port interlaced bypass torus networks

IEEE Transactions on Parallel and Distributed Systems
2012 | Journal article
EID:

2-s2.0-84869479690

Contributors: Zhang, P.; Deng, Y.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Network design considerations for exascale supercomputers

Proceedings of the IASTED International Conference on Parallel and Distributed Computing and Systems
2012 | Conference paper
EID:

2-s2.0-84878635635

Contributors: Feng, R.; Zhang, P.; Deng, Y.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Simulated performance evaluation of a 6D mesh/iBT interconnect

Proceedings - 13th ACIS International Conference on Software Engineering, Artificial Intelligence, Networking, and Parallel/Distributed Computing, SNPD 2012
2012 | Conference paper
EID:

2-s2.0-84868594460

Contributors: Feng, R.; Zhang, P.; Deng, Y.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Symmetry insights for design of supercomputer network topologies: Roots and weights lattices

International Journal of Modern Physics B
2012 | Journal article
EID:

2-s2.0-84870302494

Contributors: Deng, Y.; Ramos, A.F.; Hornos, J.E.M.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Viscous flow simulation in a stenosis model using discrete particle dynamics: A comparison between DPD and CFD

Biomechanics and Modeling in Mechanobiology
2012 | Journal article
EID:

2-s2.0-84859884942

Contributors: Feng, R.; Xenos, M.; Girdhar, G.; Kang, W.; Davenport, J.W.; Deng, Y.; Bluestein, D.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Applied Parallel Computing

2012-10 | Book
Contributors: Yuefan Deng
Source: Self-asserted source
Yuefan Deng via Crossref Metadata Search

An Ultra-scalable Supercomputer Based on MPU Architecture

2012-04-17 | Patent
PAT:

8,159,973 B2

Contributors: Yuefan Deng; Alexander Korobka; Peng Zhang
Source: Self-asserted source
Yuefan Deng

Interlacing bypass rings to torus networks for more efficient networks

IEEE Transactions on Parallel and Distributed Systems
2011 | Journal article
EID:

2-s2.0-78650883751

Contributors: Zhang, P.; Powell, R.; Deng, Y.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

Particle-based methods for multiscale modeling of blood flow in the circulation and in devices: Challenges and future directions: Sixth international bio-fluid mechanics symposium and workshop March 28-30, 2008 Pasadena, California

Annals of Biomedical Engineering
2010 | Journal article
EID:

2-s2.0-77952011367

Contributors: Yamaguchi, T.; Ishikawa, T.; Imai, Y.; Matsuki, N.; Xenos, M.; Deng, Y.; Bluestein, D.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier

A detailed analysis of communication load balance on BlueGene supercomputer

Computer Physics Communications
2009 | Journal article
EID:

2-s2.0-67650866273

Contributors: Chen, Y.; Deng, Y.
Source: Self-asserted source
Yuefan Deng via Scopus - Elsevier
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Peer review (2 reviews for 2 publications/grants)

Review activity for Biomedical signal processing and control. (1)
Review activity for The journal of supercomputing. (1)