Personal information

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Employment (3)

University at Buffalo - The State University of New York: Buffalo, NY, US

2012-09-01 to present
Employment
Source: Self-asserted source
Nikolay A. Simakov

Pittsburgh Supercomputing Center: Pittsburgh, Pennsylvania, US

2010-06-01 to 2012-07-31 | Postdoctoral Research Associate
Employment
Source: Self-asserted source
Nikolay A. Simakov

Carnegie Mellon University: Pittsburgh, US

2004-09-01 to 2010-05-30 | Research/Teaching Assistant ( Chemistry)
Employment
Source: Self-asserted source
Nikolay A. Simakov

Education and qualifications (3)

Carnegie Mellon University: Pittsburgh, PA, US

2004-09-01 to 2010-09-30 | Ph.D. ( Chemistry)
Education
Source: Self-asserted source
Nikolay A. Simakov

Moscow Institute of Physics and Technology: Moscow, RU

2002-09-01 to 2004-06-30 | M.S. (Molecular and Biological Physics)
Education
Source: Self-asserted source
Nikolay A. Simakov

Moscow Institute of Physics and Technology: Moscow, RU

1998-09-01 to 2002-06-30 | B.S. (Molecular and Biological Physics)
Education
Source: Self-asserted source
Nikolay A. Simakov

Funding (2)

Elements: Development and Dissemination of a Slurm Simulator

2020-06-01 to 2025-05-31 | Grant
Directorate for Computer & Information Science & Engineering (Alexandria, US)
GRANT_NUMBER: 2004954
Source: Self-asserted source
Nikolay A. Simakov via DimensionsWizard

EAGER: Workload Analysis of NSF Innovative HPC Program Resources

2017-11-15 to 2018-04-30 | Grant
Directorate for Computer & Information Science & Engineering (Alexandria, US)
GRANT_NUMBER: 1763033
Source: Self-asserted source
Nikolay A. Simakov via DimensionsWizard

Research resources (1)

Development and Dissemination of a Slurm Simulator

Works (34)

HPCMod: Agent-Based Modeling Framework for Modeling Users on High- Performance Computing Resources

AHFE International Conference on Human Factors in Design, Engineering, and Computing (AHFE 2024 Hawaii Edition)
2024-12-08 | Conference paper
Contributors: Nikolay Simakov
Source: Self-asserted source
Nikolay A. Simakov

Benchmarking and Continuous Performance Monitoring of Ookami, an ARM Fujitsu A64FX Testbed Cluster

Second International Workshop on HPC Testing and Evaluation of Systems, Tools, and Software (HPCTESTS 2024 at SC24)
2024-11-22 | Conference paper
Contributors: Nikolay A Simakov; Joseph P White; Matthew D Jones; Eva Siegmann; Daniel G Wood; ; Robert J Harrison
Source: Self-asserted source
Nikolay A. Simakov

First Impressions of the Sapphire Rapids Processor with HBM for Scientific Workloads

SN Computer Science
2024-06-07 | Journal article
Part of ISSN: 2661-8907
Contributors: Eva Siegmann; Robert J. Harrison; David Carlson; Smeet Chheda; Anthony Curtis; Firat Coskun; Raul Gonzalez; Daniel Wood; Nikolay A. Simakov
Source: Self-asserted source
Nikolay A. Simakov

The Data Analytics Framework for XDMoD

SN Computer Science
2024-04-20 | Journal article
Part of ISSN: 2661-8907
Contributors: Aaron Weeden; Joseph P. White; Robert L. DeLeon; Ryan Rathsam; Nikolay A. Simakov; Conner Saeli; Thomas R. Furlani
Source: Self-asserted source
Nikolay A. Simakov

Slurm Simulator Development: Balancing Speed, Accuracy, and Maintainability

International Conference on High Performance Computing in Asia-Pacific Region (HPCAsia 2024)
2024-01-25 | Conference poster
Contributors: Nikolay A Simakov; Robert L Deleon
Source: Self-asserted source
Nikolay A. Simakov

First Impressions of the NVIDIA Grace CPU Superchip and NVIDIA Grace Hopper Superchip for Scientific Workloads

Proceedings of the International Conference on High Performance Computing in Asia-Pacific Region Workshops
2024-01-11 | Conference paper | Author
Contributors: Nikolay A. Simakov; Matthew Jones; Thomas Furlani; Eva Siegmann; Robert Harrison
Source: Self-asserted source
Nikolay A. Simakov

Are we ready for broader adoption of ARM in the HPC community: Performance and Energy Efficiency Analysis of Benchmarks and Applications Executed on High-End ARM Systems

Proceedings of the HPC Asia 2023 Workshops
2023-02-27 | Conference paper | Author
Contributors: Nikolay A. Simakov; Robert DeLeon; Joseph White; Matthew Jones; Thomas Furlani; Eva Siegmann; Robert Harrison
Source: Self-asserted source
Nikolay A. Simakov

Developing Accurate Slurm Simulator

Practice and Experience in Advanced Research Computing
2022-07-08 | Conference paper
Contributors: Nikolay A. Simakov; Robert L. Deleon; Yuqing Lin; Phillip S. Hoffmann; William R. Mathias
Source: Self-asserted source
Nikolay A. Simakov

A64FX performance: experience on Ookami

2021 IEEE International Conference on Cluster Computing (CLUSTER)
2021-09 | Conference paper
Contributors: Md Abdullah Shahneous Bari; Barbara Chapman; Anthony Curtis; Robert J. Harrison; Eva Siegmann; Nikolay A. Simakov; Matthew D. Jones
Source: Self-asserted source
Nikolay A. Simakov

Ookami: Deployment and Initial Experiences

Practice and Experience in Advanced Research Computing
2021-07-17 | Conference paper
Contributors: Andrew Burford; Alan Calder; David Carlson; Barbara Chapman; Firat Coskun; Tony Curtis; Catherine Feldman; Robert Harrison; Yan Kang; Benjamin Michalowicz et al.
Source: Self-asserted source
Nikolay A. Simakov

Modernizing Titan2D, a Parallel AMR Geophysical Flow Code to Support Multiple Rheologies and Extendability

Lecture Notes in Computer Science
2019 | Book chapter | Author
Part of ISBN: 9783030343552
Part of ISBN: 9783030343569
Part of ISSN: 0302-9743
Part of ISSN: 1611-3349
Contributors: Nikolay A. Simakov; Renette Jones-Ivey; Ali Akhavan-Safaei; Hossein Aghakhani; Matthew Jones; Abani Patra
Source: Self-asserted source
Nikolay A. Simakov

Managing computational gateway resources with XDMoD

Future Generation Computer Systems
2019-09 | Journal article
Part of ISSN: 0167-739X
Contributors: Jeanette M. Sperhac; Robert L. DeLeon; Thomas R. Furlani; Steven M. Gallo; Martins Innus; Matthew D. Jones; Jeffrey T. Palmer; Abani Patra; Benjamin D. Plessinger; Ryan Rathsam et al.
Source: Self-asserted source
Nikolay A. Simakov

Microsecond Molecular Dynamics Simulations of Diphtheria Toxin Translocation T-Domain pH-Dependent Unfolding in Solution

2019-03-08 | Preprint
Contributors: Jose Flores-Canales; Nikolay A. Simakov; Maria G Kurnikova
Source: Self-asserted source
Nikolay A. Simakov

A Slurm Simulator: Implementation and Parametric Analysis

Lecture Notes in Computer Science
2018 | Book chapter
Part of ISBN: 9783319729701
Part of ISBN: 9783319729718
Part of ISSN: 0302-9743
Part of ISSN: 1611-3349
Contributors: Nikolay A. Simakov; Martins D. Innus; Matthew D. Jones; Robert L. DeLeon; Joseph P. White; Steven M. Gallo; Abani K. Patra; Thomas R. Furlani
Source: Self-asserted source
Nikolay A. Simakov

A Workload Analysis of NSF's Innovative HPC Resources Using XDMoD

2018 | Report
Contributors: Nikolay A. Simakov; Joseph P. White; Robert L. DeLeon; Steven M. Gallo; Matthew D. Jones; Jeffrey T. Palmer; Benjamin Plessinger; Thomas R. Furlani
Source: Self-asserted source
Nikolay A. Simakov

Effect of Meltdown and Spectre Patches on the Performance of HPC Applications

HPC Systems Professionals Workshop (HPCSYSPROS18) at SC18
2018 | Conference paper
Contributors: Nikolay A. Simakov; Martins D. Innus; Matthew D. Jones; Joseph P. White; Steven M. Gallo; Robert L. DeLeon; Thomas R. Furlani
Source: Self-asserted source
Nikolay A. Simakov

Federating XDMoD to Monitor Affiliated Computing Resources

2018 IEEE International Conference on Cluster Computing (CLUSTER)
2018-09 | Conference paper
Contributors: Jeanette Sperhac; Benjamin D. Plessinger; Jeffrey T. Palmer; Rudra Chakraborty; Gregary Dean; Martins Innus; Ryan Rathsam; Nikolay Simakov; Joseph P. White; Thomas R. Furlani et al.
Source: Self-asserted source
Nikolay A. Simakov

Slurm Simulator: Improving Slurm Scheduler Performance on Large HPC systems by Utilization of Multiple Controllers and Node Sharing

Proceedings of the Practice and Experience on Advanced Research Computing
2018-07-22 | Conference paper
Contributors: Nikolay A. Simakov; Robert L. DeLeon; Martins D. Innus; Matthew D. Jones; Joseph P. White; Steven M. Gallo; Abani K. Patra; Thomas R. Furlani
Source: Self-asserted source
Nikolay A. Simakov

Membrane Position Dependency of the pKa and Conductivity of the Protein Ion Channel

The Journal of Membrane Biology
2018-06 | Journal article
Part of ISSN: 0022-2631
Part of ISSN: 1432-1424
Contributors: Nikolay A. Simakov; Maria G. Kurnikova
Source: Self-asserted source
Nikolay A. Simakov

A Distal Disulfide Bridge in OXA-1 beta-Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of the Specificity Determining Omega Loop

Journal of Physical Chemistry B
2017 | Journal article
WOSUID:

WOS:000400039500008

Contributors: Simakov, Nikolay; Leonard, David A.; Smith, Jeremy C.; Wymore, Troy; Szarecka, Agnieszka
Source: Self-asserted source
Nikolay A. Simakov via ResearcherID

Workload Analysis of Blue Waters

2017 | Report
Contributors: Matthew D. Jones; Joseph P. White; Martins Innus; Robert L. DeLeon; Nikolay Simakov; Jeffrey T. Palmer; Steven M. Gallo; Thomas R. Furlani; Michael Showerman; Robert Brunner et al.
Source: Self-asserted source
Nikolay A. Simakov

Challenges of Workload Analysis on Large HPC Systems

Practice and Experience in Advanced Research Computing 2017: Sustainability, Success and Impact
2017-07-09 | Conference paper
Contributors: Joseph P. White; Martins Innus; Matthew D. Jones; Robert L. DeLeon; Nikolay Simakov; Jeffrey T. Palmer; Steven M. Gallo; Thomas R. Furlani; Michael Showerman; Robert Brunner et al.
Source: Self-asserted source
Nikolay A. Simakov

A Quantitative Analysis of Node Sharing on HPC Clusters Using XDMoD Application Kernels

Proceedings of Xsede16: Diversity, Big Data, and Science At Scale
2016 | Journal article
WOSUID:

WOS:000390305000032

Contributors: Simakov, Nikolay A.; DeLeon, Robert L.; White, Joseph P.; Furlani, Thomas R.; Innus, Martins; Gallo, Steven M.; Jones, Matthew D.; Patra, Abani; Plessinger, Benjamin D.; Sperhac, Jeanette et al.
Source: Self-asserted source
Nikolay A. Simakov via ResearcherID

Analysis of XDMoD/SUPReMM Data Using Machine Learning Techniques

2015 Ieee International Conference on Cluster Computing - Cluster 2015
2015 | Book chapter
WOSUID:

WOS:000378648100104

Contributors: Gallo, Steven M.; White, Joseph P.; DeLeon, Robert L.; Furlani, Thomas R.; Ngo, Helen; Patra, Abani K.; Jones, Matthew D.; Palmer, Jeffrey T.; Simakov, Nikolay; Sperhac, Jeanette M. et al.
Source: Self-asserted source
Nikolay A. Simakov via ResearcherID

Application kernels: HPC resources performance monitoring and variance analysis

Concurrency and Computation-Practice & Experience
2015 | Journal article
WOSUID:

WOS:000363766600038

Contributors: Simakov, Nikolay A.; White, Joseph P.; DeLeon, Robert L.; Ghadersohi, Amin; Furlani, Thomas R.; Jones, Matthew D.; Gallo, Steven M.; Patra, Abani K.
Source: Self-asserted source
Nikolay A. Simakov via ResearcherID

Open XDMoD: A Tool for the Comprehensive Management of High-Performance Computing Resources

Computing in Science & Engineering
2015 | Journal article
WOSUID:

WOS:000356900400007

Contributors: Palmer, Jeffrey T.; Gallo, Steven M.; Furlani, Thomas R.; Jones, Matthew D.; DeLeon, Robert L.; White, Joseph P.; Simakov, Nikolay; Patra, Abani K.; Sperhac, Jeanette; Yearke, Thomas et al.
Source: Self-asserted source
Nikolay A. Simakov via ResearcherID

Comprehensive, open-source resource usage measurement and analysis for HPC systems

Concurrency and Computation-Practice & Experience
2014 | Journal article
WOSUID:

WOS:000340283700010

Contributors: Browne, James C.; DeLeon, Robert L.; Patra, Abani K.; Barth, William L.; Hammond, John; Jones, Matthew D.; Furlani, Thomas R.; Schneider, Barry I.; Gallo, Steven M.; Ghadersohi, Amin et al.
Source: Self-asserted source
Nikolay A. Simakov via ResearcherID

pH-Triggered Conformational Switching of the Diphtheria Toxin T-Domain: The Roles of N-Terminal Histidines

Journal of Molecular Biology
2013 | Journal article
WOSUID:

WOS:000322296400011

Contributors: Kurnikov, Igor V.; Kyrychenko, Alexander; Flores-Canales, Jose C.; Rodnin, Mykola V.; Simakov, Nikolay; Vargas-Uribe, Mauricio; Posokhov, Yevgen O.; Kurnikova, Maria; Ladokhin, Alexey S.
Source: Self-asserted source
Nikolay A. Simakov via ResearcherID

Mechanism of the pH-Triggered Formation of Membrane-Competent State of the Diphtheria Toxin Translocation Domain Revealed by Simulations and Experiment

Biophysical Journal
2011 | Journal article
WOSUID:

WOS:000306288601498

Contributors: Flores-Canales, Jose C.; Kurnikov, Igor; Simakov, Nikolay; Kyrychenko, Alexander; Rodnin, Mykola V.; Ladokhin, Alexey S.; Kurnikova, Maria
Source: Self-asserted source
Nikolay A. Simakov via ResearcherID

Extension of Poisson-Nernst Planck Theory of Ion Conductivity with Soft-Repulsion Potential between Ions and Protein. Sensitivity of I-V Properties of alpha-Hemolysin Channel on its Penetration Depth into Membrane

Biophysical Journal
2010 | Journal article
WOSUID:

WOS:000208762003161

Contributors: Simakov, Nikolay A.; Kurnikova, Maria G.
Source: Self-asserted source
Nikolay A. Simakov via ResearcherID

Soft Wall Ion Channel in Continuum Representation with Application to Modeling Ion Currents in alpha-Hemolysin

Journal of Physical Chemistry B
2010 | Journal article
WOSUID:

WOS:000284287700047

Contributors: Simakov, Nikolay A.; Kurnikova, Maria G.
Source: Self-asserted source
Nikolay A. Simakov via ResearcherID

Calculation of Current-Voltage properties of Biological Ion Channel, using Poisson-Nernst-Planck (PNP) Theory

Biophysical Journal
2009 | Journal article
WOSUID:

WOS:000426362200506

Contributors: Simakov, Nikolay A.; Kurnikova, Maria G.
Source: Self-asserted source
Nikolay A. Simakov via ResearcherID

Calculation of current-voltage characteristics of biochannel, using potential of mean force poisson-nernst-planck (PMFPNP) method

Biophysical Journal
2007 | Journal article
WOSUID:

WOS:000243972404329

Contributors: Simakov, Nikolay A.; Kumikova, Maria G.
Source: Self-asserted source
Nikolay A. Simakov via ResearcherID

Effect of lipid composition on the "membrane response" induced by a fusion peptide

Biochemistry
2005 | Journal article
WOSUID:

WOS:000233068900024

Contributors: Volynsky, PE; Polyansky, AA; Simakov, NA; Arseniev, AS; Efremov, RG
Source: Self-asserted source
Nikolay A. Simakov via ResearcherID

Peer review (2 reviews for 1 publication/grant)

Review activity for Future generation computer systems. (2)