Nikolay Simakov, PhD

Dr. Nikolay Simakov.

Computational Scientist

Dr. Simakov joined the Center for Computational Research in 2012. He has a doctorate in Computational Chemistry from Carnegie Mellon University. He also has BA and MA in Applied Physics and Mathematics from the Moscow Institute of Physics and Technology.

Areas of Support

  • ACCESS Metrics (formerly - XDMoD - XSEDE Metrics on Demand)  A comprehensive auditing framework for the NSF ACCESS cyberinfrastructure, the follow-on to XSEDE, which aims at improving the operational efficiency and management of NSF's network of computational resources.
  • Application kernel performance monitory
  • Slurm simulator

Research Interests:

  • High-Performance Computing
  • Machine learning
  • Scientific software optimization
  • Data analytics for large datasets
  • Simulation of biomolecular systems


Dr. Simakov taught several courses at UB, namely EAS509 Statistical Learning and Data Mining-II and CDA501 Introduction to Data Driven Analysis. He also supervised several undergraduate students during their summer internship at CCR.

Selected Publications:

  • Nikolay A. Simakov, Robert L. Deleon, Yuqing Lin, Phillip S. Hoffmann, and William R. Mathias. 2022. Developing Accurate Slurm Simulator. In Practice and Experience in Advanced Research Computing (PEARC '22). Association for Computing Machinery, New York, NY, USA, Article 59, 1–4.
  • M. A. S. Bari et al., "A64FX performance: experience on Ookami," 2021 IEEE International Conference on Cluster Computing (CLUSTER), 2021, pp. 711-718, doi: 10.1109/Cluster48925.2021.00106.
  • Simakov, N.A., Jones-Ivey, R.L., Akhavan-Safaei, A., Aghakhani, H., Jones, M.D., Patra, A.K. (2019). "Modernizing Titan2D, a Parallel AMR Geophysical Flow Code to Support Multiple Rheologies and Extendability". In: Weiland, M., Juckeland, G., Alam, S., Jagode, H. (eds) High Performance Computing. ISC High Performance 2019. Lecture Notes in Computer Science(), vol 11887. Springer, Cham.
  • Simakov, N. A., White, J. P., DeLeon, R. L., Ghadersohi, A., Furlani, T. R., Jones, M. D., Gallo, S. M., and Patra, A. K. (2015) "Application kernels: HPC resources performance monitoring and variance analysis". Concurrency Computat.: Pract. Exper., 27: 5238– 5260. doi: 10.1002/cpe.3564.
  • Nikolay Simakov, David A. Leonard, Jeremy C. Smith, Troy Wymore, and Agnieszka Szarecka. "A Distal Disulfide Bridge in OXA-1 β-Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of the Specificity Determining Ω Loop". The Journal of Physical Chemistry B 2017 121 (15), 3285-3296. DOI: 10.1021/acs.jpcb.6b07884
  • Simakov, Nikolay A. and Kurnikova, Maria G.. "Graphical Processing Unit accelerated Poisson equation solver and its application for calculation of single ion potential in ion-channels". Computational and Mathematical Biophysics, vol. 1, no. 2013, 2013, pp. 151-163.
  • Nikolay A. Simakov and Maria G. Kurnikova. "Soft Wall Ion Channel in Continuum Representation with Application to Modeling Ion Currents in α-Hemolysin". The Journal of Physical Chemistry B 2010 114 (46), 15180-15190. DOI: 10.1021/jp1046062