Alexey Nikolaev
Hunter College of CUNY
695 Park Avenue, HN 1000C
New York, NY 10065

Email

a(my last name)@gradcenter.cuny.edu

Education

1. Currently enrolled in the Ph.D. Computer Science program at the Graduate Center of the City University of New York, New York, NY.
   Adviser: Saad Mneimneh.
   Area of Study: Network Science, Computational Biology, Simulation.

2. M.S. Physics, Clarkson University, Postdam, NY (2011).
   Adviser: Maria E. Gracheva.
   Area of Study: Computational Biophysics.

3. Specialist degree in Physics (Magna Cum Laude), Moscow State University, Russia (2008).
   Specialization: Computer Methods in Physics.

Employment

Clarkson University, Department of Physics

• August 2008 - July 2010. Teaching Assistant.
  • Instructor for PH131 - Physics I (Fall 2008, Fall 2009).
  • Instructor for PH132 - Physics II (Spring 2009, Spring 2010).
• July 2010 - July 2011. Research Assistant.

The City University of New York, Computer Science Program

• August 2011 - present. Research Assistant at Hunter College and CUNY Graduate Center.
  • Work with Professor Saad Mneimneh.
  • Work with Professor Amotz Bar-Noy.
• August 2013 - present. Adjunct Lecturer at Hunter College.
  • Teaching CSCI 150: Discrete Structures (Fall 2013, Spring 2014, Summer 2014, Fall 2014, Spring 2015, Summer 2015, Fall 2015, Spring 2016, Summer 2016, Spring 2017).
  • Teaching CSCI 135: Software Analysis and Design 1 (Spring 2015).
  • Teaching CSCI 136: Supervised Programming Labs (Spring 2015, Fall 2015, Spring 2016, Fall 2016, Spring 2017).

Research

Network Science: Teams and higher-order interactions. With Saad Mneimneh and Amotz Bar-Noy. Study collaborative networks of teams using an abstract simplicial complex model. Studied metrics for evaluating strength of such collaborative networks [paper ]. Proposed an evolutionary generation process for simplicial complex networks with the preferential attachment property and the facet degree distribution following a power law [poster ]. Research real-life networks of teams, such as Wikipedia Talk pages, call-graph networks in source code, DBLP. Simulated bots’ interaction and their performance with Volunteer Science project. Developed a tool for visualizing abstract simplicial complexes [github ].

Systems Biology: Stochastic approximation for Gene Regulatory Networks (GRNs). With Felisa Vazquez-Abad. A hybrid model for estimating periodic oscillations in gene regulatory networks (applied to a circadian clock GRN) and gradient estimation of the period w.r.t. the reaction rates [paper ].

Computational Biology: Protein folding. With Saad Mneimneh. A probabilistic model for predicting secondary structures in proteins.

A computer language for teaching Combinatorics. With Saad Mneimneh. Developed an interactive programming language for teaching counting principles particularly geared towards applying multiplication rule, combinations, and permutations with or without repetition [more info ] [run in the browser ].

Modeling semiconductor-electrolyte nano-devices (Master’s thesis). With Maria Gracheva. Developed a model for a semiconductor membrane with a nanopore submerged in KCl electrolyte. Its electrostatic (Poisson-Boltzmann) and dynamic (Poisson-Nernst-Planck) models. Numerical integration of the resulting system of partial differential equation. Proposed and explored the properties of a nanopore-based ionic MOSFET-like transistor.

Other topics of interest: Functional programming and language design. Process calculi and models of concurrency. Formal methods. Linear Logic. Computability and non-standard models of computation (CRNs, biocomputing, cellular automata, infinitary computability [poster ], etc.). Procedural generation and complex behaviors emerging from simple rules. Game programming [github ]. Agent-based social simulation.

Publications

• “Controlled Growth of Simplicial Complex Networks.” Alexey Nikolaev, Saad Mneimneh, Amotz Bar-Noy, Ram Ramanathan. IEEE International Workshop on Network Science for Communication Networks (NetSciCom). Atlanta, GA, USA, May 2017.

• “Counting with Code.” Saad Mneimneh and Alexey Nikolaev. ACM Journal of Computing Sciences in Colleges, April 2017 (also presented at CCSCNE 2017)

• “Testing Higher-Order Network Structures in an Online Experiment.” Jason Radford, Amotz Barnoy, Alexey Nikolaev, Saad Mneimneh, David Lazer, Ram Ramanathan. CSCW Companion 2016: 377-380.

• “Stochastic approximation for regulating circadian cycles, a precision medicine viewpoint.” Alexey Nikolaev and Felisa J. Vazquez-Abad. Proc. 2015 Winter Simulation Conference. December 2015.

• “Measuring the Strength of Networks of Teams: Metrics and Properties.” Ali Assarpour et al. Proc. IEEE NetSciCom 2015 (colocated with INFOCOM), Hong Kong, April 2015.

• “Poisson-Nernst-Planck model for an ionic transistor based on a semiconductor membrane”, A. Nikolaev, M. Gracheva, Journal of Computational Electronics (Special Issue) 13(4), p. 818-825 (2014).

• “A mathematical model for secondary structure in proteins.” Alexey Nikolaev and Saad Mneimneh. BIBE 2013, 1-6.

• Masters thesis: “Poisson-Nernst-Planck Model for Simulating Ionic Current through the Nanopore in a Semiconductor Membrane”, 2011.

• “Simulation of ionic current through the nanopore in a double-layered semiconductor membrane” A. Nikolaev, M. E. Gracheva, Nanotechnology, 2011, 22 (16) 165202.

• “On formation of sharp transition layers in two-dimensional reaction-diffusion models” (Russian), N.N. Nefedov, A. Nikolaev, et al., ZhVMiMF, 2007, 47 (8), 1356-1364.

Posters and Talks

• Poster “Controlled evolution of collaborative networks: is it a good idea?”, A. Nikolaev, S. Mneimneh, A. Bar-Noy, R. Ramanathan. NetSci-X 2017, January 15th (2017).
• Talk “A Hybrid Stochastic Model for Self-Regulated Biochemical Systems”, A. Nikolaev, F. Vazquez-Abad, 4th Rutgers Applied Probability Conference, October 3rd (2015).
• Poster “Simulation of Infinite Time Turing Machines on a Classical Turing Machine”, A. Nikolaev, Computer Science Student Workshop 2013, CUNY, New York, New York, May 3rd (2013).
• Talk “A Probabilistic Model for Deriving Structure of Proteins from Their Sequence Information”, A. Nikolaev, S. Mneimneh, STAR-W 2013: STudents Algoritmic Reserach Workshop, CUNY, New York, New York, March 22nd (2013).
• Talk “From Sequences to Structures: A Computational Probability Approach Based on Percolation Theory”, A. Nikolaev, S. Mneimneh, INFORMS Computing Society Conference 2013, Santa Fe, New Mexico, January 6th - 8th (2013).
• Poster “Simulation of ionic current through the nanopore in a double layered semiconductor membrane”, A. Nikolaev, M. E. Gracheva, Biophysical Society Meeting, Baltimore, Maryland, March 5th - 9th (2011).
• Talk “Ionic current in semiconductor nanopores: Designing the most efficient devices”, Clarkson University, Physics Department Colloquium, October 8th (2010).
• Poster “Modeling of ionic currents in a semiconductor nanopore”, A. Nikolaev, M. E. Gracheva, Biophysical Society Meeting, San Francisco CA, February 20th - 28th (2010).
• Talk “Modeling of a semiconductor membrane with a nanopore in a KCl solution” A. Nikolaev, Clarkson University, Physics Department Colloquium, November 13th (2009)
• Talk “Computational model of controlled translocation of DNA molecule through a nanopore membrane with tunable electrostatic potential”, A. Nikolaev, M. E. Gracheva, American Physical Society, Pittsbugh PA, March 16th - March 20th (2009).
• Poster “Controlled DNA translocation through a nanopore membrane with different electrostatic landscapes”, A. Nikolaev, M. E. Gracheva, Biophysicsl Society Meeting, Boston MA, February 28th - March 4th (2009).
• Talk “Simple Model for Controlled DNA Translocation through a Nanopore” A. Nikolaev, Clarkson University, Physics Department Colloquium, January 30th (2009)
• Talk “Investigation of processes of phase and component division in lipid films”, N. Grachev, A. Nikolaev, et al., XIII Conference “Mathematics. Computer. Education”, Russia (2006).
• Talk “Thermodynamics and asymptotic theory: phase and component division in binary sistems”, N. Grachev, A. Nikolaev, Conference ’Lomonosov - 2006’, Moscow, Russia (2006).