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


a(my last name)


  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.


Clarkson University, Department of Physics

The City University of New York, Computer Science Program


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 pdf]. Proposed an evolutionary generation process for simplicial complex networks with the preferential attachment property and the facet degree distribution following a power law [poster pdf]. 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 pdf].

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 pdf], etc.). Procedural generation and complex behaviors emerging from simple rules. Game programming [github ]. Agent-based social simulation.


Posters and Talks