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

The City University of New York, Computer Science Program

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 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.

Publications

Posters and Talks