Alexey Nikolaev
Hunter College of CUNY
695 Park Avenue, HN 1000C
New York, NY 10065
a(my last name)@gradcenter.cuny.edu
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.
M.S. Physics, Clarkson University, Postdam, NY (2011).
Adviser: Maria E. Gracheva.
Area of Study: Computational Biophysics.
Specialist degree in Physics (Magna Cum Laude), Moscow State University, Russia (2008).
Specialization: Computer Methods in Physics.
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.
“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.
“Simulation of ionic current through the nanopore in a double-layered semiconductor membrane” A. Nikolaev, M. E. Gracheva, Nanotechnology, 2011, 22 (16) 165202.