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.
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).
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
Proposed an evolutionary generation process for simplicial complex networks with
the preferential attachment property and the facet degree distribution following a power law
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
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.
“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).