A large part of my research involves development of scientific software, either to directly simulate a given system, or to post-process and analyze the data produced by publicly available packages like LAMMPS or HOOMD Blue.

I have an extensive background in advanced numerical techniques and strong knowledge of C/C++, Python, Fortran 77/90 and Unix/Linux shell scripting. I am also proficient in parallel programming with MPI/OpenMP as well as in graphics card programming.

Scientific codes I have developed

(listed in a reversed chronological order)

  • Membrane
    a flexible object-oriented Monte Carlo code for initializing, simulating, and analyzing multicomponent charged elastic and liquid membranes
    around 35,000 lines of C++ and 12,000 lines of Python code
  • NPT integrator, Morse and electrostatic potentials for HOOMD-Blue
    approximately 2,000 lines of GPU CUDA C code
  • NanoBuilder
    object-oriented toolkit for rapid construction of initial configurations for simulations of nanoparticle/copolymer systems
    approximately 15,000 lines of Python code
  • NanoAnalyzer
    a library of Python classes for data analysis of coarse grained molecular dynamics simulations
    approximately 3,000 lines of Python code
  • GreenCarlo
    a Monte Carlo simulation of charged lipid bilayer using fast Green’s function method
    approximately 5,000 lines of C++ code
  • ColloidMC
    Monte Carlo simulation of colloid systems
    around 3000 lines of C++ code.
  • CGBuild
    Python toolkit for generating initial configuration for molecular dynamics simulations of coarse grained proteins and lipids
    approximately 5000 lines of Python code
  • FLEX
    set of tools for solving and analyzing fluctuation exchange approximation (FLEX) equations for superconductors
    approximately 18,000 lines of ANSI C and 1,000 lines of Python code, parallelized with OpenMP and MPI
  • MDSim
    a general purpose molecular dynamics code
    over 17,000 lines of C++ code, parallelized with MPI
  • BdG
    solver for Bogoliubov-de Gennes equations for type II superconductors in external magnetic field
    approximately 5,000 lines of Fortran 90 code
  • RRN
    conductivity calculation of a random resistor network
    over 4000 lines of C code parallelized using MPI
  • Aligner
    a simple OpenGL based tool for alignment of structures produced in molecular dynamics simulations
    around 2000 lines of C++ OpenGLcode
  • Disorder
    Monte Carlo code for simulation of Ising and Heisenberg spin models with correlated disorder
    approximately 4,000 lines of C/C++ code

...and many many more short programs and scripts.

If you are interested to learn more about any of those codes, please send me an e-mail.