76 Elm st. apt 114

Jamaica Plain, MA 02130

(h) 617-524-0374 (m) 510-604-1688




Kirill N. Shokhirev, Ph.D.


Research Interests

Mathematical, statistical, and computational modeling of complex systems



Analysis, modeling and numerical simulation of biological and physical systems. Scientific programming using MATLAB, C++, Fortran in Windows and Linux environments




1997 - 2005

University of California

Berkeley, CA

PhD Program in Physics

  MA Physics, May 2000

  PhD Physics, December 2005

Thesis: Estimation of the orientation of short lines with a realistic population of cortical neurons

Advisor: Prof. Donald A. Glaser


1994 - 1997

University of Arizona

Tucson, AZ

BS in Physics and Mathematics


1992 - 1994

Novosibirsk State University

Novosibirsk, Russia

Undergraduate program in Physics


Professional Experience


Physical Sciences Inc.

Andover, MA


        Developed and tested data fusion algorithms and simulation environment for detection and localization of radiological sources in an urban environment

        Advanced data fusion optimization methods for Chemical-Biological sensor networks by utilizing information-theoretical analysis, algorithm development and numerical simulation

2006 - 2008

Magma Design Automation

San Jose, CA

Member of Technical Staff (research engineer )

        Developed computational methods and algorithms for simulating optical and diffusion phenomena in micro-lithography

        Developed calibration framework for testing model results against experimental data. Implemented original algorithms (C++ and MATLAB) and integrated new code with existing software




1997 - 2005

University of California

Berkeley, CA

Postdoctoral researcher

        Modeled orientation estimation in human visual cortex

        Developed parallel computational tools for studying the visual system


Graduate Student Researcher

        Investigated interaction among cortical feature maps and their influence on orientation perception and motion detection

        Analyzed models of population coding and information processing in the human visual system

        Designed algorithms and computer software for large-scale simulation of populations of interacting neurons

        Developed probabilistic models of visual illusions


Graduate Student Instructor

        Assisted in teaching of an upper-division course on computational modeling of biological systems

        Developed new instructional materials and methods. Supervised the computer laboratory for the course


Graduate Student Researcher

        Developed theoretical models and data analysis software for ultra-low temperature experiments on Josephson effect in superfluid 3He.


Shokhirev K. N., Kumar T., & Glaser D. A. Cortical feature maps and the population vector estimator of orientation. in preparation

Shokhirev K. N., Kumar T., & Glaser D. A. The influence of cortical feature maps on the encoding of the orientation of a short line. Accepted for publication: Journal of Computational Neuroscience

Shokhirev, K. N., Kumar, T., & Glaser, D. A. (2003). Estimation of the parameters of a visual stimulus from the responses of a realistic population of model visual neurons [Abstract]. Journal of Vision, 3(12), 81a, http://journalofvision.org/3/12/81/, doi:10.1167/3.12.81.

Shokhirev K N, Glaser D A Interaction among cortical maps [Abstract]

NEUROCOMPUTING 44: 993-1000 JUN 2002

Dharmasena G, Phillips TR, Shokhirev KN Parker GA, Keil M Vibrationally and rotationally resolved angular distributions for F+H2 -> HF(ν, j) + H reactive scattering. JOURNAL OF CHEMICAL PHYSICS 106(23): 9950-9953 JUN 15 1997



References are available upon request




MATLAB, C, C++, Java, FORTRAN, MPI, distributed computing, data analysis, data fusion, algorithms, numerical model, scientific programming, simulation, vision, neuroscience, image processing, computational biology , Windows, Linux, Eclipse