Staff Profiles

Anton Arkhipov, Ph.D.

Associate Investigator

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Anton Arkhipov joined the Allen Institute in 2013 as an assistant investigator in the Modeling, Analysis, and Theory group. He is leading efforts to carry out biophysically detailed simulations of individual neurons as well as large-scale neuronal circuits from the mouse visual system. The main focus of his research is on integration of experimental anatomical and physiological data to build sophisticated, highly realistic computational models of cortical circuitry, with the aim of elucidating mechanisms underlying processing of visual information in the cortex. Before joining the Allen Institute he was a Postdoctoral Fellow at D. E. Shaw Research in New York City, where he used a specialized supercomputing architecture to perform computational studies of structure-function relationships in proteins, with the emphasis on cancer-associated cell-surface receptors. Arkhipov received his B.S. and M.S. in Physics from Moscow Institute of Physics and Technology and a Ph.D. in Physics from the University of Illinois at Urbana-Champaign.


Research Interests

Anton Arkhipov applies high-performance computing to simulate neuronal activity in the mouse visual system. Using experimentally observed neuronal morphologies, connectivity patterns, and electrophysiological properties, he constructs highly detailed, biophysically accurate models of neuronal circuits. The main aim is to build powerful models that, on the one hand, reproduce major features of in vivo experimental recordings from anesthetized and awake mice and, on the other, allow for testable predictions about mechanisms involved in processing of the visual information in the cortex.


  • Computational Neuroscience
  • Theoretical and Computational Biophysics
  • High-performance Computing

Research Programs

  • Modeling, Analysis & Theory

Selected Publications

Inferring cortical function in the mouse visual system through large-scale systems neuroscience

July 5, 2016

Hawrylycz M, Anastassiou C, Arkhipov A, Berg J, Buice M, Cain N, Gouwens NW, Gratiy S, Iyer R, Lee JH, Mihalas S, Mitelut C, Olsen S, Reid RC, Teeter C, de Vries S, Waters J, Zeng H, Koch C; Barber C, Becker L, Berg B, Bernard A, Bertagnolli D, Bickley K, Bleckert A, Blesie N, Bodor A, Bohn P, Bowles N, Brouner K, Bumbarger D, Caldejon S, Casal L, Casper T, Cetin A, Chapin M, Chatterjee S, Cheng A, da Costa N, Cross S, Cuhaciyan C, Daigle T, Dang C, Danskin B, Desta T, Dee N, Denman D, Dolbeare T, Donimirski A, Dotson N, Durand S, Farrell C, Feng D, Fisher M, Fliss T, Garner A, Garrett M, Garw

Architecture and membrane interactions of the EGF receptor

January 2013

Arkhipov A, Shan Y, Das R, Endres NF, Eastwood MP, et al

Conformational coupling across the plasma membrane in activation of the EGF receptor

January 2013

Endres NF, Das R, Smith AW, Arkhipov A, Kovacs E, et al

Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization

May 2012

Shan Y, Eastwood MP, Zhang X, Kim ET, Arkhipov A, et al

Molecular dynamics simulations of the complete satellite tobacco mosaic virus

March 2006

Freddolino PL, Arkhipov AS, Larson SB, McPherson A, Schulten K