Put me inside SSC. Let's test superstring theory, Oh yoi yoi accelerate the protons, stir it twice and then just add me. - Gogol Bordello

Home Department: Beckman Institute

Office Address: Beckman Institute, Room 3143

Office Phone: (217) 244-7403

Home Page: perilla.me

Email Address: juan [at] ks [dot] uiuc [dot] edu



  • The molecular architecture of HIV
  • Molecular mechanisms of cell-signaling processes.
  • Mechanisms of folding and signaling function by membrane receptors.
  • Conformational and phase changes in biomolecules.
  • Protein-protein interactions in biological membranes.
  • Theoretical and computational methods.
  • Medical imaging for treatment and diagnosis

Selected Publications

Mature HIV-1 capsid structure courtesy of David Goodsell

  • CryoEM and Computer Simulations Reveal a Novel Kinase Conformational Switch in Bacterial Chemotaxis Signaling.
    C. Keith Cassidy, Benjamin A. Himes, Frances J. Alvarez, Jun Ma, Gongpu Zhao, Juan R. Perilla, Klaus Schulten and Peijun Zhang
    eLife, 2015, in press
  • Dynamic allostery governs cyclophilin A-HIV capsid interplay.
    Manman Lu, Guangjin Hou, Huilan Zhang, Christopher L. Suiter, Jinwoo Ahn, In-Ja L. Byeon, Juan R. Perilla, Christopher J. Langmead, Ivan Hung, Peter L. Gor'kov, Zhehong Gan, William Brey, Christopher Aiken, Peijun Zhang, Klaus Schulten, Angela M. Gronenborn and Tatyana Polenova
    Proceedings of the National Academy of Sciences USA, 2015, in press
  • Chemical Visualization of Human Pathogens : The Retroviral Capsids.
    Juan R. Perilla*, Boon Chong Goh*, John Stone and Klaus Schulten
    Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, SuperComputing'15. IEEE Press, 2015
  • Atomic modeling of an immature retroviral lattice using molecular dynamics and mutagenesis.
    Boon Chong Goh*, Juan R. Perilla*, Matthew R. England, Katrina J. Heyrana, Rebecca C. Craven and Klaus Schulten.
    * co-first authors
    Structure, 2015, 23,1414-1425
  • Molecular dynamics simulations of large macromolecular complexes.
    Juan R. Perilla, Boon Chong Goh, C. Keith Cassidy, Bo Liu, Rafael C. Bernardi, Till Rudack, Hang Yu, Zhe Wu and Klaus Schulten
    Current Opinion in Structural Biology, 2015, 31, 64-74
  • Computing ensembles of transitions with molecular dynamics simulations.
    Juan R. Perilla and Thomas B. Woolf
    In Molecular Modeling of Proteins - Methods in Molecular Biology, Springer, 2015; ISBN: 978-1-4939-1464-7
  • Ictal propagation of high frequency activity is recapitulated in interictal recordings: Effective connectivity of epileptogenic networks recorded with intracranial EEG.
    A. Korzeniewskaa, M.C. Cervenkaa, C.C. Jounya, J.R. Perilla, J. Harezlakc, G.K. Bergeya, P.J. Franaszczuka, N.E. Crone.
    Neuroimage, 2014, 101, 96-113
  • Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.
    Gongpu Zhao* , Juan R. Perilla*, Ernest L. Yufenyuy*, Xin Meng, Bo Chen, Jiying Ning, Jinwoo Ahn, Angela Gronenborn, Klaus Schulten, Christopher Aiken, and Peijun Zhang.
    * Equal contribution authors
    Nature, 2013, 497 , 643-646
  • Molecular dynamics simulations of transitions for ECD Epidermal Growth Factor Receptors show key differences between human and drosophila forms of the receptors
    Juan R. Perilla, Daniel Leahy, and Thomas Woolf.
    Proteins: Structure, Function, and Bioinformatics, 2013, 81, 1113-1126
  • Towards the prediction of order parameters from molecular dynamics simulations in proteins
    Juan R. Perilla and Thomas B. Woolf.
    Journal of Chemical Physics , 2012, 136 , 164101
  • Computing ensembles of transitions from stable states: Dynamic importance sampling
    Juan R. Perilla*; Oliver Beckstein; Elizabeth J. Denning; Thomas B. Woolf*.
    * Corresponding authors
    Journal of Computational Chemistry, 2011, 32, 196-209
  • Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open <-> Closed Transitions
    Oliver Beckstein*; Elizabeth J. Denning*; Juan R. Perilla*; Thomas B. Woolf*.
    * Corresponding authors
    Journal of Molecular Biology, 2009, 394, 160-176
  • Del socavón a la vida (From the cave to life). Baseline to the eradication and prevention of child labor in artisan minery in Colombia.
    United Nations Development Programme, 2003, ISBN: 958-701-350-6.

  • Journal Covers

    Mature HIV-1 capsid structure by cryo-EM and all-atom MD. Mature HIV-1 capsid structure by cryo-EM and all-atom MD. Mature HIV-1 capsid structure by cryo-EM and all-atom MD.

    Protein Data Bank Entries

  • Molecule of the month: HIV Capsid
  • Structure of HIV-1 capsid protein by cryo-EM - Single hexamer
  • Structure of HIV-1 Capsid Protein by Cryo-EM - Hexamer of hexamers
  • Atomic-level structure of the entire HIV-1 capsid
  • Atomic-level structure of the entire HIV-1 capsid
  • News Coverage

  • Build your own paper model of the HIV-1 capsid
  • Wit, grit and a supercomputer yield chemical structure of HIV capsid
  • BBC Health News - HIV Capsid Structure Revealed
  • Gizmodo - How a Supercomputer May Have Finally Unlocked a Way to Beat HIV
  • Popular Science - Supercomputer Creates Atom-By-Atom Model Of HIV Virus Shell
  • Beckman Institute News Release
  • National Institutes of Health (NIH) -Imaging HIV's Inner Shell
  • National Science Foundation (NSF) - Cracking the Code of HIV; Providing An Up-Close View of the Enemy
  • CHARMM (Chemistry at HARvard Macromolecular Mechanics)

  • Dynamic Importance Sampling (DIMS). CHARMM36 release, August 2007
  • A major mode for editing CHARMM scripts in Emacs: charmm-mode. Installation instructions.

Lectures and Presentations

  • Structure, Dynamics, and Function of the HIV Capsid at the All-atom Level. 2014 FASEB virus assembly and structure conference.
  • Unveiling the structure of the HIV-1 capsid. 2013 GPU Technology Conference.
  • Structural Analysis of Supramolecular Assemblies by Hybrid Methods. 2013 Keystone Symposia, Lake Tahoe, CA
  • CUDA Research Fast Forward. NVIDIA Booth, SuperComputing 2011, Seattle, WA
  • Towards finding a better reaction coordinate: NtrC and DIMS. Biophysical Society 55th Annual Meeting, 2011. Baltimore, MD
  • Dynamic importance sampling calculations on ECD Epidermal Growth Factor Receptor conformational changes. Biophysical Society 55th Annual Meeting, 2011. Baltimore, MD
  • Computing Transitions in Macromolecular Systems: Dynamic Importance Sampling. Biophysical Society 53th Annual Meeting, 2009. Boston, MA
  • Understanding the conformational changes in Ca-ATPase using Coarse-grained and All-atom simulations with Dynamic Importance Sampling. Biophysical Society 53th Annual Meeting, 2009. Boston, MA
  • Medical imaging

  • Language Mapping in Multilingual Patients: Electrocorticography and Cortical Stimulation During Naming.
    Mackenzie C. Cervenka, Dana F. Boatman-Reich, Julianna Ward, Piotr J. Franaszczuk, and Nathan E. Crone. Frontiers in human neuroscience, 2011, 5:13
  • Choices of references used for EEG measures of effective connectivity to localize seizure foci. American Epilepsy Society, 2011. Baltimore, MD
  • Propagation of Intracranial Electroencephalographic Activity between Neocortex and Subcortical Structures as an Indicator of Seizure Onset. American Epilepsy Society, 2010. San Antonio, TX
  • Legacy

  • Quark top production and detection in ATLAS(LHC). Revista Colombiana de Física, 2006, 38, 1276-1280