Juan Roberto Perilla

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

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

Education

Research

  • 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

Publications

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

  • 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.
    Nature , in press
  • 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, in press
  • 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.   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.   Journal of Molecular Biology, 2009, 394, 160-176

    • Legacy

  • Quark top production and detection in ATLAS(LHC). Revista Colombiana de Física, 2006, 38, 1276-1280
  • Del socavón a la vida (From the cave to life). Baseline to the eradication and prevention of child labor in artisan minery in Colombia. 2003, ISBN: 958-701-350-6.

CHARMM (Chemistry at HARvard Macromolecular Mechanics)

  • Dynamic Importance Sampling (DIMS).
  • A major mode for editing CHARMM scripts in Emacs: charmm-mode.

Lectures and Presentations

  • 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-APTase 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