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) 244-3157

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

  • 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

  • Choices of references used for EEG measures of effective connectivity to localize seizure foci. American Epilepsy Society, 2011. Baltimore, MD
  • 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
  • Propagation of Intracranial Electroencephalographic Activity between Neocortex and Subcortical Structures as an Indicator of Seizure Onset. American Epilepsy Society, 2010. San Antonio, TX
  • 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
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