Juan Roberto Perilla
Home Department: Beckman Institute
Office Address: Beckman Institute, Room 3143
Office Phone: (217) 244-7403
Email Address: juan [at] ks [dot] uiuc [dot] edu
- Ph. D in Biophysics and Biophysical Chemistry
Johns Hopkins University - School of Medicine, 2011
- B.S. Physics
Universidad Nacional de Colombia, 2005
- 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
- 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
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.
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.
- 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
- 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
- Dynamic Importance Sampling (DIMS). CHARMM36 release, August 2007
- A major mode for editing CHARMM scripts in Emacs: charmm-mode. Installation instructions.
Protein Data Bank Entries
CHARMM (Chemistry at HARvard Macromolecular Mechanics)
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-APTase using Coarse-grained and All-atom simulations with Dynamic Importance Sampling. Biophysical Society 53th Annual Meeting, 2009. Boston, MA
- 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
- Quark top production and detection in ATLAS(LHC). Revista Colombiana de Física, 2006, 38, 1276-1280