Presentations
At the 235th American Chemical Society National Meeting in New Orleans, LA, our group gave the following presentations:
"Using inter-residue distances to predict protein structure", Christina
"Computational Studies of Structure-Activity Relationships in FF Neuropeptide", Georgios
"Computational Studies of the interaction of sulfoindocyanine dye Cy3 with single- and double-stranded DNA", Lena
"Advanced multicanonical replica exchange simulations", Dan
"Enhanced sampling via replica methods", Adrian
"A computational study of the flap dynamics of HIV-1 protease subtype B vs. C"(poster), Dwight
"Mixed quantum/classical studies of Trypanosoma Cruzi's Trans-sialidase" (poster), Jason
"Structure-Activity Relationships in FF Neuropeptide studied with computational simulations" (poster), Georgios
"Computational Studies of the interaction of sulfoindocyanine dye Cy3 with single- and double-stranded DNA" (poster), Lena
Awards
Dan and Georgios received a Chemical Physics Center Travel Grant from the University of Florida.
Dan, Christina, Lena, and Georgios received a Graduate Student Council Travel Grant from the University of Florida.
Presentations
At the 48th Sanibel Symposium on St. Simons Island, GA, our group gave the following presentations:
"Using inter-residue distances to predict protein structure" (poster), Christina
"Implementation of Multicanonical Replica Exchange into AMBER" (poster), Dan
"Computational study of the interaction of sulfoindocyanine dye Cy3 with single- and double-stranded DNA" (poster), Lena
"Structure-Activity Relationships in FF Neuropeptide" (poster), Georgios
"Design of Novel Materials based on Liquid Crystals" (poster), Maria Ana
Mehrnoosh received the A. F. Wentworth Honors Scholarship
Lena received the Crow-Stasch Writing Award for excellence in scientific publication.
January 2008
Publications
Daniel Sindhikara, Yilin Meng, Adrian E. Roitberg. Exchange frequency in replica exchange molecular dynamics. J. Chem. Phys. 128, 024103 (2008)
Seonah Kim, Adrian E.Roitberg. Simulating Temperature Jumps for Protein Folding. J. Phys. Chem. B (2008)
Visitors
Maria Ana Castro from the University of Buenos Aires
Santiago de Lella from the University of Buenos Aires and Tucuman
Christina defended her thesis "New protein structure prediction method using inter-residue distances and a theoretical investigation of the isomerization mechanism of azobenzenes and disubstituted azobenzenes".
November 2007
Awards
Christina received the Procter & Gamble Award for excellence in graduate research
October2007
Presentations
At the 2007 Pan-American Workshop on Molecular and Material Science: Theoretical and computational aspects, in Cuernavaca, Mexico, Georgios presented a poster titled "Structure-Activity Relationships of FLPs Neuropeptides"
Mehrnoosh presented a poster titled "Structure-Activity Analysis of Neuropeptide FF" at an HHMI Poster Session.
August 2007
Presentations
At the 234th American Chemical Society National meeting in Boston, MA, our group gave the following presentations:
"QM/MM Study of the Catalytic Mechanism of Trypanosoma cruzi trans-sialidase" (poster), Ozlem
“Comparison of semi-empirical quantum mechanics methods applied to biological molecules: Potential and free energy surfaces of alanine and glycine Dipeptides in vacuum and in water” (poster), Gustavo
"Trypanosoma cruzi trans-sialidase Binding Investigated by Molecular Dynamics Simulations and QM/MM Calculations" (oral), Ozlem
"How much experimental data is needed to predict protein structure?" (oral), Christina
“Evaluation of different quantum mechanics methods applied to biological molecules: Potential and free energy surfaces of alanine and glycine dipeptides in vacuum and in water” (oral), Gustavo
At the 2nd CMM 'Users Meet Developers' Workshop on QM/MM Simulations in Philadelphia, PA, Gustavo presented a talk titled “Dissociation of the Angeli's salt in explicit water: An application of the PUPIL package as an interface between Amber and Gaussian”
Awards
Ozlem and Christina received a Chemical Physics Center Travel Grant from the University of Florida.
Christina received the Chemical Computing Group Excellence Award.
Dolghih, E., A. E. Roitberg, J. L., Krause. Fluorescence Resonance Energy Transfer in Dye-Labeled DNA. J. Photochem Photobiol. A 2007;190:321-327
July 2007
Seonah defended her thesis "Simulating Temperature Jumps for Protein Folding Studies".
June 2007
Awards
Dan received the National Science Foundation Eastern Asian and Pacific Summer Institute Fellowship to study in Japan with Dr. Yuko Okamoto at Nagoya University.
Visitors
Jason Swails visiting undergraduate student from the State University of New York at Binghamton
Jovan Livada visiting undergraduate student from Hamilton College
Jesse Edwards visiting professor from Florida A&M University
T. Dwight McGee visiting undergraduate student from Florida A&M University
Charlyne Jean visiting undergraduate student from Florida A&M University
At the 83rd Annual America Chemical Society – Florida Regional Section Meeting and Exposition in Orlando, FL, our group gave the following presentations:
"Using distances between a-carbons to predict protein structure” (oral), Christina
“Structure-Activity Relationships of FLPs Neuropeptides” (poster), Georgios
“Evaluation of Different Semi-Empirical Methods Applied to Biological Molecules: Free Energy Surfaces of Alanine Dipeptide in Water” (oral), Gustavo
April 2007
Awards
Dan was named the 2006-2007 Campus-wide Teaching Assistant of the Year by the University of Florida
Publications
Gustavo de M.Seabra, Ross C. Walker, Marcus Elstner, David A.Case, Adrian E. Roitberg. Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package. Journal of Physical Chemistry A. 111 (26):5655-5664 (2007)
March 2007
Presentations
At the 233rd American Chemical Society National Meeting in Chicago, IL, Gustavo gave a talk titled “Angeli’s Salt Decomposition: A Multi-scale Study”
Awards
Mehrnoosh received the HHMI Scholar Award.
February 2007
Presentations
At the 47th Sanibel Symposium on St. Simons Island, GA, our group gave the following presentations:
"The Mechanism of Trypanosoma cruzi trans-sialidase: A Computational Point of View" (poster), Ozlem
“Structure-Activity Relationships of FLPs Neuropeptides” (poster), Georgios
“Effect of Chromophore Orientation on Fluorescence Resonance Energy Transfer” (poster), Lena
"Free energy surfaces of Alanine dipeptide in vacuum and in water studied by SCC-DFTB and QM/MM" (poster), Gustavo
“Folding Kinetics by Temperature-jump Simulations of Two Related 14-Residue Peptides” (poster), Seonah
“Exchange Attempt Frequency in Replica Exchange Molecular Dynamics and Measures of Convergence” (poster), Dan
"Replica Exchange Molecular Dynamics Simulations on pH-Dependence of Protein Structure and Dynamics" (poster), Yilin
At the Quantitative Computational Biophysics Workshop at Florida State University in Tallahassee, FL, Gustavo presented a poster titled "Free energy surfaces of Alanine dipeptide in vacuum and in water studied by SCC-DFTB and QM/MM"
Awards
Dan received a Chemical Physics Center Travel Grant from the University of Florida.
January 2007
Presentations
At the 20th Enzyme Mechanisms Conference held in St. Pete Beach, FL, Özlem presented a poster titled "Computational Mechanistic Study of Trypanosoma cruzi trans-sialidase".
December 2006
Awards
Dan was named Teaching Assistant of the Year by the UF Department of Physics
September 2006
Presentations
At the CISCO-UF Collaborative meeting in Gainesville, Seonah presented a talk titled “Protein folding kinetics”.
August 2006
Awards
Özlem received the 2006-2007 Ruegamer Fellowship from the University of Florida.
May 2006
Publications
Crecca, C. R., Roitberg, A. E., Theoretical Study of the Isomerization Mechanism of Azobenzene and Disubstituted Azobenzene Derivative, J. Phys. Chem. A, 2006;110:8188-8203
Awards
Dan received the AAPT Outstanding Physics TA of 2006 awardMarch 2006
At the 231st American Chemical Society National Meeting in Atlanta, GA, our group gave the following presentations:
"Exploring the Mechanism of Trypanosoma cruzi trans-sialidase" (poster), Özlem
"Theoretical Study of the Isomerization Mechanism of Azobenzene and Disubstituted Azobenzene Derivatives" (poster), Christina
"Conformational Diversity of FLPs Neuropeptides" (poster), Georgios
"Implementation of SCC-DFTB in Amber", Gustavo
“Conformational sampling and folding in polyalanine peptides ” (poster), Seonah
"Free Energy Calculation from Non-equilibrium Simulations" (poster), Hui
Awards
Ozlem, Seonah, and Christina received a Chemical Physics Center Travel Grant from the University of Florida.
Hui received the Department of Physics Graduate Travel Award.