| Date | Speaker | Title |
|---|---|---|
| January 5 | Yuhui Cheng UCSD |
Synapse Modeling with Finite Element Method |
| January 12 | Jennifer Bui UCSD |
Conformational Transitions of Flexible Protein upon Protein-Protein Binding Interactions |
| January 19 | Lou Noodleman UCSD |
Quantum Chemical Studies of the Photocycle and Spectral Tuning in Photoactive Yellow Protein |
| January 26 | - | No Group Meeting |
| February 2 | Donald Hamelberg UCSD |
Relating local energy landscape roughness and kinetic rates |
| February 9 | Sanjib Senapati UCSD |
Acetylcholinesterase in a Unique Conformation |
| February 16 | - | No Group Meeting |
| February 23 | John Mongan UCSD |
Generalized Born Beyond the van der Waals Surface: The Neck Correction |
| March 2 | Jessica MJ Swanson UCSD |
Bridging Explicit and Implicit Solvation Models |
| March 9 | David Cerutti UCSD |
GRAPPLE 2.0: Swiftius, Altius, Fortius |
| March 16 | - | No Group Meeting |
| March 23 | Ivaylo Ivanov UCSD |
Characterization of non-biological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all atom molecular dynamics. |
| March 31 | Dave Zhang UCSD |
Activation mechanism of nicotinic acetylcholine receptor revealed by ligand unbinding |
| April 6 | Barry Grant UCSD |
Stripping Down the Kinesin Molecular Motor |
| April 13 | Kay Hamacher UCSD |
Computation of amino-acid specific fluctuations - application to HIV1-Protease |
| April 20 | Tushar Jain UCSD |
Principal Component Analysis: Searching for Conformational Population |
| April 27 | - | No Group Meeting |
| May 4 | Alex Perryman UCSD |
Computer-Assisted Protein Structure Studies: Hunting Down the Hidden Secrets of HIV |
| May 11 | Xiao-Lin Cheng UCSD |
Channel opening motion of alpha7 nAChR as suggested by normal mode analysis |
| May 18 | Chia-En Chang UCSD |
1. HIV-1 protease internal motion and ligand encounter: Brownian dynamics in a coarse-grained model 2. The missing term in protein-ligand docking |
| May 25 | Joachim Dzubiella UCSD |
Classical (dynamic) Density Functional Theory: any use for Biochemistry? |
| June 1 | Jie Liu UCSD |
Discover dynamically the transcriptional regulatory network |
| June 8 | Anushka Michailova and Kathy Lu UCSD |
3D model of synchronous calcium signals in ventricular myocyte |
| June 15 | Ben-zhuo Lu UCSD |
Calculation of PB force on solvated molecule in boundary element method frame |
| June 22 | Justin Gullingsrud UCSD |
All-atom and coarse-grained molecular dynamics studies of protein kinase A regulation |
| June 29 | - | No Group Meeting |
| July 6 | - | No Group Meeting |
| July 13 | - | No Group Meeting |
| July 20 | Cameron Mura UCSD |
3D models of fibrillar Hfq and other Sm-like proteins |
| July 27 | Donald Hamelberg UCSD |
Role of flexibility in the proteolytic machinery of HIV-1 |
| August 3 | William McLaughlin UCSD |
Transgressing the Scales: Predictions of Protein Interaction Partners with Help from MM/PBSA |
| August 10 I |
Jingfang Huang UNC Chapel Hill |
A New Version of Fast Multipole Method for Screened Coulomb Interactions in Three Dimensions |
| August 10 II |
Kevin Litchfield UCSD |
MD studies on the Barnase-Barstar System: Testing the Transferability and Convergence of Free Energy Estimates using MM-PBSA. |
| August 17 | - | No Group Meeting |
| August 24 I |
Stuart E. Murdock U Southampton |
BioSimGrid, An Environent to Archive and Analyse Biosimulation Data |
| August 24 II |
Steven Johnston U Southampton |
Data management in BioSimGrid |
| August 31 | David Minh UCSD |
1. A Smattering of X-Ray Scattering 2. External Entropy Loss Upon Protein-Protein Binding |
| September 7 | John Mongan UCSD |
The Wonderful World of Generalized Born |
| September 14 | Xiyun Zhang UCSD |
Free Energies of TS Binding and the Origins of Enzyme Catalysis |
| September 20 | Sanjib Senapati UCSD |
Why is the syn-isomer of TZ2PA6 the sole product in AChE environment? |
| September 27 | David Cerutti UCSD |
Making Predictions within the MM-PBSA Framework |
| October 4 | Alemayehu Abebe UCSD |
Dynamics of an Enzyme and a Peptide-DMPC Complex |
| October 11 | Tongye Shen UCSD |
Elasticity of Biomolecules |
| October 18 | - | No group meeting |
| October 25 | Yuhui Cheng UCSD |
Analysis of Synaptic Transmission in the Neuromuscular Junction |
| November 1 | Jessica MJ Swanson UCSD |
Exploring Implicit Solvation Models |
| November 8 | David Zhang UCSD |
Potenitals of mean force for ACh unbinding from alpha7 nAChR ligand-binding domain |
| November 15 | Benzhuo Lu UCSD |
On the energy analysis of the dynamics of the catalytic subunit of PKA |
| November 22 | Ivaylo Ivanov UCSD |
Dynamics of Proliferating Cell Nuclear Antigen |
| November 29 | Barry Grant UCSD |
1. Comparative analysis of homologous protein structures 2. Phosphate release in Myosin: forcing the backdoor |
| December 6 | - | No Group Meeting |
| December 13 | Tushar Jain UCSD |
Configurational-Bias Sampling for Predicting Side-chain Conformations in Proteins |
| December 20 | - | No group meeting |
| December 27 | - | No group meeting |