Department of Chemistry, University of Minnesota

Group meetings will be held each Thursday at 1:30pm in the reserved meeting room (unless otherwise announced). Note to speakers: please make sure your Title and any Supplementary Reading/Material have been posted prior to your scheduled talk. For further information, contact Hugh Heldenbrand.

Date Speaker Topic Time/Place
12/10 Violeta Lopez TBA 1:30/Smith 101J
12/03 Hugh Heldenbrand TBA 1:30/Smith 101J
11/26 Tim Giese TBA 1:30/Smith 101J
11/19 George Giambasu Clustering: Science or Art? 1:30/Smith 101J
11/12 Postponed TBA 1:30/Smith 101J
11/05 Andreas Goetz, SDSC Subsystem approaches for simulations of complex molecular systems 1:30/Smith 101J
10/29 Postponed TBA 1:30/Smith 101J
10/22 Kiniu Wong Reaction Mechanism of Acid Catalysis by Hammerhead Ribozyme from a 3-D QM/MM Free-Energy Profile 1:30/In Lab
10/15 Brian Radak Some more thoughts about WHAM 1:30/Smith 101J
10/08 Taisung Lee Some thoughts about umbrella sampling 1:30/Smith 101J
10/01 Erich Kuechler Parameterization for the OPNQ QM/MM Model 1:30/Smith 101J
09/24 Ming Huang Development of Pseudo Atom Model and AM1d-PhoT2 Model for QM/MM Simulation of RNA Catalysis 1:30/Kolthoff 668A
09/17 Hugh Heldenbrand The continued search for van der Waals parameters for charged nucleobases 1:30/Smith 101J
09/10 Tim Giese Comparison between Kohn-Sham density functional and potential energy expansion methods using local density approximation, GGA (generalized gradient approximation), and meta-GGA functionals 1:30/Smith 101J
09/03 Special Seminar: Alan Grossfield Antimicrobial lipopeptides: characterizing a novel class of membrane-binding antibiotics using molecular dynamics simulations 1:00/Smith 101J
08/27 George Giambasu Exploring Conformational Transitions 1:30/283 Kolthoff
05/28 Kiniu Wong A Fast Converging TI (Thermodynamic Integration) Method Based on Free-Energy Perturbation in the Hamiltonian Space. 1:30/Smith 101J
05/21 Cancelled IMA talks 1:30/Smith 101J
05/14 Maria Nagan HDV 1:30/Smith 101J
05/07 Adam Moser So much data your eyes will bleed 2:00/Smith 101J
04/30 Taisung Lee Finding the second metal ion in HHR 1:30/Smith 101J
04/17 Erich Kuechler Charge-dependent non-bonded non-electrostatic interactions in QM/MM simulations 1:30/Smith 101J
04/09 Hugh Heldenbrand van der Waals parameters for charged nucleobases 1:30/Smith 101J
04/02 Tim Giese Implementation of the de novo Kohn-Sham density functional method 1:30/Smith 101J
03/26 Cancelled TBA 1:30/Smith 101J
03/19 Cancelled TBA 1:30/Smith 101J
03/12 George Giambasu Finding our way on (free) energy landscapes 1:30/Smith 101J
03/05 Ming Huang Practice Oral Examination 1:30/Smith 101J
02/27 Kiniu Wong Updates on the Development, Implementation and Application of Ab Initio QM/MM and Path-Integral Free-Energy Simulations on RNA Catalysis by Hammerhead Ribozyme 1:30/568A Kolthoff Hall
02/19 Maria Nagan HIV Peptide RNA Water Analysis 1:30/Smith 101J
02/12 Adam Moser Proton Affinity and Gas Phase Basicity: Some challenges and questions 1:30/Smith 101J
02/05 Tai-Sung Lee What p53 is and what we are going to do with it 1:30/Smith 101J
01/29 Ming Huang Pseudo Atom Model and AM1d-Phot2 Model 1:30/Smith 101J
01/22 Hugh Heldenbrand/Erich Kuechler Oral Exam Practice 1:30/Smith 101J
01/15 Hugh Heldenbrand Oral Exam Practice 1:30/Smith 101J
01/08 Tim Giese Kohn-Sham potential energy expansion ab initio performace using LDA, GGA, and meta-GGA functionals and parameter free approximations for next generation semiempirical model development 1:30/Smith 101J
12/11 George Giambasu Hinge points of the L1 Ligase: identification and impact on catalysis 1:30/Smith 101J
12/04 Nina Barnett Calculating pKa from a Statistical Mechanical Standpoint 1:30/Smith 101J
11/20 Carlos Silva Lopez Mechanism of Catalysis in Hammerhead 1:30/Smith 101J
11/13 Kin-Yiu Wong Ab Initio QM/MM and Path-Integral Free-Energy Profile Calculations: RNA Catalysis by Hammerhead Ribozyme 3:00/Kolthoff 668A
11/06 Meeting with Dr. Frisch Visiting scientist 1:30/Smith 117/119
10/30 Carlos Silva Lopez Cancelled 1:30/Smith 101J
10/23 Olalla Nieto Faza Ewald Sums 1:30/Smith 221
10/16 Brian Skjerven COSMO and Multigrid Methods 1:30/Smith 117/119
10/09 Hugh Heldenbrand Dr. Valadkhan's ncRNA 1:00/Lab
10/02 Adam Moser Thermodynamic Cycles and other topics 1:30/Smith 101J
09/11 Tai-Sung Lee Origin of mutational effects at various positions on hammerhead ribozyme catalysis from molecular dynamics simulations 1:00/Smith 101J
09/04 Francesca Guerra Steps towards improved semi-empirical quantum models for phosphoryl transfer reactions 1:00/Smith 101J
08/28 Meeting Cancelled Meet the Teacher Day 1:00/Smith 101J
08/21 Meeting Cancelled ACS Conference 1:00/Smith 101J
08/14 Darrin York Linear-scaling electronic structure theory: a primer, and next generation quantum model for biocatalysis 1:00/Smith 101J
08/07 Erich Kuechler SCF/QMMM Interaction 1:00/Smith 221
07/31 Ming Huang Parameter Optimization 1:00/Smith 221
07/24 Meeting Cancelled Safety Training Refresher 1:00/Smith 221
07/17 Hugh Heldenbrand Hammerhead simulations/VMD 1:00/Lab
07/10 Tim Giese Solid Harmonics/SphericalHarmonicsMod 1:00/Smith 221
07/03 George Giambasu FEP Calculations 1:00/Yorklab
06/26 Nina Barnett TBA 1:00/Smith 221
06/19 Yun Liu Practice Thesis Defense 1:30/Smith 221
06/12 Yun Liu Practice Thesis Defense 1:00/Smith 221
06/05 Meeting Cancelled TBA 1:00/Smith 221
05/29 Informal Meeting Calculus of variations problems and intro to ES theory for first years lab
05/15 Adam Moser TBA
05/08 Tim Giese Development of a new tight-binding model. I. Atomic calculations
04/24 Ming Huang TBA
03/27 Francesca Guerra TBA
03/20 Yun Liu TBA
03/13 Xiaoying Lu TBA
03/06 Brian Skjerven Multigrid method for solving COSMO
02/21 Tai-Sung Lee TBA
02/14 George Giambasu TBA
01/31 Adam Moser Group Introduction
01/24 Tim Giese Electrostatics
2007
12/13 Francesca Guerra TBA
12/06 Yun Liu Hydrolysis of Tri-Phosphate Methyl Ester in Aqueous Solution and the Role of Magnesium
11/15 Carlos Silva Lopez TBA
10/18 Olalla Nieto Faza Ewald sums II. Document in LaTeX/Manuscripts/ewald_sums
10/11 Adam Moser TBA
10/04 Hyunju Lee TBA
09/27 Xiaoying Lu Thio effect in Hammerhead Ribozyme
09/06 George Giambasu Ligase
08/30 Tai-Sung Lee Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation
04/18 George Giambasu TBA
04/11 Elena Formoso Estensoro TBA
04/05 Adam Moser Dr. Wolfenden's Solvation Idea - his paper
03/22 Yun Liu Theoretical Studies on Hydrolysis of Tri-Phosphate Methyl Ester in Gas Phase and Aqueous Solution
03/15 George Giambasu Practice Oral Exam
03/01 Tai-Sung Lee Hammerhead Solvation
02/22 Tai-Sung Lee How to use up SUs
02/15 Francesca Guerra Phosphate transistion state search
01/25 Tim Giese Introduction to Gaussian functions and integral evaluation
2006
01/18 George Giambasu HDV Ribozyme Dynamics
11/16 Adam Moser Substituted cytosine; See Dannenberg_JAmChemSoc_2000_v122_p2062
11/9 Yun Liu Free energy barrier and KIE of Ras-catalyzed GTP hydrolysis
10/26 Kin-Yiu Wong Introduction to Quantum Transition State Theory, Feynman Path Integrals, and Variational Perturbation Theory
10/19 Tai-Sung Lee New results providing insight into the role of Mg2+ in Hammerhead rybozyme.
10/12 Francesca Guerra PMF profiles of methylphosphate and meta-nitro-benzylphosphate
10/05 Tim Giese Numerical quadrature, Part II: 3D, multicenter
09/28 Tim Giese HTML Q&A / How-to: Editing the group webpage
09/07 George Giambasu TBA
08/17 Carlos Silva Lopez TBA
08/10 Olalla Nieto Faza QM/MM biasing potentials with mndo and smooth cosmo
08/03 Adam Moser Proton Affinity and Gas Phase Basicity of DNA/RNA Bases
07/27 Yun Liu Kinetic isotope effects in Ras-catalyzed GTP hydrolysis: structure of transition state
07/20 Tai-Sung Lee Possible roles of the Mg2+ ion in Hammerhead RNA inferred from molecular dynamics simulations


A list of previous group meeting talks can be found here:
2003-2004 academic year