Lorentz Center - Progress in ab initio modeling of biomolecules: methods and applications from 3 Jul 2006 through 7 Jul 2006
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    Progress in ab initio modeling of biomolecules: methods and applications
    from 3 Jul 2006 through 7 Jul 2006

 
What is needed in a Proposal for a Lorentz Center Workshop

Preliminary program

 

Monday 3 July

09:30 10:00 Registration

10:00 10:10 Opening

 

10:10 11:00 M. Swart

Computational Study on the Structure of DNA

 

11:00 11:30 Coffee & Tea

 

11:30 12:20 U. Landman

Microscopic simulations of macroscopic consequences:

fixing the continuum and hybrid methods

 

12:30 13:30 Lunch

 

14:00 15:00 Poster session

15:00 15:50 A. Magistrato

Understanding Anticancer Drug-DNA Interactions via

Molecular Dynamics Simulations

 

15:50 16:10 Coffee & Tea

 

16:10 16:40 C. Gossens

DNA-Binding of Ruthernium-arene anticancer drugs

16:40 17:10 A. Karawajczyk

The Mechanism of the Bleomycin Activity

 

17:10 18:30 Wine & cheese party

 

Tuesday 4 July

09:00 09:50 B. Ensing

Metadynamics as a Tool for Exploring Free Energy Landscapes of Chemical Reactions

09:50 10:40 G. Bussi

Free energy landscapes from combined metadynamics and parallel tempering

 

10:40 11:10 Coffee & Tea

 

11:10 12:00 U. Roehrig

Amyloid Bibril Formation Studied by Molecular Dynamics and Metadynamics Simulations

12:00 12:30 S. Raugei

A Quantum chemistry study of the redox potential and
electronic properties of Rubredoxin

12:30 13:30 Lunch

 

15:00 16:00 Discussion group

 

16:00 16:20 Coffee & Tea

 

16:20 17:10 E.J. Meijer

Structure, dynamics and proton transfer in aqueousion solutions

17:10 18:00 C. Rovira

Substrate distortion in the Michaelis complexes of glycoside

hydrolases


Wednesday 5 July

09:00 09:50 C. Filippi

Excitations in (bio)molecules from quantum Monte Carlo

09:50 10:40 V. Tozzini

Variation of color and photodynamics within the family of intrinsically fluorescent proteins

 

10:40 11:10 Coffee & Tea

 

11:10 11:40 M. Guglielmi

Microsolvation effects on protonated tryptophan

11:40 12:20 E. Leenders

Protonation of the chromophore in the photoactive yellow protein

 

12:30 13:30 Lunch

 

15:00 15:30 L. Guidoni

Absorption Spectra in Solution by Quantum Monte Carlo/Molecular

Mechanics (QMC/MM)

15:30-16:00 M. Zaccheddu

Green Flourescent Protein: Shedding Light with Quantum Monte

Carlo

 

16:00 16:20 Coffee & Tea

 

16:30 prompt Departure by tour bus to Conference Dinner

(BBQ at the beach starting at 17:30)

 

Thursday 6 July

09:00 09:50 J. Ireta

Why helices are right-handed and beta-sheets left-handed? :

Insight from first-principles calculations.

09:50 10:40 L. Colombi Ciacchi

Selective inhibition of CDK proteins by small ligands:

the roles of hydrogen bonding, solvation, and dispersion forces

 

10:40 11:00 Coffee & Tea

 

11:00 11:50 C. Molteni

Mutagenesis computer experiments on ligand gated ion channels

11:50 12:30 P. Bolhuis

  Transition path sampling of biomolecular processes using ab initio and
  classical molecular dynamics

 

12:30 13:30 Lunch

 

14:30 15:20 D. Sebastiani

Ab-initio modeling of environmental packing effects of

biomolecules in their environment: solvation and crystal NMR

chemical shift

15:20 16:00 J. Neugebauer

Environmental Effects on Molecular Properties Modeled by Frozen-

Densiy Embedding

 

16:00 16:30 Coffee & Tea

 

16:30 17:00 I-Chun Lin

17:00 17:30 P. K. Wawrzyniak

A DFT Study of the Special Pair in Bacterial Reaction Center:

Effect of Histidine Protonation on the Chemical Shifts


Friday 7 July

09:00 09:50 F. Krajewski

A new stochastic linear scaling electronic structure method

and accurate sampling with noisy forces

09:50 10:30 G. Canters

Theoretical analysis of structure and function of Cu containing

Redox proteins: azurin and quercetinase

 

10:30 11:00 Coffee & Tea

 

11:00 11:50 J. VandeVondele

A Combination of Linear Scaling and QM/MM techniques for the

study of electron transfer reactions in biological systems and solar

cells



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