Program
Locations
Morning lectures: Beckman Institute Auditorium
Coffee breaks: 1003 Beckman Institute
Afternoon and evening computer labs: 252 Everitt Lab / 406B1
Engineering Hall
campus map
Handouts
Running Simulations During the Afternoon Hands-on Sessions (html ,pdf)
Four Ways to Run NAMD at SS03 (html, pdf)
Collaborative Exercises
Energies
Echoes
Mon, 6/2: Introduction to Protein Structure and Dynamics
(K. Schulten)
| 07:30-12:00 | Registration |
| 08:30-09:00 | Welcome, Opening Remarks, and
Overview (pdf)
|
| 09:00-10:00 | Molecular Graphics Perspective of
Protein Structure and Function (pdf) |
| 10:00-11:00 | Molecular Dynamics Method (part 1 -
pdf; part
2 - pdf)
(J. Phillips and J. Gullingsrud) |
| Coffee Break | |
| 11:30-12:30 | Equilibrium Properties of Proteins
(pdf) |
| 12:30-12:45 | Daily Q & A |
| Lunch Break | (12:45-13:30 Staff
Meeting, 3169 BI ) |
| 13:45-14:30 | Overview of Technical Resources (pdf) (T. Skirvin, K. Vandivort,
R. Brunner) [Beckman Institute Auditorium] |
| 14:30-15:30 | Hands-on -- Molecular Graphics
Tutorial 1 (html, pdf)
(E. Villa, F. Khalili) |
| 15:45-17:00 | Hands-on -- Molecular Graphics
Tutorial 2 (html,
pdf)
(E. Villa, F. Khalili) |
| 19:00-21:00 | Free Session -- Model Your Own System (E. Villa,
J. Gullingsrud, M. Sotomayor, M. Dittrich) |
Tue, 6/3: Statistical Mechanics of Proteins (I. Kosztin)
| 09:00-11:00 | Registration |
| 09:00-10:00 | Equilibrium and Nonequilibrium
Properties of Proteins (pdf) |
| 10:00-11:00 | Coherent Motion in Proteins:
Temperature Echoes (pdf, paper)
|
| Coffee Break | |
| 11:30-12:30 | Simulated Cooling of Proteins (pdf) |
| 12:30-12:45 | Daily Q & A |
| Lunch Break | (12:45-13:30 Staff
Meeting, 3169 BI ) |
| 14:30-15:30 | Hands-on -- Molecular Dynamics
Tutorial 1 (html,
pdf)
(A. Aksimentiev, D. Lu) |
| 15:45-17:00 | Hands-on -- Molecular Dynamics
Tutorial 2 (html,
pdf)
(A. Aksimentiev, D. Lu) |
| 18:00-20:00 | Banquet [Beckman Institute Atrium]
(closed event; nametags required) |
Wed, 6/4: Steered Molecular Dynamics of Proteins
(K. Schulten)
| 09:00-10:00 | Introduction and Examples (pdf) |
| 10:00-11:00 | Mechanical Proteins (pdf) |
| Coffee Break | |
| 11:30-12:30 | Determining Potentials (pdf) |
| 12:30-12:45 | Daily Q & A |
| Lunch Break | (12:45-13:30 Staff
Meeting, 3169 BI ) |
| 14:30-15:30 | Hands-on -- Molecular Dynamics
Tutorial 3 (html,
pdf)
(S. Park, M. Gao) |
| 15:45-17:00 | Hands-on -- Stretching Deca-Alanine
(html,
pdf)
(S. Park, M. Gao) |
| 19:00-21:00 | Free Session -- Model Your Own System
(A. Aksimentiev, J. DeSouza, B. Isralewitz, J. Cohen) |
Thu, 6/5: Simulating Membrane Channels (E. Tajkhorshid)
| 09:00-10:00 | Introduction and Examples (pdf) |
| 10:00-11:00 | Transport in Aquaporins (pdf) |
| Coffee Break | |
| 11:30-12:30 | Nanotubes (pdf)
|
| 12:30-12:45 | Daily Q & A |
| 12:45 | Summer School Photo |
| Lunch Break | (12:45-13:30 Staff
Meeting, 3169 BI ) |
| 14:30-15:30 | Hands-on -- Water Channel 1 (html, pdf)
(F. Zhu, J. Cohen) |
| 15:45-17:00 | Hands-on -- Water Channel 2 (html, pdf)
(F. Zhu, J. Cohen) |
| 17:30-19:00 | Demonstration of Aquaporin channel
and Haptic Device IMD (3 demos) [3151 BI] |
| 19:00-21:00 | Free Session -- Model Your Own System (D. Lu, F. Zhu)
|
Fri, 6/6: Quantum Chemistry of Proteins (T. Martinez)
| 09:00-10:00 | Introduction and Examples (pdf) |
| 10:00-11:00 | Ab Initio and Semiempirical Quantum
Chemistry (pdf) |
| Coffee Break | |
| 11:30-12:30 | QM/MM Methods and Direct Dynamics (pdf)
|
| 12:30-12:45 | Daily Q & A |
| Lunch Break | (12:45-13:30 Staff
Meeting, 3169 BI ) |
| 14:30-15:30 | Hands-on -- Introduction to QM
Simulations (html,
pdf)
(M. Dittrich, S. Olsen) |
| 15:45-17:00 | Hands-on -- Computational
Determination of Proton Affinities (html,
pdf)
(M. Dittrich, S. Olsen) |
| 19:00-21:00 | Free Session -- Model Your Own System
(C. Kanchanawarin, M. Gao) |
Sat, 6/7 Bus Trip to Chicago (Optional, Not Funded by
School, Sign up Early)
Sun, 6/8
| 14:00-21:00 | Free Session -- Model Your Own System
|
Mon, 6/9: Parameters for Classical Force Fields
(Z. Schulten)
| 09:00-10:00 | Introduction and Examples (pdf)
|
| 10:00-11:00 | Introduction to Classical Force
Fields (pdf)
|
| Coffee Break | |
| 11:30-12:30 | Methods of Parameterization (pdf)
|
| 12:30-12:45 | Daily Q & A |
| Lunch Break | (12:45-13:30 Staff
Meeting, 3169 BI ) |
| 14:30-15:30 | Hands-on -- System Setup of HisH with
the Molecular Modeling Package Moe (html, pdf)
(R. Amaro, F. Autenrieth, R. Braun) |
| 15:45-17:00 | Hands-on -- Semiempirical Parameter
Generation with Spartan (html, pdf)
(R. Amaro, F. Autenrieth, R. Braun) |
| 17:30-19:00 | Demonstration of Aquaporin channel
and Haptic Device IMD (3 demos) [3151 BI] |
| 19:00-21:00 | Free Session - Model Your Own System (G. Zheng,
S. Kumar) |
Tue, 6/10: Bioinformatics of Proteins (Z. Schulten)
| 09:00-10:00 | Protein Structure Prediction and
Function html, (pdf)
|
| 10:00-11:00 | Sequence and Structure Alignment
Algorithms (pdf)
|
| Coffee Break | |
| 11:30-12:30 | Sequence and Structural Analysis
Tools on the Web (pdf)
|
| 12:30-12:45 | Daily Q & A |
| Lunch Break | (12:45-13:30 Staff
Meeting, 3169 BI ) |
| 14:30-15:30 | Hands-on -- Bioinformatics
Introduction on Class II tRNA Synthetases (html, pdf)
(F. Autenrieth, B. Isralewitz, T. Pogorelov) |
| 15:45-17:00 | Hands-on -- Sequence and Structural
Alignment Methods (html, pdf)
(F. Autenrieth, B. Isralewitz, T. Pogorelov) |
| 19:00-21:00 | Free Session -- Model Your Own System (D. Hardy,
F. Khalili) |
Wed, 6/11: Simulation of Lipids (M. Klein); Parallel
Computing (L. Kale)
| 08:55-09:00 | Entries for Beauty Contest are due
| | 09:00-10:00 | Atomic Level Simulation of Membranes
(pdf) (M. Klein)
|
| 10:00-11:00 | Coarse Grained Modeling of Lipid
Phases (pdf)
(M. Klein) |
| Coffee Break | |
| 11:30-12:30 | Introduction to Parallel Computing
Issues (pdf)
(L. Kale) |
| 12:30-12:45 | Daily Q & A |
| 12:45-12:50 | Announcement of Beauty Contest
Finalists |
| Lunch Break | (12:50-13:30 Staff
Meeting, 3169 BI ) |
| 14:30-15:30 | Hands-on -- Case Studies in Effective
Parallelization of MD Simulations (pdf) (L. Kale)
|
| 15:45-16:30 | Optional - Introductory Lessons on
Cluster Building (pdf);
Choose-up for Section 1, 2, or 3 (T. Skirvin, J. Stone, J. Phillips)
|
| 16:30-18:30 | Optional - Hands-on -- Build Your Own
Cluster 1 (html,
pdf)
(T. Skirvin, J. Stone, J. Phillips) (5602 BI) |
| 19:00-21:00 | Free Session -- Model Your Own System
(R. Braun, D. Brandon) |
Thu, 6/12: Numerical Algorithms (T. Schlick, R. Skeel)
| 09:00-10:00 | Force Evaluation, Integrators, and
Propagators (Slides, Notes)
(R. Skeel) |
| 10:00-11:00 | Optimization Techniques (pdf, HW) (T. Schlick)
|
| Coffee Break | |
| 11:30-12:30 | Monte Carlo Methods (pdf, HW) (T. Schlick)
|
| 12:30-12:45 | Feedback Forms |
| Lunch Break | (12:45-13:30 Staff
Meeting, 3169 BI ) |
| 14:30-15:30 | Hands-on -- Numerical Laboratory (pdf)
(D. Hardy, R. Engle, J. Marriott, W. Wang) |
| 15:30-17:30 | Optional - Hands-on -- Build Your Own
Cluster 2 (html,
pdf)
(T. Skirvin, J. Stone, J. Phillips) (5602 BI) |
| 17:30-19:30 | Optional - Hands-on -- Build Your Own
Cluster 3 (html,
pdf)
(T. Skirvin, J. Stone, J. Phillips) (5602 BI) |
| 15:30-17:00 | NCSA
Cave Tours (6 Tours) [3510 BI] |
| 19:30-21:00 | Beauty Contest
[Beckman Institute Auditorium]
The certificate of the summer
school will be handed out. |
Fri, 6/13: Modeling Large Systems (K. Schulten)
| 09:00-10:00 | Molecular Machines of the Living Cell
(pdf) |
| 10:00-11:00 | Light Harvesting in Photosynthesis
(pdf) |
| Coffee Break | |
| 11:30-12:00 | ATP Synthase (pdf) |
| 12:00-12:15 | Daily Q & A |
| 12:15-12:45 | Concluding Remarks |
| Lunch Break | (12:45-13:30 Staff
Meeting, 3169 BI ) |
| 13:00-14:30 | NCSA
Cave Tours (6 Tours) [3510 BI] |
| 14:30-15:30 | Hands-on -- Excitation Transfer (html, pdf) (M. Sener,
C. Kanchanawarin) |
| 15:45-17:00 | Hands-on -- Electron Transfer (html ,pdf) (M. Sener,
C. Kanchanawarin) |
|
