Molecular simulation is an important technique to analyze and interpret molecular phenomena across many disciplines. Small-angle scattering (SAS) utilizing either X-ray or neutron sources is a valuable method to characterize shape, interactions, and properties of many soft-matter systems. Modeling of SAS data is typically done using analytical functions and/or dummy-ball (DB) models. While these methods are simple, they have proven to be quite robust and have allowed for a tremendous expansion of SAS studies to a wide variety of systems. Atomistic modeling can be used to interpret SAS data and inherently provides structural and atomic interactions that are unavailable using analytical or DB models. In addition, atomistic models can allow the use of experimental and computational constraints on the SAS data. The goal of this introductory course is to use modern simulation methods and software tools to predict and analyze small-angle scattering data of soft-matter systems, focusing particularly on biological systems. Participants will be introduced to modern simulation tools such as VMD and NAMD. The bulk of the course will introduce SASSIE, a software framework designed to facilitate the use of atomistic modeling to interpret scattering data.
The course will involve a mixture of lectures and examples with student lessons. Examples will involve various protein and DNA molecules, as well as their complexes. Advanced simulation methods for glycosylated proteins, lipidic systems, and coarse-grain methods can be accommodated depending on demand. The emphasis will be on structure building, ensemble molecular simulation, calculation of scattering profiles, and comparison to experimental data.
Day 1: Introduction to molecular modeling using force-fields.
Day 2: SASSIE.
Day 3: Advanced building examples and student projects.
Students are encouraged to contact the course organizers in advance to discuss their systems as a portion of the course will involve helping students set-up initial models for their own projects.
| Time | Lead | Activity | File |
|---|---|---|---|
| Noon - 12:15 PM | SJP | Course Welcome | |
| 12:15 - 12:30 PM | JEC | Course Introduction | lecture_0.pdf |
| 12:30 - 1:30 PM | JEC | Lecture 1: Coordinates to Structure | lecture_1.pdf |
| 1:30 - 1:45 PM | Break | ||
| 1:45 - 2:30 PM | JB | Lab I: VMD | lab_I.pdf |
| 2:30 - 4:30 PM | JB | Lab II: PSFGEN/NAMD | lab_II_windows.pdf |
| 4:30 - 5:30 PM | JEC | Lecture 2: MD | lecture_2.pdf |
| 5:30 - 7:30 PM | DWW | Lab III: NAMD | lab_III_windows.pdf |
Files needed for day 1: uk_2017_day_1_files.zip
Answers for labs on day 1: uk_2017_day_1_answers.zip
| Time | Lead | Activity | File |
|---|---|---|---|
| 9:00 - 9:30 AM | JEC | Lecture 3: MMC & SASSIE Overview | lecture_3.pdf |
| 9:30 - 10:00 AM | GKH/SJP | Lab IV: SASSIE-web Basics | lab_IV.pdf |
| 10:00 - 10:15 AM | Break | ||
| 10:15 - Noon | DWW | Lab V: SASSIE-web Quick Start | lab_V.pdf |
| Noon - 1:00 PM | Lunch | ||
| 1:00 - 2:45 PM | SB | Lab VI: SASSIE-web Workflows | lab_VI.pdf |
| 2:45- 3:00 PM | Break | ||
| 3:00 - 3:15 PM | SB | Lecture 4: Advanced SASSIE-web | lecture_4.pdf |
| 3:15 - 6:00 PM | SB | Lab VII: Advanced SASSIE-web | lab_VII.pdf |
| 6:00 - 7:30 PM | ALL | Extra time |
Files needed for day 2: uk_2017_day_2_files.zip
Answers for labs on day 2: uk_2017_day_2_answers.zip
| Time | Lead | Activity | File |
|---|---|---|---|
| 9:00 - 9:20 AM | JEC | Lecture 5: Advanced Structure Building | lecture_5.pdf |
| 9:20 - 10:00 AM | SB | Lab VIII: Advanced Structure Building | lab_VIII_windows.pdf |
| 10:00 - 10:15 AM | Break | ||
| 10:15 - 11:30 AM | SB | Lab VIII-2: Advanced Structure Building | |
| 11:30 - Noon AM | ALL | Breakout Sessions; Student Projects; Lab IX & X (optional) | lab_IX_membrane_builder.pdf lab_X_normal_modes.pdf |
| Noon - 1:00 PM | Lunch |
Files needed for Day 3: uk_2017_day_3_files.zip
Answers for labs on Day 3: uk_2017_day_3_answers.zip