UK 2017


January 23-25, 2017

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.

Monday 1/23/2017

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:

Answers for labs on day 1:

Tuesday 1/24/2017

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:

Answers for labs on day 2:

Wednesday 1/25/2017

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:

Answers for labs on Day 3:

Take-Home Exam: Antibody Build & Simulation

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