APS 2016

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Atomistic Modeling of Small-Angle Scattering Data Using SASSIE-web

September 21-23, 2016
Advanced Photon Source, Argonne National Laboratory, Argonne, IL

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 additional, atomistic models can allow the use of experimental and computational constraints on the SAS data.

The goal of this three day introductory course is to use modern simulation methods and software tools to predict and analyze small-angle scattering data of soft-matter systems, focussing particularly on biological systems. Participants will be gain experience with modern simulation tools such as VMD, NAMD. The latter half of the course will introduce SASSIE, a software framework designed to facility 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, dna, and 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: Intermediate MD, SASSIE and advanced building methods.

Day 3: Advanced MS, SASSIE 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.

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Wednesday 9/21/2016

Time Lead Activity File
9:00 - 9:30 AM JEC Course Introduction lecture_0.pdf
9:30 - 10:30 AM JEC Lecture 1: Coordinates to Structure lecture_1.pdf
10:30 - 10:45 AM Break
10:45 - Noon ALL Lab 0: Software Installation and SASSIE-web Basics lab_0.pdf; basic_osx_linux_commands.pdf; basic_windows_commands.pdf
Noon - 1:00 PM Lunch
1:00 - 2:45 PM SK/ALL Lab I: VMD lab_I.pdf
2:45 - 3:00 PM Break
3:00 - 5:00 PM SK/ALL Lab II: PSFGEN/NAMD lab_II_osx_linux.pdf; lab_II_windows.pdf

Files needed for day 1: aps_2016_day_1_files.zip

Answers for labs on day 1: aps_2016_day_1_answers.zip

Thursday 9/22/2016

Time Lead Activity File
9:00 - 10:00 AM JEC Lecture 2: MD II lecture_2.pdf
10:00 - 10:15 AM Break
10:15 - Noon SB/CJ Lab III: NAMD lab_III_osx_linux.pdf lab_III_windows.pdf
Noon - 1:00 PM Lunch
1:00 - 1:30 PM JEC Lecture 3: MMC & SASSIE Overview lecture_3.pdf
1:30 - 3:00 PM SK/ALL Lab IV: SASSIE-web Quick Start lab_IV.pdf
3:00 - 3:15 PM Break
3:15 - 5:00 PM SK/ALL Lab V: SASSIE-web Workflows lab_V.pdf

Files needed for day 2: aps_2016_day_2_files.zip

Answers for labs on day 2: aps_2016_day_2_answers.zip

Friday 9/23/2016

Time Lead Activity File
9:00 - 9:30 AM SCH Lecture 4: Advanced SASSIE-web lecture_4.pdf
9:30 - 10:00 AM SCH/CJ Lab VI-1: Advanced SASSIE-web lab_VI.pdf lab_VI.html
10:00 - 10:15 AM Break
10:15 - 11:30 AM SCH/CJ Lab VI-2: Advanced SASSIE-web lab_VI.pdf
11:30 - Noon AM JEC Lecture 5: Advanced Structure Building lecture_5.pdf
Noon - 1:00 PM Lunch
1:00 - 3:00 PM SK/ALL Lab VII: Advanced Structure Building lab_VII_osx_linux.pdf lab_VII_windows.pdf
3:00 - 3:15 PM Break
3:15 - 5:00 PM SB/ALL Lab VIII: Breakout Sessions: Student Projects and Advanced MD Labs lab_VIII_membrane_builder.pdf lab_VIII_normal_modes.pdf

Files needed for Day 3: aps_2016_day_3_files.zip

Answers for labs on Day 3: aps_2016_day_3_answers.zip

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