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Introduction into SASSIE2

SASSIE: Software to Model AUC & SAS Data Using Atomistic Ensembles from Molecular Simulations.

Presenters: Emre Brookes, University of Montana, USA, and Stephen Perkins, Division of Biosciences, University College London, UK

Molecular simulation is an important technique to analyze and interpret molecular phenomena across many disciplines. AUC & Small-angle scattering (SAS) utilizing either light or neutron sources are valuable methods to characterize shape, interactions, and properties of many soft-matter systems. Modeling of AUC & SAS data is often 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 AUC & SAS studies to a wide variety of systems. Atomistic modeling can be used to interpret AUC & 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 experimental data. The goal of this introductory course is to use modern simulation methods and software tools to predict and analyze AUC & small-angle scattering data of biological systems. The bulk of the course will introduce SASSIE, a software framework designed to facilitate the use of atomistic modeling to interpret AUC & 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. The emphasis will be on structure building, ensemble molecular simulation, calculation of AUC & scattering profiles, and comparison to experimental data.

Session 1: Introduction to molecular modeling using force-fields.
Session 2: SASSIE.
Session 3: Calculating AUC and SAS Profiles from Simulation.
Session 4: Advanced Topics

This workshop will be presented during the four sessions on Monday, at 9:00-11:00,11:30-13:30, 14:30-16:30 and 17:00-19:00 (sessions 7-10).