US-SOMO Hydrodynamic Modelling
UltraScan Solution Modeler Hydrodynamic Modelling Workshop
Presenters: Saeed
Mortezazadeh, University of Lethbridge, Canada (in-person), Emre Brookes, University of
Montana, USA (remote), and Mattia Rocco,
Retired, Ospedale Policlinico San Martino, Genova, Italy (remote)
DescriptionUltraScan Solution Modeler (US-SOMO)[1,2] processes atomic and lower-resolution bead model representations of biological and other macromolecules to compute various hydrodynamic parameters, such as the sedimentation and diffusion coefficients, relaxation times and intrinsic viscosity. This allows the researcher to validate structural models against experimental data. The tools available in US-SOMO have been shown to provide the best known computations of hydrodynamic parameters from experiment [3]. The US-SOMO hydrodynamics workshop will consist of three sessions. In the first session, attendees will be given an introduction to computational hydrodynamics and techniques. In the second session, users will utilize US-SOMO to compute hydrodynamics parameters from structures and to use automated batch processing to compute over multiple structures. It is suggested that attendees attend both sessions, as earlier material will not be covered again during the 2 session course. Registered attendees will receive detailed software installation instructions in the week prior to the workshop. This 2 session workshop will be presented on Sunday at 14:30-16:00 and 17:00-19:00 (sessions 3 and 4). [1] Brookes, E. and Rocco, M., 2018. Recent advances in the UltraScan SOlution MOdeller (US-SOMO) hydrodynamic and small-angle scattering data analysis and simulation suite. European Biophysics Journal, 47(7), pp.855-864. doi: 10.1007/s00249-018-1296-0. [2] Rocco, M., Brookes, E. & Byron, O. US-SOMO: Methods for Construction and Hydration of Macromolecular Hydrodynamic Models. In: Encyclopedia of Biophysics, Roberts, G. & Watts, A., European Biophysical Societies (eds). Springer, Berlin, Heidelberg (2021). doi: 10.1007/978-3-642-35943-9_292-1 [3] Rocco M, Byron O., 2015, "Hydrodynamic Modeling and Its Application in AUC.", Methods Enzymol. 2015;562:81-108. doi: 10.1016/bs.mie.2015.04.010.