Tentative Schedule

8:45-9:00: Coffee and bagels

9:00-9:15: Introductions (organizers and participants) and overview of workshop content

9:15-10:00: Introduction to Multi-scale RNA simulations
Prof. Paul Whitford, Northeastern University

10:00-10:30: Orientation to Computing Facilities and Introduction to Linux
Prof. Alan Chen, SUNY Albany
If you have never used Linux, we suggest that you read this site prior to attending the workshop (at least sections 2.1 and 2.2). It’s ok if you don’t get all of it, we will be there to help. [ and]
Another useful interactive tutorial may be found at codeacademy (lessons 1 and 2 are most useful)

10:30-11:15: SHAPE-directed RNA secondary structure prediction
Angela Yu (Julius Lucks lab), Northwestern University
RNA secondary structure prediction using SHAPE data. A brief introduction to RNA secondary structure prediction methods and the basics of SHAPE experiments will be reviewed, with an emphasis on how SHAPE chemical probing data can be used to improve the prediction accuracy. Recent developments in reconstructing the secondary and tertiary folding pathways of the E. coli Signal Recognition Particle (SRP) RNA from cotranscriptional SHAPE-Seq data will be highlighted.

11:15-12:00:Hands-on Session 1: Secondary structure prediction of RNA
Angela Yu, Northwestern University
This session will focus on using the RNAstructure suite of tools to predict model RNA thermodynamic structures and ensembles of RNA structures.

12:00-1:00: Boxed Lunch will be provided

1:00-1:30:Hands-on Session 2: Introduction to Visualization of Simulations
Sri Ranganathan, RNA Institute @ SUNY Albany
Viewing time-trajectories of atomic motion is a standard component of simulation analysis. This session will provide hands-on experience with standard visualization tools that will help to bridge the communication gap between experimentalists and theorists during collaboration.

1:30-2:15: Theoretical Considerations when Using Simplified/Coarse-grained Models: An interactive discussion
Prof. Paul Whitford, Northeastern University
In this session, we will introduce the concepts that are the basis for using simulations with simplified models. Applications to protein and RNA folding and RNA dynamics will be presented. Please bring your own questions for discussion. This discussion is intended for all backgrounds.

2:15-3:15:Hands-on Session 3: Using Coarse-Grained Models
Paul Whitford, Mariana Levi, Northeastern University
RNA-protein assemblies are often composed of large collections of molecules (e.g. ribosomes and spliceosomes).  Many times, one desires methods for obtained a first glimpse into the structural dynamics about an experimentally-obtained structure.  In this session, we will introduce how to perform coarse-grained simulations, in order to identity collective motions in large-scale assemblies.

3:15-4:00: All-atom Explicit-solvent Simulations: An interactive discussion
Prof. Alan Chen, SUNY Albany
Discussion will include a brief history of large-scale molecular dynamics simulations, an introduction to available software packages and the energy functions that are employed, basic terminology, and best practices.

4:00-4:30:  Ab initio simulations of RNA oligonucleotides and building blocks using the Oak Ridge Leadership Computing Facility (OLCF) Supercomputers.
Ada Sedova, Ph.D, Oak Ridge National Lab
Solid-state vibrational dynamics of nucleic acid building blocks in the polycrystalline state and solution-state molecular dynamics of RNA tetramers using explicit water and ions at the density functional theory (DFT) level. Comparison to experiment, including neutron vibrational spectroscopy, and to classical molecular dynamics is discussed.