CCB Brown Bag Seminar

SPEAKERS:

Sidney Holden, Ph.D., Flatiron Research Fellow, Biological Transport & Networks 

CONTINUUM MODELING FOR DENSE BIOLOGICAL NETWORKS: Space-filling networks play crucial roles for their hosts by distributing and collecting resources and waste with remarkable efficiency. They balance transport performance with material cost, and remain robust to damage and fluctuating metabolic demands. Continuum models offer insights into their function and design at the macroscale, without needing to track each individual junction and vessel. This is particularly useful for biological networks with thousands, and up to millions of vessels: the human vasculature system is up to two thousand times the length of Fifth Avenue! I’ll present a continuum model for wave-like or diffusive dynamics on dense random networks, with an application to the embryonic vasculature of our group’s newest colleague: the quail.ontinuum 

Vikram K. Mulligan, Ph.D., Research Scientist, Biomolecular Design 

MASALA 1.0: A VERSATILE PLATFORM FOR RAPID DEVELOPMENT AND EXPERIMENTATION WITH NEW MACROMOLECULAR MODELLING APPROACHES: For nearly 30 years, the Rosetta software suite has been one of the leading software packages for designing and validating proteins and synthetic heteropolymers.  However, Rosetta’s aging infrastructure, monolithic architecture, and steep developer learning curve have all worked to slow experimentation with new macromolecular modeling methods in recent years. In this presentation, I will describe the Masala software suite, a set of C++ libraries intended to be a successor to Rosetta, but which can also be used as extension libraries for existing software, including Rosetta. I will describe Masala’s versatile, plugin-based architecture, which allows novice developers to implement new methods with a minimum level of familiarity with the Masala code base and without tedious rounds of recompiling and relinking. I will also describe the automated tools for generating a stable API, permitting Masala to be used as a support library for other software. Finally, I will present a proof of principle in which we used Masala to experiment with new quantum algorithms for solving the NP-hard heteropolymer sequence design problem, and to build a practical workflow for using quantum computing seamlessly in a Rosetta design script.