biological models

Modeling and Automated Storytelling of Mesoscale Molecular Models

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KAUST

In my talk, I will present techniques that allow biologists to model a mesocale entity in a rapid way in the timeframe of a few minutes to hours. This way we have created the first complete atomistic model of the SARS-CoV-2 virion that we are these days sharing with the worldwide scientific community. Mesoscale represents a scalar gap that is currently not possible to accurately image with neither microscopy nor X-ray crystallography approaches. For this purpose, scientists characterize it by observations from the surrounding nanoscale and the microscale. From this information, it is possible to reconstruct a three-dimensional model of a biological entity with a full atomistic model. The problem is that these models are enormously large and are not possible to model with traditional methods from computer graphics within a reasonable time.

A Whole-genome Model of DNA Replication in Human Cells

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B5 L5 R5209

DNA replication is a fundamental cellular process and its precise regulation is crucial for maintaining genomic integrity. Inspired by the mathematical parallelism between DNA replication and the nucleation problem in one-dimensional crystal growth kinetics, we introduce a model that maps whole-genome replication dynamics based on the firing rate profiles of replication origins and fork movement.