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PICS Colloquium: “Modeling and simulations of protein conformational changes and virus entry”

Zoom - email kathom@seas.upenn.edu

Abstract: Virus infections remain major threats to human health worldwide. Viruses are intracellular parasites, and must enter host cells and deliver their genetic material to initiate infection. Virus entry is a highly complex process that may involve hundreds of trans-membrane and peripheral membrane proteins. This highly complex process is dictated by various events, such as […]

PICS Colloquium: “Network-Based Characterization, Modeling, and Control of Fluid Flows”

Zoom - email kathom@seas.upenn.edu

The network of interactions in a sea of vortices gives rise to the amazingly rich dynamics of fluid flows. To describe these interactions, we consider the use of mathematical tools from the emerging field of network science that is comprised of graph theory, dynamical systems, data science, and control theory. In this presentation, we discuss […]

PICS Colloquium: “Protein dynamics and energy landscape engineering”

Zoom - email kathom@seas.upenn.edu

Abstract: Experiments only reveal a few of a protein’s structures with the atomic detail required to rationally engineer mutations and drugs. However, a protein actually has a vast landscape of uncharted conformations that present untapped opportunities for manipulating its function. My lab is developing simulation methods, called Markov state models (MSMs), that provide unprecedented access […]

PICS Colloquium: “How reproducible is your research?”

Zoom - email kathom@seas.upenn.edu

Abstract: Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are […]

PICS Colloquium: “Kinetic theory for superparameterization of sea ice dynamics”

PICS Conference Room 534 - A Wing , 5th Floor 3401 Walnut Street, Philadelphia, PA, United States

Arctic sea ice comprises of many ice floes whose dynamics is driven by oceanic/atmospheric currents and floe-floe interaction. Models of the effective sea ice dynamics  at large scales typically employ hydrodynamic equations of motion, such as mass and momentum conservation, with complex constitutive laws attempting to capture the rheology of sea ice as a continuum. Although hydrodynamic sea ice models […]

PICS Colloquium: “A model for external aerodynamics based on building-block flows”

PICS Conference Room 534 - A Wing , 5th Floor 3401 Walnut Street, Philadelphia, PA, United States

Abstract: A wall model for large-eddy simulation is proposed by devising the flow as a collection of building blocks, whose information enables the prediction of the stress as the wall.  The core assumption of the model is that simple canonical flows (such as turbulent channel flows, boundary layers, pipes, ducts, speed bumps, etc) contain the […]

CIS Seminar: “Sketching Algorithms”

Wu and Chen Auditorium (Room 101), Levine Hall 3330 Walnut Street, Philadelphia, PA, United States

Abstract: A "sketch" is a data structure supporting some pre-specified set of queries and updates to a database while consuming space substantially (often exponentially) less than the information theoretic minimum required to store everything seen, and thus can also be seen as some form of functional compression. A "streaming algorithm" is simply a data structure […]

MSE Seminar: “Lansdcapes of Glass”

Auditorium, LRSM Building 3231 Walnut Street, Philadelphia, PA, United States

If cooled sufficiently quickly, the disorder of a liquid can be "quenched" or locked in place; the resulting amorphous solid is glass. Although it appears to be solid on human timescales, glass continues to creep due to thermal vibrations at the molecular scale. Consider now a pile of sand; it too is a disordered system, […]

PICS Colloquium: “From atoms to emergent mechanisms with information bottleneck and diffusion probabilistic models”

Zoom - email kathom@seas.upenn.edu

Abstract: The ability to rapidly learn from high-dimensional data to make reliable predictions about the future is crucial in many contexts. This could be a fly avoiding predators, or the retina processing terabytes of data guiding complex human actions. Modern day artificial intelligence (AI) aims to mimic this fidelity and has been successful in many domains […]

PICS Colloquium: “Molecular organization in biology: What can computer simulations teach us?”

PICS Conference Room 534 - A Wing , 5th Floor 3401 Walnut Street, Philadelphia, PA, United States

Abstract: The formation of membraneless organelles (MLOs) via phase separation of proteins and nucleic acids has emerged as an essential process with which cells can maintain spatiotemporal control. Despite enormous progress in understanding the role of MLOs in biological function in the last ten years or so, the molecular details of the underlying phenomena are […]