Towards predictive "whole-cell" models of cellular behavior
Markus Covert
Stanford University
Wednesday, September 3, 4:00 PM, C215 ESC
Abstract:
Francis Crick first called for a coordinated worldwide scientific effort to determine a “complete solution” of the bacterium Escherichia coli. We have been working for some years now to complete a model of E. coli that takes into account all of the known functions of every well-annotated gene, in order to better understand and predict the behavior of this scientifically-relevant and industrially-significant model organism. I will discuss our ongoing efforts to improve this model, most recently with new modeling added to better describe growth rate control, transcription unit architecture and tRNA metabolism. I will then highlight our newest “whole-colony” models, a multi-scale modeling effort in which every individual within a simulated colony is running the latest version of the whole-cell model, to calculate population-level emergent behaviors based on molecular interactions and events as the colony responds to the sudden introduction of antibiotics.
Biographical Sketch:
Markus Covert is the Ram Shriram Chair and Professor of Bioengineering at Stanford University. Over the course of his career, his lab has generated several new exciting technologies to measure, analyze, and mathematically model the behaviors of individual cells. The lab is probably best known for constructing the first "whole-cell" computational model, which explicitly represents all known gene functions and molecules in a bacterial cell - an advance which was highlighted by the journal Cell as a highlight publication of the 40-year history of that journal. Markus is the author of the textbook Fundamentals of Systems Biology: from Synthetic Circuits to Whole-Cell Models. He has received several awards for his efforts to develop new technologies, in particular the NIH Director's Pioneer Award, and the Paul G. Allen Family Foundation Distinguished Investigator and Discovery Center awards. He has also consulted in industry, including on the scientific advisory board of Emerald Cloud Labs, and as an inaugural Ambassador at X Labs, (previously Google [X]). Finally, Markus has taught one of the most popular courses at Stanford for several years, an integrated “lecture, lab and lunch” course entitled Bon Appétit, Marie Curie! The Science of Haute Cuisine, and has taught this course in Paris twice through the Stanford's Bing Overseas Studies Program (BOSP).
Acoustics
Michelle Swearingen
US Army Corps of Engineers (USACE)
Wednesday, September 10, 4:00 PM, C215 ESC
Abstract:
Biographical Sketch:
Experimental nuclear physics
Chris Crawford
University of Kentucky
Wednesday, October 1, 4:00 PM, C215 ESC
Abstract:
Dr. Crawford's research focuses on experimental nuclear physics:
- precision tests of fundamental symmetries
- hadronic weak interaction (HWI), hadronic structure
- cold and ultra-cold neutrons, polarized targets
Symmetries help us to understand our physical universe, reducing diverse phenomena to universal laws. Noether's theorem makes a connection between continuous symmetries and conserved currents, such as energy and momentum. In particle physics, the difference in particle masses is attributed to spontaneous symmetry breaking.
Although discrete symmetries such as P (spatial parity), T (time reversal), and C (charge conjugation) are outside the scope of Noether's theorem, they offer a unique perspective of quantum mechanics. While classical laws are invariant under these discrete transformations, their trajectories are always continuous. In contrast, quantum transitions occur between discrete states, enabling new concepts such as spin angular momentum.
Of the four fundamental forces, P,C, and CP-violation have been observed only in the weak interaction. We are running a series of experiments at the Spallation Neutron Source (SNS), ORNL to measure P-violation in the weak nucleon-nucleon interaction (HWI), which is sensitive to quark-quark correlations in the proton and neutron. We are also involved in a precision measurement of the electric dipole moment of the neutron, which violates both P and T symmetries. This observable is sensitive to new physics at the same energy scale as the Large Hadron Collider (LHC) at Cern.
Biographical Sketch:
Exo-planets
Jason Steffen
UNLV
Wednesday, October 8, 4:00 PM, C215 ESC
Abstract:
Dr. Steffen studies various properties of exoplanets and exoplanetary systems (systems of planets that orbit distant stars). He has been a part of NASA’s Kepler mission since 2008 and works primarily with Kepler data. Dr. Steffen is looking forward to the launch of NASA’s TESS mission, which is a successor to Kepler.
Biographical Sketch:
Dr. Jason Steffen has been a member of the science team for NASA's Kepler mission since 2008. A native of Utah, He received his bachelor of science in Physics and Mathematics from Weber State University and his master's and doctoral degree in physics from the University of Washington, Seattle. Dr. Steffen spent a decade as the Brinson Fellow at Fermilab and the Lindheimer Fellow at Northwestern University, both near Chicago, and recently moved back West as an Assistant Professor of Physics at the University of Nevada, Las Vegas. Dr. Steffen is an author on over 60 publications and has been privileged to contribute to many recent discoveries in exoplanet science.
LCLS-II
Arianna Gleason
SLAC
Wednesday, October 22, 12:00 PM, C215 ESC
Abstract:
Biographical Sketch:
Arianna Gleason is a Staff Scientist in the Fundamental Physics Directorate of the SLAC National Accelerator Laboratory and is Adjunct Faculty in the Geological Science Department, Stanford University, where she focuses on dynamic mesoscale materials properties. She obtained her Ph.D. in 2010 from the University of California, Berkeley, working on high-pressure mineral physics and on planetary sciences. Her research applies ultrafast x-ray probes to study dynamic materials processes related to geoscience, planetary science, and fusion-energy research. She recently received a DOE’s Early Career Award.
Physics Education Research
Zhongzhou Chen
UCF Department of Physics
Wednesday, October 29, 12:00 PM, C215 ESC
Abstract:
Biographical Sketch:
Dr. Zhongzhou Chen earned his Ph.D. in physics from University of Illinois Urbana Champaign in 2012, specializing in physics education and multimedia learning. In 2013 he joined the RELATE group at MIT as a postdoc, conducting educational research in Massive Open Online Courses (MOOCs) on the edX platform, mentored by Prof. David Pritchard. His current research focuses on analyzing student learning data to improve the effectiveness of online learning, and designing online-learning environments to enhance the quality of measurement and data collection.
The Physics of Football
Timothy Gay
University of Nebraska
Wednesday, November 5, 12:00 PM, C215 ESC
Abstract:
Biographical Sketch:
We are interested in polarized electron physics. Our work involves studies of polarized electron scattering from atoms and molecules, the understanding of chiral and dichroic effects in such targets, the development of novel sources of polarized electrons and electron polarimeters, and investigations of the fundamental nature of the electron. Our group collaborates with scientists at Los Alamos National Laboratory and the Thomas Jefferson National Laboratory. We are funded by the Experimental Atomic, Molecular, and Optical Physics Program and the Accelerator Science Program in the Physics Division of the National Science Foundation.
Determining the Astrophysical Origins of White-Dwarf Supernovae with JWST Infrared Spectroscopy
Lindsey Kwok
Northwestern University
Wednesday, November 12, 4:00 PM, C215 ESC
Abstract:
Biographical Sketch:
Cosmology
Gustavo Marques Tavares
University of Utah
Wednesday, December 3, 12:00 PM, C215 ESC
Abstract:
Biographical Sketch:
We welcome anyone who wish to attend, and typically serve refreshments ten minutes before the colloquium begins. Speakers generally keep their presentation accessible to undergraduate physics students.