Calendar

Upcoming events

Minflux Webinar

100x sharper than a confocal microscope, 100x faster tracking than a camera – that is MINFLUX.

Don’t miss the chance to learn what MINFLUX is capable of! Join us on zoom for this session.

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STC-QCB Seminar: Massimiliano Esposito (University of Luxembourg) "Nonequilibrium thermodynamics of chemical reaction networks and bioenergetics"

Beckman 3269 3rd Floor Tower Room

Contact name: Lisa Johnson
Contact email: lisa3@illinois.edu
Contact phone: 217-300-9574

I will start by introducing the fundamentals of thermodynamics of open chemical reaction networks (CRNs) and discuss how this theory can be used to assess the energetic cost of various biologically relevant operations. I will then present a circuit theory of CRNs which, like electrical circuit theory, can be used to describe complex CRNs in terms of modules characterized by the chemical analogues of a current-voltage characteristics and of Kirchhoff current and voltage laws. Energy transduction in central metabolism will be discussed as an application. 

 

References:

- R. Rao and M. Esposito, "Nonequilibrium Thermodynamics of Chemical Reaction Networks: Wisdom from Stochastic Thermodynamics", Phys. Rev. X  6, 041064 (2016)

- F. Avanzini, N. Freitas and M. Esposito, "Circuit Theory for Chemical Reaction Networks", Phys. Rev. X 13, 021041 (2023)

- A. Wachtel, R. Rao and M. Esposito, "Free-Energy Transduction in Chemical Reaction Networks: From Enzymes to Metabolism", J. Chem. Phys. 157, 024109 (2022)

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STC-QCB Seminar: Markus Covert (Stanford University) "Whole-cell modeling of E. coli: from simulation to discovery"

Beckman 3269 3rd Floor Tower Room

Contact name: Lisa Johnson
Contact email: lisa3@illinois.edu
Contact phone: 217-300-9574

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.

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Intro to Parallel Computing on HPC Systems Workshop

Contact name: Bruno Abreu
Contact email: babreu@illinois.edu

This workshop will explore parallel programming and computing on HPC systems at the introductory level. Attendees will learn how to parallelize and run C/C++/Fortran applications using shared memory parallelism with OpenMP through hands-on exercises and access to the Illinois Campus Cluster. General terminology, parallel computing concepts and ideas, measuring performance, identifying bottlenecks, and other relevant topics will be discussed.

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LAS Dean’s Distinguished Lecture: Zaida (Zan) Luthey-Schulten

Illini Union Ballroom

"Bringing a cell to life on a computer and in Minecraft" is the title of Dr. Zaida (Zan) Luthey-Schulten's LAS Dean's Distinguished Lecture. A professor of chemistry, she is also director of the NSF Science and Technology Center in Quantitative Cell Biology at the Beckman Institute. The lecture will be presented in person at the Illini Union Ballroom and also streamed via Zoom. The lecture is free, but registration is requested for inperson and required to get the Zoom link. Register here.

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Biological Physics / iPoLS / STC-QCB Seminar: Giovanni Pavan () ""

Beckman 3269 3rd Floor Tower Room

Contact name: Lisa Johnson
Contact email: lisa3@illinois.edu
Contact phone: 217-300-9574

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Minflux Seminar - In Person

IGB 114

100x sharper than a confocal microscope, 100x faster tracking than a camera – that is MINFLUX.

Don’t miss the chance to learn what MINFLUX is capable of! Come join us in Room 114 at the Institute for Genomic Biology.

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STC-QCB Seminar: Bin Zhang (MIT), "Multiscale Simulations of Biocondensates and Genome Organization"

Beckman 3269 3rd Floor Tower Room

Contact name: Lisa Johnson
Contact email: lisa3@illinois.edu
Contact phone: 217-300-9574

Coarse-grained models enable large-scale simulations of complex biomolecular systems over long timescales. We have introduced bottom-up approaches based on contrastive learning to parameterize these models using atomistic simulations, and top-down approaches based on maximum entropy optimization to parameterize them from experimental data. We performed coarse-grained simulations to study the liquid-liquid phase separation of biomolecules, which has emerged as a fundamental principle for organizing various cellular structures. In addition, we simulate the 3D conformations of the human genome to understand its organizational principles and the role of chromatin structure in gene regulation. Our studies help elucidate the molecular determinants for the stability, internal organization, and coarsening of biocondensates, and the contribution of various condensates to genome organization.

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QCB Lunch & Learn: Mentoring

Beckman 3269 3rd Floor Tower Room

Contact name: Center for Quantitative Cell Biology
Contact email: qcb@beckman.illinois.edu

Join us for lunch and and training on becoming an effective mentor - a relationship critical to developing the next generation of researchers. Dr. Sharlene Denos, QCB Team Leader, Broader Impacts, will lead this training using materials from the Center for Improvement of Mentored Experiences in Research (CIMER). Attendance required for QCB postdocs and grad students.

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Strategic Planning with Giant Leap Consulting

Beckman Institute

Contact name: Center for Quantitative Cell Biology
Contact email: qcb@beckman.illinois.edu

This event is only for QCB members and invited guests.

STC-QCB Seminar: Joshua Rabinowitz (Princeton University) TBD

Beckman 3269 3rd Floor Tower Room

Contact name: Lisa Johnson
Contact email: lisa3@illinois.edu
Contact phone: 217-300-9574

No more information

QCB Lunch & Learn

Beckman 3269 3rd Floor Tower Room

Contact name: Center for Quantitative Cell Biology
Contact email: qcb@beckman.illinois.edu

Join us for lunch and an informative speaker. More information coming soon!

Biological Physics / iPoLS / STC-QCB Seminar: Luke Chao (Harvard University) ""

Beckman 3269 3rd Floor Tower Room

Contact name: Lisa Johnson
Contact email: lisa3@illinois.edu
Contact phone: 217-300-9574

No more information

STC for Quantitative Cell Biology Computational Workshop

Contact name: Chris Zwilling
Contact email: zwillin1@illinois.edu

The NSF Science and Technology Center for Qualitative Cell Biology Computational Workshop is hosting a computational workshop. More details coming soon!

Advanced Computational Workshop

University of Illinois Urbana-Champaign

Contact name: Center for Quantitative Cell Biology
Contact email: qcb@beckman.illinois.edu

Save the date and plan to join us at the University of Illinois Urbana-Champaign for an advanced computational workshop. This workshop is targeted to those who have been using computational tools for a while and want to increase their knowledge and skills. It is not for beginners. More information coming soon!

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Midwest Advanced MINFLUX and Super Resolution Workshop

Carl R. Woese Institute for Genomic Biology

Contact name: Chris Zwilling
Contact email: zwillin1@illinois.edu

The NSF Science and Technology Center for Qualitative Cell Biology is hosting a Midwest Advanced MINFLUX and Super Resolution Workshop. The workshop will highlight STED and MINFLUX technology through talks and hands-on sessions with the MINFLUX and STEDYCON system.

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NSF Site Visit

Beckman Institute

Contact name: Center for Quantitative Cell Biology
Contact email: qcb@beckman.illinois.edu

This meeting is only for QCB members and invited guests.