Dynamics Club
Launched in Jan 2022, Dynamics Club is a forum for junior scientists to discuss nonlinear dynamics in biology and physiology. Our monthly seminars are mostly on Zoom, with hybrid access to occasional in-person visit. All are welcome!
Currently, we have 290 members. If you’re new, sign up here!
Call for 2024 speakers is still open: please fill in the form to indicate your preferences.
Job opportunities:
- A postdoctoral position is available with Dr. Russell Rockne at City of Hope (Details).
- A postdoctoral position is available with Dr. Jeremy Purvis at UNC Chapel Hill (Details).
- A postdoctoral position is available with Dr. Sheng-hong Chen at Academia Sinica, Taiwan (Details).
Key References (PDFs are available online):
Nonlinear Dynamics and Chaos by Steven Strogatz
Modeling Life by Alan Garfinkel, Jane Shetsov and Yina Guo (Course Materials)
Upcoming Events in May:
Guest lecture: What do elevated levels of albumin in urine mean?
Speaker: Dr. Aurelie Edwards (Research Professor; Boston University)
Date and Time: May 24 (Fri) at 10am PT / 1pm ET
Virtual event on Zoom (Meeting ID: 927 4378 5517, Passcode: 147406)
Abstract:
The kidneys normally filter a very small fraction of large plasma proteins, since these proteins play important roles (in transport, immune function, maintaining blood volume, etc.) and should not be excreted. The presence of significant amounts of albumin in urine signifies dysfunction, but it is difficult to interpret, since many factors – such as capillary permeability, filtration rates, shear stress, concentration, receptor kinetics – impact the renal handling of albumin. In this talk, we will describe how mathematical modeling of albumin transport in kidney tubules can provide essential insight into the mechanisms underlying urinary loss of albumin, particularly in diabetes. We will focus on how changes in plasma filtration rates and downregulation of the albumin receptors megalin and cubilin contribute to raising albumin excretion in early-stage diabetes and uni-nephrectomy, a model of living kidney donation.
Matching a network model of the yeast cell cycle to multiple dynamic behaviors of mutant datasets
Speaker: Dr. Breschine Cummins (Assistant Professor; Montana State University)
Date and Time: May 29 (Wed) at 11am PT / 2pm ET
Hybrid event: Boyer Hall 130 and on Zoom (Meeting ID: 915 5371 7489, Passcode: 589284)
Abstract:
Modeling biological systems holds great promise for speeding up the rate of discovery in systems biology by predicting experimental outcomes and suggesting targeted interventions. However, this process is dogged by an identifiability issue, in which network models and their parameters are not sufficiently constrained by coarse and noisy data to ensure unique solutions. In this work, we evaluated the capability of a simplified yeast cell-cycle network model to reproduce multiple observed transcriptomic behaviors under genomic mutations. We matched time-series data from both cycling and checkpoint arrested cells to model predictions using an asynchronous multi-level Boolean approach. We showed that this single network model, despite its simplicity, is capable of exhibiting dynamical behavior similar to the datasets in most cases, and we demonstrated the drop in severity of the identifiability issue that results from matching multiple datasets.
Scheduled Sessions:
| Date | Topic | Speaker(s) |
| Jun 4 | Guest lecture: Pulsed stimuli entrain p53 to synchronize single cells and modulate cell-fate determination | Dr. Eric Batchelor (University of Minnesota) |
| Jun | Mathematical modeling of macrophage polarization | Dr. Anna-Simone J. Frank (University of Bergen) |
| Jul | Blood pressure pulsations modulate central neuronal activity via mechanosensitive ion channels | Dr. Luna Jammal Salameh (University of Regensburg) |
| Aug | Guest lecture: TBA | Dr. Susanna Röblitz (University of Bergen) |
| Sep | Causality without correlation in biology | Dr. Gerald Pao (Okinawa Institute for Science and Technology) |
| Oct | Homoclinic action potentials in neural encoding and synchronization | Dr. Janina Hesse (Leibniz Institute for Resilience, Mainz) |
| Nov | Plausible, robust biological oscillations through allelic buffering | Dr. Feng-Shu Hsieh (Academia Sinica) |
| Dec | Nonlinear dynamics of pattern formation and of oscillator synchronization during embryonic development | Dr. Laurent Jutras-Dubé (Rockefeller University) |
Past Events in 2024
| Date | Topic | Speaker(s) | Materials |
| Jan 10 | Optimal transport in single-cell genomics with moscot | Dominik Klein (Theis Lab; Helmholtz Munich) | Preprint |
| Feb 12 | Context-dependent regulation of lipid accumulation in adipocytes by a HIF1a-PPARg feedback network | Dr. Michael Zhao (EMBL) | PubMed |
| Mar 20 | A bioelectrical phase transition patterns the first vertebrate heartbeats | Bill Jia (Cohen/Megason Lab; Harvard) | PubMed |
| Apr 24 | Modeling inter-individual differences in circadian timekeeping based on wrist-wearable data | Dr. Ruby Kim (University of Michigan) |
Past Events in 2023
Past Events in 2022