Congratulations, Dr. Stanifer!

Congratulations to Dr. Ethan Stanifer, who successfully defended his thesis entitled, “Investigating the relationships between disorder, structure, and dynamics in amorphous systems” on June 25th!

Manning research group: BlackLivesMatter

As a research lab, we have taken time away from work for #shutdownSTEM and Juneteenth reflect on how we can actively promote anti-racism. We must start by acknowledging that BlackLivesMatter and that systemic racism negatively impacts people of color in many ways, including raising significant barriers that impede them as they perform scientific research and progress in academia.  We love doing science, and all people deserve that thrill of discovery. How many great scientists are we missing because systemic racism blocked them from that path?Moreover, research demonstrates that science and engineering are better when science is more diverse: https://www.pnas.org/content/101/46/16385 . And there are plenty of examples of times when science and technology has failed us because the scientists/designers were not diverse: https://reporter.rit.edu/tech/bigotry-encoded-racial-bias-technology .Given this, we must take active steps to make our research group and society more inclusive, and very specific more inclusive of Black and Brown students and scientists. Small steps include expanding our work on partnerships between Minority Serving Institutions and Primarily White Institutions, contributing to the Physics Department’s Diversity and Inclusion Committee, and advocating for changes to GRE and other departmental testing requirements. We can ensure that the speakers we invite to give seminars are diverse, and we can participate in mentoring and outreach programs.  We can engage in public policy debates as private citizens. This is a process, so we are still engaged in thinking about changes we can make to improve. Please stay tuned.

Manuscript on rigidity transitions in anisotropic tissues and fruit fly convergent extension appears in PNAS

A great collaboration with Karen Kasza’s group at Columbia has led to a paper we’re excited about that just appeared in Proceedings of the National Academy of Sciences. Our former REU (research experiences for undergraduates) student Leo Sutter is a co-author, as are former postdocs Matthias Merkel and Gonca Erdemci-Tandogan. Here’s a link to a news article about the research : https://thecollege.syr.edu/news-all/news-2020/physics-behind-tissue-growth-embryo/
And here’s a link to the manuscript: Xun Wang*, Matthias Merkel*, Leo B. Sutter*, Gonca Erdemci-Tandogan, M. Lisa Manning, Karen E. Kasza. “A solid-to-fluid transition is predicted by cell shape and alignment in an anisotropic tissue of the developing fly embryo”, Proceedings of the National Academy of Sciences May 2020, , https://doi.org/10.1073/pnas.1916418117 , arXiv: https://arxiv.org/abs/2005.07283 (2020).

Manuscript describing two kinds of nonlinear behavior in jammed particulate matter appears in PRR!

Former postdoctoral associate Peter Morse, former graduate student Sven Wijtmans, and Lisa Manning worked with Martin Van Hecke’s lab to understand how contact changes correlate with plasticity in jammed soft spheres.  We found that contact changes are not one-to-one with plastic events, even in the limit of zero pressure. This is interesting because in hard spheres those two types of events always occur together.  We also show that the statistics of nonlinear plastic events show the same scaling as the linear response, again highlighting the zero-pressure limit is singular.

Peter Morse, Merlijn van Deen, Sven Wijtmans, Martin Van Hecke, M. L. Manning, “Two classes of events in sheared particulate matter,”  Physical Review Research 2 023179https://link.aps.org/doi/10.1103/PhysRevResearch.2.023179 arXiv:1907.10198 (2020).

Manuscript about microtubule bridges in formation of Kupffer’s vesicle, spearheaded by Hehnly lab, appears in Nature Communications.

Former postdoctoral associate Gonca Erdemci-Tandogan and Lisa Manning worked with Heidi Hehnly’s lab (SU Biology) and Jeff Amack’s lab (SUNY Upstate Cell and Developmental Biology) to understand cytokinetic bridges that occur during formation of Kupffer’s vesicle, the organ responsible for left-right symmetry breaking in zebrafish. The manuscript recently appeared in Nature Communications: https://www.nature.com/articles/s41467-020-15002-8

Manuscript on small-scale demixing in confluent biological tissues appears in Soft Matter

Our paper, “Small-scale demixing in confluent biological tissues” just appeared in Soft Matter.

Surface tension governed by differential adhesion can drive fluid particle mixtures to sort into separate regions, i.e., demix. Does the same phenomenon occur in confluent biological tissues? We begin to answer this question for epithelial monolayers with a combination of theory via a vertex model and experiments on keratinocyte monolayers. Vertex models are distinct from particle models in that the interactions between the cells are shape-based, as opposed to distance-dependent. We investigate whether a disparity in cell shape or size alone is sufficient to drive demixing in bidisperse vertex model fluid mixtures. Surprisingly, we observe that both types of bidisperse systems robustly mix on large lengthscales. On the other hand, shape disparity generates slight demixing over a few cell diameters, a phenomenon we term micro-demixing. This result can be understood by examining the differential energy barriers for neighbor exchanges (T1 transitions). Experiments with mixtures of wild-type and E-cadherin-deficient keratinocytes on a substrate are consistent with the predicted phenomenon of micro-demixing, which biology may exploit to create subtle patterning. The robustness of mixing at large scales, however, suggests that despite some differences in cell shape and size, progenitor cells can readily mix throughout a developing tissue until acquiring means of recognizing cells of different types.

https://pubs.rsc.org/en/Content/ArticleLanding/2020/SM/C9SM01084J#!divAbstract

Manuscript on non-linear response of ordered biological tissues appears in Soft Matter

Our paper, “Linear and nonlinear mechanical responses can be quite different in models for biological tissues” just appeared in Soft Matter.

The fluidity of biological tissues – whether cells can change neighbors and rearrange – is important for their function. In traditional materials, researchers have used linear response functions, such as the shear modulus, to accurately predict whether a material will behave as a fluid. Similarly, in disordered 2D vertex models for confluent biological tissues, the shear modulus becomes zero precisely when the cells can change neighbors and the tissue fluidizes, at a critical value of control parameter s0* = 3.81. However, the ordered ground states of 2D vertex models become linearly unstable at a lower value of control parameter (3.72), suggesting that there may be a decoupling between linear and nonlinear response. We demonstrate that the linear response does not correctly predict the nonlinear behavior in these systems: when the control parameter is between 3.72 and 3.81, cells cannot freely change neighbors even though the shear modulus is zero. These results highlight that the linear response of vertex models should not be expected to generically predict their rheology. We develop a simple geometric ansatz that correctly predicts the nonlinear response, which may serve as a framework for making nonlinear predictions in other vertex-like models.

https://pubs.rsc.org/en/content/articlelanding/2020/sm/c9sm01068h#!divAbstract

Manuscript on the role of cell divisions in confluent tissue fluidization appears in Soft Matter

Our paper, “Glassy dynamics in models of confluent tissue with mitosis and apoptosis” just appeared in Soft Matter.

Recent work on particle-based models of tissues has suggested that any finite rate of cell division and cell death is sufficient to fluidize an epithelial tissue. At the same time, experimental evidence has indicated the existence of glassy dynamics in some epithelial layers despite continued cell cycling. To address this discrepancy, we quantify the role of cell birth and death on glassy states in confluent tissues using simulations of an active vertex model that includes cell motility, cell division, and cell death. Our simulation data is consistent with a simple ansatz in which the rate of cell-life cycling and the rate of relaxation of the tissue in the absence of cell cycling contribute independently and additively to the overall rate of cell motion. Specifically, we find that a glass-like regime with caging behavior indicated by subdiffusive cell displacements can be achieved in systems with sufficiently low rates of cell cycling.

https://pubs.rsc.org/en/content/articlelanding/2019/sm/c9sm00916g#!divAbstract

Julia Giannini and Ethan Stanifer Awarded BioInspired Institute Poster Session Prizes

The BioInspired Institute held it’s kickoff event on October 11, featuring PI pitch talks, a brainstorming session, and a poster session for students and postdocs. At the poster session Julia and Ethan were awarded prizes for the presentation of their respective work entitled “Predicting crowd dynamics using local structure” and “Structural evolution of amorphous systems during large scale deformation.”

Read more about the BioInspired Institute here:

https://news.syr.edu/blog/2019/04/25/bioinspired-institute-brings-together-faculty-with-related-research-interests-from-across-the-university/