Manning Research Group
@manningresearch.bsky.social
Manning Research Group at Syracuse University: theory and computation focused on cells, grains, tissues, glasses, and other out-of-equilibrium disordered matter
In addition to altering lumen shape changes, are dynamical forces sufficient to change individual cell shapes to drive KV remodeling involved in LR patterning?
Yes, notochord ablation reduces the AP distribution as compared to controls. The 3D vertex model predicts this.
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Yes, notochord ablation reduces the AP distribution as compared to controls. The 3D vertex model predicts this.
12/n
July 17, 2025 at 1:43 PM
In addition to altering lumen shape changes, are dynamical forces sufficient to change individual cell shapes to drive KV remodeling involved in LR patterning?
Yes, notochord ablation reduces the AP distribution as compared to controls. The 3D vertex model predicts this.
12/n
Yes, notochord ablation reduces the AP distribution as compared to controls. The 3D vertex model predicts this.
12/n
These shape changes are generic – they can also be seen in a simpler hydrodynamic model of a membrane surrounded by a highly viscous medium, also with anterior pushing forces and posterior pulling forces.
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July 17, 2025 at 1:43 PM
These shape changes are generic – they can also be seen in a simpler hydrodynamic model of a membrane surrounded by a highly viscous medium, also with anterior pushing forces and posterior pulling forces.
11/n
11/n
The experiments match the simulation predictions! In notochord ablation experiments, the lumen elongates along the anterior-posterior axis (RgAP/RgLRincreases), while posterior cells ablations extend the lumen along the left-right axis (RgAP/RgLR decreases).
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July 17, 2025 at 1:43 PM
The experiments match the simulation predictions! In notochord ablation experiments, the lumen elongates along the anterior-posterior axis (RgAP/RgLRincreases), while posterior cells ablations extend the lumen along the left-right axis (RgAP/RgLR decreases).
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In simulations, we identify a set of model parameters (star in phase diagram) that generate the lumen shape seen in control experiments, where KV is pushed from the anterior by the notochord (orange cells) and pulled by posterior cells (purple cells).
July 17, 2025 at 1:43 PM
In simulations, we identify a set of model parameters (star in phase diagram) that generate the lumen shape seen in control experiments, where KV is pushed from the anterior by the notochord (orange cells) and pulled by posterior cells (purple cells).
Laser ablation of the notochord reduces the speed of KV in comparison to control experiments. That suggests that we were able to reduce the forces on the KV at the anterior part of KV.
We next ask how these reduced forces affect the shape of the KV lumen and KV cells
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We next ask how these reduced forces affect the shape of the KV lumen and KV cells
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July 17, 2025 at 1:43 PM
Laser ablation of the notochord reduces the speed of KV in comparison to control experiments. That suggests that we were able to reduce the forces on the KV at the anterior part of KV.
We next ask how these reduced forces affect the shape of the KV lumen and KV cells
7/n
We next ask how these reduced forces affect the shape of the KV lumen and KV cells
7/n
To test our hypothesis, we developed 3D models and laser ablation experiments to:
1) quantify how perturbing structures around KV impact its motion
2) measure cell and organ shape in these cases
3) show that observed in vivo shape changes match those predicted from the 3D model
6/n
1) quantify how perturbing structures around KV impact its motion
2) measure cell and organ shape in these cases
3) show that observed in vivo shape changes match those predicted from the 3D model
6/n
July 17, 2025 at 1:43 PM
To test our hypothesis, we developed 3D models and laser ablation experiments to:
1) quantify how perturbing structures around KV impact its motion
2) measure cell and organ shape in these cases
3) show that observed in vivo shape changes match those predicted from the 3D model
6/n
1) quantify how perturbing structures around KV impact its motion
2) measure cell and organ shape in these cases
3) show that observed in vivo shape changes match those predicted from the 3D model
6/n
To answer this question, we study Kupffer’s Vesicle (KV). KV is composed of a single layer of epithelial cells surrounding a fluid-filled lumen, located in tailbud of zebrafish, and it moves through surrounding tailbud tissue slowly, at about a micron per minute.
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July 17, 2025 at 1:43 PM
To answer this question, we study Kupffer’s Vesicle (KV). KV is composed of a single layer of epithelial cells surrounding a fluid-filled lumen, located in tailbud of zebrafish, and it moves through surrounding tailbud tissue slowly, at about a micron per minute.
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Yay! New paper out in PNAS: www.pnas.org/doi/10.1073/... . How do dynamical forces generated by tissue movement affect organ morphology changes during embryonic development?
Using Kupffer’s vesicle in zebrafish embryo we showed that dynamical forces produce shape changes in a developing organ.
Using Kupffer’s vesicle in zebrafish embryo we showed that dynamical forces produce shape changes in a developing organ.
July 17, 2025 at 1:43 PM
Yay! New paper out in PNAS: www.pnas.org/doi/10.1073/... . How do dynamical forces generated by tissue movement affect organ morphology changes during embryonic development?
Using Kupffer’s vesicle in zebrafish embryo we showed that dynamical forces produce shape changes in a developing organ.
Using Kupffer’s vesicle in zebrafish embryo we showed that dynamical forces produce shape changes in a developing organ.
Congratulations to research assistant Tyler Hain, who was just awarded the 2022 Syracuse University Oustanding Teaching Assistant Award!
December 16, 2024 at 11:02 PM
Congratulations to research assistant Tyler Hain, who was just awarded the 2022 Syracuse University Oustanding Teaching Assistant Award!
Really interesting talk on experiences as a woman in physics and also active matter by Cristina Marchetti @cris_marchetti_ at the Women in Science and Engineering 20(+2) year celebration at Syracuse University. Thanks, Cristina! #SUWISE22
December 16, 2024 at 11:02 PM
Really interesting talk on experiences as a woman in physics and also active matter by Cristina Marchetti @cris_marchetti_ at the Women in Science and Engineering 20(+2) year celebration at Syracuse University. Thanks, Cristina! #SUWISE22
10/ We solve self-consistency equation, which is a weighted integral over the edge tension distribution, for this k_m, and then use it to calculate the shear modulus.
December 16, 2024 at 11:02 PM
10/ We solve self-consistency equation, which is a weighted integral over the edge tension distribution, for this k_m, and then use it to calculate the shear modulus.
9/ i.e. imagine the honeycomb lattice undergoes a uniform expansion so L_1 = u_0 + L_0*, and then we replace one edge by a spring k_a, which would change its length. We want to find a new k_m for the surrounding network that would on average keep the length the same.
December 16, 2024 at 11:01 PM
9/ i.e. imagine the honeycomb lattice undergoes a uniform expansion so L_1 = u_0 + L_0*, and then we replace one edge by a spring k_a, which would change its length. We want to find a new k_m for the surrounding network that would on average keep the length the same.
6/ In such rigid systems, there is a distribution P(T) of tensions T on the edges, and which we find is well-fitted by a Gamma distribution.
December 16, 2024 at 11:01 PM
6/ In such rigid systems, there is a distribution P(T) of tensions T on the edges, and which we find is well-fitted by a Gamma distribution.
4/ Here, we develop an EMT for a random regular network, in this case a disordered 2D network where each vertex is connected to exactly three edges, and map it onto an ordered network with the same connectivity (a honeycomb lattice).
December 16, 2024 at 11:01 PM
4/ Here, we develop an EMT for a random regular network, in this case a disordered 2D network where each vertex is connected to exactly three edges, and map it onto an ordered network with the same connectivity (a honeycomb lattice).
8/ We find that localized bursts of deformation (with index B) during the avalanche DO occur at these soft spots (with index S). Here, overlap between the two is measured using mutual information.
December 16, 2024 at 11:01 PM
8/ We find that localized bursts of deformation (with index B) during the avalanche DO occur at these soft spots (with index S). Here, overlap between the two is measured using mutual information.
6/ Here, we study how the linear response (e.g. eigenvalues \lambda) evolves DURING the avalanche (e.g. over time t). The eigenspectrum is a hot mess. There are often multiple negative eigenvalues(n_n) and the resulting dynamics do not always track the most unstable eigenvector.
December 16, 2024 at 11:01 PM
6/ Here, we study how the linear response (e.g. eigenvalues \lambda) evolves DURING the avalanche (e.g. over time t). The eigenspectrum is a hot mess. There are often multiple negative eigenvalues(n_n) and the resulting dynamics do not always track the most unstable eigenvector.
4/ This results in a clustering of an avalanche into localized bursts that are clustered in space (X,Y) and time.
December 16, 2024 at 11:01 PM
4/ This results in a clustering of an avalanche into localized bursts that are clustered in space (X,Y) and time.
3/ We can robustly separate this data into space-time clusters using a slightly modified persistent homology algorithm, where we identify the “birth”(B) and “death”(D) of peaks in D2min (or a test function \phi), and then prune the birth-death tree based on the volume of peaks.
December 16, 2024 at 11:01 PM
3/ We can robustly separate this data into space-time clusters using a slightly modified persistent homology algorithm, where we identify the “birth”(B) and “death”(D) of peaks in D2min (or a test function \phi), and then prune the birth-death tree based on the volume of peaks.
2/ Fellow scientists have observed that avalanches appear to proceed via localized bursts of deformation. Using the “D2min” metric defined by Falk and Langer we see (like others) that there is “burstiness” in time (bottom plot) and space (insets).
December 16, 2024 at 11:01 PM
2/ Fellow scientists have observed that avalanches appear to proceed via localized bursts of deformation. Using the “D2min” metric defined by Falk and Langer we see (like others) that there is “burstiness” in time (bottom plot) and space (insets).
7/ Previous work has shown that low-connectivity spring and fiber networks “strain-stiffen”, becoming orders of magnitude stiffer at a critical value of the applied strain. Similarly, vertex and Voronoi models become rigid at a critical value of the cell shape parameter.
December 16, 2024 at 11:00 PM
7/ Previous work has shown that low-connectivity spring and fiber networks “strain-stiffen”, becoming orders of magnitude stiffer at a critical value of the applied strain. Similarly, vertex and Voronoi models become rigid at a critical value of the cell shape parameter.
6/ In paper 1, we show the answer is “it depends” and describe specific criteria for when 1st order rigidity or 2nd order rigidity is sufficient to ensure energetic rigidity. We demonstrate that in some cases neither is sufficient, which may open avenues for metamaterials design
December 16, 2024 at 11:00 PM
6/ In paper 1, we show the answer is “it depends” and describe specific criteria for when 1st order rigidity or 2nd order rigidity is sufficient to ensure energetic rigidity. We demonstrate that in some cases neither is sufficient, which may open avenues for metamaterials design
3/One way to derive Maxwell constraint counting is to consider a frame or network composed of joints connected by bars, and ask if any perturbation to the joints results in extension or compression of the bars to first order. If so, the structure is “first-order rigid”.
December 16, 2024 at 11:00 PM
3/One way to derive Maxwell constraint counting is to consider a frame or network composed of joints connected by bars, and ask if any perturbation to the joints results in extension or compression of the bars to first order. If so, the structure is “first-order rigid”.
2/Many of us are familiar with Maxwell constraint counting, which predicts that a material becomes rigid when the number of constraints equals the number of degrees of freedom. This, for example, correctly predicts the onset of jamming in granular matter.
December 16, 2024 at 11:00 PM
2/Many of us are familiar with Maxwell constraint counting, which predicts that a material becomes rigid when the number of constraints equals the number of degrees of freedom. This, for example, correctly predicts the onset of jamming in granular matter.
Our new manuscript develops a method for predicting material failure in active solids with the application of predicting and preventing disasters (like crushing and trampling events) in dense human crowds🧍♂️🧍♀️- J. Giannini, E. Stanifer, M. L. Manning - DOI: 10.1039/D1SM01675J
December 16, 2024 at 11:00 PM
Our new manuscript develops a method for predicting material failure in active solids with the application of predicting and preventing disasters (like crushing and trampling events) in dense human crowds🧍♂️🧍♀️- J. Giannini, E. Stanifer, M. L. Manning - DOI: 10.1039/D1SM01675J
Postdoctoral opportunity in theoretical biophysics/soft matter in the Manning Lab with @amacklab and @LovelessRadio
December 16, 2024 at 11:00 PM
Postdoctoral opportunity in theoretical biophysics/soft matter in the Manning Lab with @amacklab and @LovelessRadio