Jupiter Algorta
@jupiteralgorta.bsky.social
Mathematician exploring the fascinating world of cellular migration and biology. Combining equations and experiments to understand how cells move and interact. 🧫🔬👨🏻💻
If you're curious about how cells make decisions in complex environments, and how mathematical models can capture such behaviour, our preprint is now live!
Check it out here: www.biorxiv.org/content/10.1...
Check it out here: www.biorxiv.org/content/10.1...
Investigating Local Negative Feedback of Rac Activity by Mathematical Models and Cell Motility Simulations
For polarization and directed migration, cells use a combination of local positive feedback and long-range inhibition. We have previously used mathematical models to show the ability of this core…
www.biorxiv.org
May 6, 2025 at 6:09 PM
If you're curious about how cells make decisions in complex environments, and how mathematical models can capture such behaviour, our preprint is now live!
Check it out here: www.biorxiv.org/content/10.1...
Check it out here: www.biorxiv.org/content/10.1...
Following a hypothesis proposed by Orion and Jason, I tested multiple models and formalisms to explain how cell reversal could be explained.
The key was adding a negative feedback loop (a Rac inhibitor) to the molecules driving cell motion.
With this, simulations finally matched experiments.
The key was adding a negative feedback loop (a Rac inhibitor) to the molecules driving cell motion.
With this, simulations finally matched experiments.
May 6, 2025 at 6:09 PM
Following a hypothesis proposed by Orion and Jason, I tested multiple models and formalisms to explain how cell reversal could be explained.
The key was adding a negative feedback loop (a Rac inhibitor) to the molecules driving cell motion.
With this, simulations finally matched experiments.
The key was adding a negative feedback loop (a Rac inhibitor) to the molecules driving cell motion.
With this, simulations finally matched experiments.
But when the light expands from part of the cell to illuminate the whole cell, real cells reverse rotation, something previous model(s) failed to predict.
This and other puzzling results led us to revise such models to better understand how cells reorient.
This and other puzzling results led us to revise such models to better understand how cells reorient.
May 6, 2025 at 6:09 PM
But when the light expands from part of the cell to illuminate the whole cell, real cells reverse rotation, something previous model(s) failed to predict.
This and other puzzling results led us to revise such models to better understand how cells reorient.
This and other puzzling results led us to revise such models to better understand how cells reorient.
When the light hits one side of the cell, it smoothly reorients toward it.
In simple environments, a previous polarity model captured this motion well.
In simple environments, a previous polarity model captured this motion well.
May 6, 2025 at 6:09 PM
When the light hits one side of the cell, it smoothly reorients toward it.
In simple environments, a previous polarity model captured this motion well.
In simple environments, a previous polarity model captured this motion well.
In 2023, Dr. Orion Weiner and Dr. Jason Town (UCSF) showed how to guide cells with light, using “optogenetic” stimulation upstream of Rac t o steer neutrophils .
Before diving deeper, here’s what you’ll see:
Left = experiment, right = simulation.
Green = cell edge, blue = light stimulus.
Before diving deeper, here’s what you’ll see:
Left = experiment, right = simulation.
Green = cell edge, blue = light stimulus.
May 6, 2025 at 6:09 PM
In 2023, Dr. Orion Weiner and Dr. Jason Town (UCSF) showed how to guide cells with light, using “optogenetic” stimulation upstream of Rac t o steer neutrophils .
Before diving deeper, here’s what you’ll see:
Left = experiment, right = simulation.
Green = cell edge, blue = light stimulus.
Before diving deeper, here’s what you’ll see:
Left = experiment, right = simulation.
Green = cell edge, blue = light stimulus.
Previous models of cell polarity capture basic movements, but not flexibility. When the chemical signal changes direction, they stay locked in place. Our revised model (right) reorients and tracks the new direction. We’re releasing the full story today as a preprint – link below.
May 6, 2025 at 6:09 PM
Previous models of cell polarity capture basic movements, but not flexibility. When the chemical signal changes direction, they stay locked in place. Our revised model (right) reorients and tracks the new direction. We’re releasing the full story today as a preprint – link below.
A cell navigating a chemical gradient is like being blindfolded in a dense forest, trying to find a clearing by feeling slight changes in the breeze. No map, no clear path. And yet, immune cells can find their way. I build models to understand how.
May 6, 2025 at 6:09 PM
A cell navigating a chemical gradient is like being blindfolded in a dense forest, trying to find a clearing by feeling slight changes in the breeze. No map, no clear path. And yet, immune cells can find their way. I build models to understand how.
In 2023, Dr. Orion Weiner and Dr. Jason Town (UCSF) showed how to guide cells with light, using “optogenetic” stimulation upstream of Rac t o steer neutrophils .
Before diving deeper, here’s what you’ll see:
Left = experiment, right = simulation.
Green = cell edge, blue = light stimulus.
Before diving deeper, here’s what you’ll see:
Left = experiment, right = simulation.
Green = cell edge, blue = light stimulus.
May 6, 2025 at 6:01 PM
In 2023, Dr. Orion Weiner and Dr. Jason Town (UCSF) showed how to guide cells with light, using “optogenetic” stimulation upstream of Rac t o steer neutrophils .
Before diving deeper, here’s what you’ll see:
Left = experiment, right = simulation.
Green = cell edge, blue = light stimulus.
Before diving deeper, here’s what you’ll see:
Left = experiment, right = simulation.
Green = cell edge, blue = light stimulus.
Previous models of cell polarity capture basic movements, but not flexibility. When the chemical signal changes direction, they stay locked in place. Our revised model (right) reorients and tracks the new direction. We’re releasing the full story today as a preprint – link below.
May 6, 2025 at 6:01 PM
Previous models of cell polarity capture basic movements, but not flexibility. When the chemical signal changes direction, they stay locked in place. Our revised model (right) reorients and tracks the new direction. We’re releasing the full story today as a preprint – link below.
A cell navigating a chemical gradient is like being blindfolded in a dense forest, trying to find a clearing by feeling slight changes in the breeze. No map, no clear path. And yet, immune cells can find their way. I build models to understand how.
May 6, 2025 at 6:01 PM
A cell navigating a chemical gradient is like being blindfolded in a dense forest, trying to find a clearing by feeling slight changes in the breeze. No map, no clear path. And yet, immune cells can find their way. I build models to understand how.
If any of this interests you, I invite you to visit Morpheus's home page: morpheus.gitlab.io and feel free to contact me at jupitera@math.ubc.ca.
Morpheus
Multicellular Simulation
morpheus.gitlab.io
January 20, 2025 at 10:07 PM
If any of this interests you, I invite you to visit Morpheus's home page: morpheus.gitlab.io and feel free to contact me at jupitera@math.ubc.ca.
Here’s a short video of one of my simulated cells responding to optogenetic inputs: the green shows Rac concentration on the cell edge, and the blue dashed circles indicate the regions of optogenetic stimulation, mimicking their experimental setup.
January 20, 2025 at 10:07 PM
Here’s a short video of one of my simulated cells responding to optogenetic inputs: the green shows Rac concentration on the cell edge, and the blue dashed circles indicate the regions of optogenetic stimulation, mimicking their experimental setup.
This project involves crafting intricate PDEs and implementing them in Morpheus to test and elaborate on what they’ve observed in the lab.
January 20, 2025 at 10:07 PM
This project involves crafting intricate PDEs and implementing them in Morpheus to test and elaborate on what they’ve observed in the lab.
My role has been to model their cells and demonstrate how incorporating this hypothesis enhances the ability of virtual cells to realign their fronts during chemotaxis. Additionally, I’ve been working to explain Jason’s most surprising results.
January 20, 2025 at 10:07 PM
My role has been to model their cells and demonstrate how incorporating this hypothesis enhances the ability of virtual cells to realign their fronts during chemotaxis. Additionally, I’ve been working to explain Jason’s most surprising results.
In 2023, Jason published a paper presenting compelling evidence for a local inhibitor of Rac within its downstream effects, along with extensive data and some unexpected results from different light stimulation configurations.
January 20, 2025 at 10:07 PM
In 2023, Jason published a paper presenting compelling evidence for a local inhibitor of Rac within its downstream effects, along with extensive data and some unexpected results from different light stimulation configurations.
Most recently, I have been collaborating with Dr. Orion Weiner and Dr. Jason Town to model HL-60 neutrophil-like cells modified to respond to optogenetic stimulation.
January 20, 2025 at 10:07 PM
Most recently, I have been collaborating with Dr. Orion Weiner and Dr. Jason Town to model HL-60 neutrophil-like cells modified to respond to optogenetic stimulation.
Soon you’ll be able to read about it in a review paper I co-authored with Dr. Leah Keshet, Jack M. Hughes, and Ali Fele-Paranj. The paper has been accepted and will be featured in the next Cold Spring Harbor Perspectives volume on Cell Migration. Here’s a video of the project in action:
January 20, 2025 at 10:07 PM
Soon you’ll be able to read about it in a review paper I co-authored with Dr. Leah Keshet, Jack M. Hughes, and Ali Fele-Paranj. The paper has been accepted and will be featured in the next Cold Spring Harbor Perspectives volume on Cell Migration. Here’s a video of the project in action:
This project was particularly refined as it incorporated two stages of cellular differentiation, governed by internal gene expressions, and cell sorting driven by differential cell-cell adhesion forces.
January 20, 2025 at 10:07 PM
This project was particularly refined as it incorporated two stages of cellular differentiation, governed by internal gene expressions, and cell sorting driven by differential cell-cell adhesion forces.
Another interesting project I developed in Morpheus over the years was a simulation of mammalian embryo development, starting from a single zygote cell and progressing to the 128-cell stage.
January 20, 2025 at 10:07 PM
Another interesting project I developed in Morpheus over the years was a simulation of mammalian embryo development, starting from a single zygote cell and progressing to the 128-cell stage.
I highly recommend trying out this tool and following along with the tutorial. By the end, you should be able to craft simulations like this one where I have two cells that follow a chemical gradient through chemotaxis:
January 20, 2025 at 10:07 PM
I highly recommend trying out this tool and following along with the tutorial. By the end, you should be able to craft simulations like this one where I have two cells that follow a chemical gradient through chemotaxis:
I demonstrate this in the video tutorials I created a few years ago, which you can find here (though I still need to complete Part 3, it provides a great starting point): www.youtube.com/watch?v=DLNj.... Yes, I know… I had my head shaved at the time, and it looks a bit weird!
Morpheus Tutorial - Part 1 Description, Space, and Time
YouTube video by Jupiter Algorta
www.youtube.com
January 20, 2025 at 10:07 PM
I demonstrate this in the video tutorials I created a few years ago, which you can find here (though I still need to complete Part 3, it provides a great starting point): www.youtube.com/watch?v=DLNj.... Yes, I know… I had my head shaved at the time, and it looks a bit weird!
The software features a user-friendly graphical interface, where users can simply drag and drop elements to build and customize their virtual cellular environments.
January 20, 2025 at 10:07 PM
The software features a user-friendly graphical interface, where users can simply drag and drop elements to build and customize their virtual cellular environments.
In 2014, a group at TU Dresden—Jörn Starruß, Walter de Back, Lutz Brusch, and Andreas Deutsch—created Morpheus, a software designed to allow users to implement their models with little to no programming knowledge.
January 20, 2025 at 10:07 PM
In 2014, a group at TU Dresden—Jörn Starruß, Walter de Back, Lutz Brusch, and Andreas Deutsch—created Morpheus, a software designed to allow users to implement their models with little to no programming knowledge.
Over the years, CPM has evolved to include increasingly complex descriptions and fascinating dynamics, making it an indispensable tool for exploring cellular behaviour. With its growing popularity, many software tools and packages were developed to facilitate the implementation of CPM.
January 20, 2025 at 10:07 PM
Over the years, CPM has evolved to include increasingly complex descriptions and fascinating dynamics, making it an indispensable tool for exploring cellular behaviour. With its growing popularity, many software tools and packages were developed to facilitate the implementation of CPM.