japanese slime mold experiment

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January 27, 2022

Using a 'virtual slime mold' to design a subway network less prone to disruption

by Tyler Irving, University of Toronto

Researchers use ‘virtual slime mould’ to design a TTC subway network less prone to disruption

It doesn't have a brain and survives on rotting vegetable matter—but it could offer valuable insights into city planning, according to a team of University of Toronto researchers.

Physarum polycephalum is a slime mold, a single-celled amoeboid organism that grows as a greenish-yellow system of veins. These veins form a tubular network that is optimized to transfer nutrients efficiently throughout the entire organism.

Slime molds first "forage" broadly over an area, then refine their tubular network to optimize for transport of the nutrients. Now, researchers believe the slime mold's efficient organic structure could provide a model for optimizing other networks—including those designed to move people and goods around a city.

"Humans aren't the only ones dealing with the challenge of designing efficient, resilient networks," says Raphael Kay, who joined U of T's Faculty of Applied Science & Engineering as a master's candidate after completing his undergraduate degree at the John H. Daniels Faculty of Architecture, Landscape, and Design.

"In architecture school, we were taught by human architects the lessons of past human architecture. But the slime mold has been shaped by hundreds of millions of years of evolution, so in that sense, they are far more experienced at solving certain architectural problems than we humans ever could be."

Kay, who is supervised by Ben Hatton, an associate professor in the department of materials science and engineering, is not the first to think this way. Back in 2010, a team of researchers from Japan and the U.K. fed a slime mold with nutrients arranged to imitate the nodes of the Tokyo subway system . The resulting network was strikingly similar to the real thing, and sparked the emergence of what is now known as biologically inspired adaptive network design. Other researchers have since conducted similar studies in the context of their own regional rail or road transportation networks.

Kay, along with Anthony Mattacchione, a master of architecture student, built on this work by creating a computer model that simulates the way slime molds construct their network. They validated the model by comparing its results to those of a real slime mold grown on an agar plate, which they fed with oatmeal.

The results of their work were published this week in Scientific Reports .

The networks created by the model were evaluated using three key metrics:

Cost, a function of the overall length of all segments
Mean travel time, the average length between any two points
Vulnerability, the average increase in travel time caused by the removal of a segment

Looking at the ratios between these metrics, the team saw good correlation with the actual slime mold: the deviation between the model and the living organism was less than four percent.

While other teams have created similar models, what sets this one apart is the way it was explicitly aimed at architects, city planners and other professionals who might be interested in incorporating lessons from nature into their design process. For example, the user could specify a maximum cost or minimum travel time and generate a selection of networks designed to meet those needs. (Kay says he and Mattacchione first conceptualized the model for a graduate architecture course taught by Assistant Professor Maria Yablonina at the John H. Daniels Faculty of Architecture, Landscape, and Design.)

To test the virtual slime mold model, the team programmed it to create two sample networks derived from real-world situations. One set of points was derived from the locations of various roller coasters and food stands at Canada's Wonderland, a local amusement park. The other was based on the locations of 17 key subway stations in Toronto.

"In the Canada's Wonderland example, our model generated a network that, for the same cost, would provide a travel time 10 percent faster than the real-life network and 80 percent more resilient in the event that one of the segments gets blocked," says Kay.

"For the subway, the most striking finding was that for a network with the same travel time as the real thing, our network was 40 percent less susceptible to disruption."

The results may not be that surprising to those who have used these real-life networks, which weren't necessarily designed with resilience to disruption as a top priority. Kay and Hatton say they are not advocating for these networks to be re-designed from scratch, but rather using them as examples of where their model could offer insights on the best places to add segments, as well as to inform future designs.

"Another advantage of our model is that it can generate the attractor nodes itself, without the need for designer input," says Kay. "For example, you can upload the population density of a real neighborhood or city, and then have it determine the network nodes that might best serve this population."

The team is considering making the model available on an open-source basis to anyone who wants to use it.

Hatton says it has potential to bring together expertise and insights from disciplines that have traditionally been thought of as separate. "Raphael and Anthony developed a really useful tool, which I think is pretty accessible to anyone," he says. "You could imagine it being used not just for transportation networks, but freight networks or energy networks. It turns out they are trying to optimize networks in the same kind of way as the slime mold."

Journal information: Scientific Reports

Provided by University of Toronto

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Slime Mold Grows Network Just Like Tokyo Rail System

Talented and dedicated engineers spent countless hours designing Japan’s rail system to be one of the world’s most efficient. Could have just asked a slime mold.

Every day, the rail network around Tokyo has to meet the demands of mass transport, ferrying millions of people between distant points quickly and reliably, notes study coauthor Mark Fricker of the University of Oxford. “In contrast, the slime mold has no central brain or indeed any awareness of the overall problem it is trying to solve, but manages to produce a structure with similar properties to the real rail network.”

The researchers then borrowed simple properties from the slime mold’s behavior to create a biology-inspired mathematical description of the network formation. Like the slime mold, the model first creates a fine mesh network that goes everywhere, and then continuously refines the network so that the tubes carrying the most cargo grow more robust and redundant tubes are pruned.

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The behavior of the plasmodium “is really difficult to capture by words,” comments biochemist Wolfgang Marwan of Otto von Guericke University in Magdeburg, Germany. “You see they optimize themselves somehow, but how do you describe that?” The new research “provides a simple mathematical model for a complex biological phenomenon,” Marwan wrote in an article in the same issue of Science .

Fricker points out that such a malleable system may be useful for creating networks that need to change over time, such as short-range wireless systems of sensors that would provide early warnings of fire or flood. Because these sensors are destroyed when disaster strikes, the network needs to efficiently re-route information quickly. Decentralized, adaptable networks would also be important for soldiers in battlefields or swarms of robots exploring hazardous environments, Fricker says.

The new model may also help researchers answer biological questions, such as how blood vessels grow to support tumors, Fricker says. A tumor’s network of vessels start out as a dense, unstructured tangle, and then refine their connections to be more efficient.

Images: Science/AAAS

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NOT EXACTLY ROCKET SCIENCE

Slime mould attacks simulates Tokyo rail network

In a Japanese laboratory, a group of scientists is encouraging a rapidly expanding amoeba-like blob to consume Tokyo. Thankfully, the blob in question is a “slime mould” just around 20cm wide, and “Tokyo” is represented by a series of oat flakes dotted about a large plastic dish. It’s all part of a study on better network design through biological principles. Despite growing of its own accord with no plan in mind, the mould has rapidly produced a web of slimy tubes that look a lot like Tokyo’s actual railway network.

The point of this simulation isn’t to reconstruct the monster attacks of popular culture, but to find ways of improving transport networks, by recruiting nature as a town planner. Human societies depend on good transport networks for ferrying people, resources and information from place to place, but setting up such networks isn’t easy. They have to be efficient, cost-effective and resistant to interruptions or failure. The last criterion is particularly challenging as the British public transport system attests to, every time a leaf or snowflake lands on a road or railway.

Living thing also rely on transport networks, from the protein tracks that run through all of our cells to the gangways patrolled by ant colonies. Like man-made networks, these biological ones face the same balancing act of efficiency and resilience, but unlike man-made networks, they have been optimised through millions of years of evolution. Their strategies have to work – if our networks crash, the penalties are power outages or traffic jams; if theirs crash, the penalty is death.

To draw inspiration from these biological networks, Atsushi Tero from Hokkaido University worked with the slime mould Physarum polycephalum . This amoeba-like creature forages for food by sending out branches (plasmodia) from a central location. Even though it forms vast, sprawling networks, it still remains as a single cell. It’s incredibly dynamic. Its various veins change thickness and shape, new ones form while old ones vanish, and the entire network can crawl a few centimetres every hour.

For a mindless organism, the slime mould’s skill at creating efficient networks is extraordinary. It can find the most effective way of linking together scattered sources of food, and it can even find the shortest path through a maze . But can it do the same for Tokyo’s sprawling cityscape?

Tero grew Physarum in a wet dish at a place corresponding to Tokyo, with oat flakes marking the locations of other major cities in the Greater Tokyo Area. Physarum avoids bright light, so Tero used light to simulate mountains, lakes and other prohibitive terrain on his miniature map. The mould soon filled the space with a densely packed web of plasmodia. Eventually, it thinned out its networks to focus on branches that connected the food sources. Even by eye, these final networks bore a striking similarity to the real Tokyo rail system.

The mould’s abilities are a wonder of self-optimisation. It has no sense of forward-planning, no overhead maps or intelligence to guide its moves. It creates an efficient network by laying down plasmodia indiscriminately, strengthening whatever works and cutting back on whatever doesn’t. The approach seems as haphazard as a human planner putting railway tracks everywhere, and then removing the ones that aren’t performing well. Nonetheless, the slime mould’s methods (or lack thereof) produced a network with comparable cost, efficiency and tolerance for faults to the planned human attempt.

Tero tried to emulate this slime mould’s abilities using a deceptively simple computer model, consisting of an randomly meshed lattice of tubes. Each tube has virtual protoplasm flowing through it, just as the branches of the slime mould do. The faster the flow rate, the wider the tube becomes. If the flow slows, the tubes thin and eventually disappear.

Tweaking the specific conditions of the model produced networks that were very similar to those of both live Physarum and Tokyo’s actual rail system. Tweaking it further allowed Tero to boost the system’s efficiency or resilience, while keeping its costs as low as possible. This, perhaps, is the engineering of the future – a virtual system inspired by a biological one that looks a lot like a man-made one.

Reference: Tero et al. 2010. Rules for Biologically Inspired Adaptive Network Design. Science 10.1126/science.1177894

More on slime moulds: Predatory slime mould freezes prey in large groups

Images : from AAAS/Science

YEAR-LONG ADVENTURE for every explorer on your list

Brainless Slime Mold Builds a Replica Tokyo Subway

When scientists talk up learning about transportation networks from nature, it’s often ants that get the praise for being so much more organized and efficient than we humans with our silly gridlock. But a team of Japanese researchers found, for a new study in Science , that you don’t even need a brain to be to a traffic genius. Single-celled slime molds, they found, can build networks as complex as the Tokyo subway system.

The mold explored slowly at first, but like any good transportation engineer it began to figure out traffic patterns. To continue growing and exploring, the slime mold transforms its Byzantine pattern of thin tendrils into a simpler, more-efficient network of tubes: Those carrying a high volume of nutrients gradually expand, while those that are little used slowly contract and eventually disappear [ ScienceNOW Daily News ]. When the mold got its system settled, researchers say, it looked rather similar to the actual Tokyo subway system, as you can see in the illustration.

The scientists didn’t just marvel at the slime mold’s mapped-out network; they also tried to capture its technique in math, Wolfgang Marwan added in an accompanying piece in Science . Marwan called the mathematical model “beautifully useful.” He added that: “It quantitatively mimics phenomena that can be neither captured nor quantified by verbal description alone” [ Scientific American ]. But will slime mold subways start to show us how we ought to be building our transport systems or other networks? Perhaps not so fast, says Portland State University’s Melanie Mitchell. “This paper uses only one relatively simple example,” she cautions. “It’s not obvious that similar experiments would work as well for matching other transport networks” [ ScienceNOW Daily News ] .

Image: Science/AAAS

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Brainless slime mold grows in pattern like Tokyo’s subway system

A group of researchers led by Toshiyuki Nakagaki from the Hokkaido University in Japan, placed Physarum polycephalum in a petri-dish scattered with oat flakes. The position of food scraps was deliberately placed to replicate the locations of some of the most visited site in Tokyo. In the first few hours, the slime mold’s size grew exponentially, and it branched out through the entire edible map. Within a few days, the size of its branches started to shrink, and the slime mold established a complex branching network between the oats on the petri-dish. Despite growing and expanding without a central coordination system like the brain, the mould had re-created an interconnected network made of slimes that looks almost exactly like the efficient, well-designed Tokyo subway system.

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Slime Mold Beats Humans at Perfecting Traffic Networks

Since the best city planners around the world have not been able to end traffic jams, scientists are looking to a new group of experts: slime mold.

That's right, a species of gelatinous amoeba could help urban planners design better road systems to reduce traffic congestion , a new study found.

A team of researchers studied the slime mold species Physarum polycephalum and found that as it grows it connects itself to scattered food crumbs in a design that’s nearly identical to Tokyo’s rail system.

Slime mold is a fungus-like, single-celled animal that can grow in a network of linked veins, spreading over a surface like a web. The mold expands by dividing its nuclei into more and more nuclei, though all are technically enclosed in one large cell.

"Some organisms grow in the form of an interconnected network as part of their normal foraging strategy to discover and exploit new resources," wrote the researchers in a paper published in the Jan. 22 issue of the journal Science. Slime mold has evolved to grow in the most efficient way possible to maximize its access to nutrients.

"[It] can find the shortest path through a maze or connect different arrays of food sources in an efficient manner with low total length, yet short average minimum distance between pairs of food sources," wrote the scientists, led by Atsushi Tero from Hokkaido University in Japan.

To test whether slime-mold networks behave anything like train and car traffic networks , the researchers placed oat flakes in various spots on a wet surface so that the resulting layout corresponded to the cities surrounding Tokyo. They even added areas of bright light (which slime mold tends to avoid) to correspond to mountains or other geologic features that the trains would have to steer around.

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The scientists let the mold organize itself and spread out around these nutrients, and found that it built a pattern very similar to the real-world train system connecting those cities around Tokyo. And in some ways, the amoeba solution was more efficient. What's more, the slime mold built its network without a control center that could oversee and direct the whole enterprise; rather, it reinforced routes that were working, and eliminated redundant channels, constantly adapting and adjusting for maximum efficiency.

To take advantage of what nature and evolution have spent millennia perfecting, the researchers fed information about the slime mold's feeding and growing habits into a computer model, and hope to use it to design more efficient and adaptive transportation networks.

"The model captures the basic dynamics of network adaptability through interaction of local rules, and produces networks with properties comparable to or better than those of real-world infrastructure networks," Wolfgang Marwan of Otto von Guericke University in Germany, who was not involved in the project, wrote in an accompanying essay in the same issue of Science.

"The work of Tero and colleagues provides a fascinating and convincing example that biologically inspired pure mathematical models can lead to completely new, highly efficient algorithms able to provide technical systems with essential features of living systems."

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How a Brainless Slime Mold Recreated the Tokyo Rail System

What's the best way to design a new subway network or road system? It might be using slime mold. Yes, slime molds—the single-celled, brainless organisms that you might have seen covering a log on a hike in the woods—happen to be excellent urban planners.

For over a decade, researchers have been studying how slime molds spread out to look for food via the most efficient paths. When the mold finds something to eat, the path to that spot gets stronger, not unlike the way a line of ants will zero in on a picnic sandwich. Scientists in Japan decided to see how the mold would navigate the Tokyo area, and set up a "map" with oak flakes—slime mold's favorite food—marking local cities. Within a day, the mold had essentially recreated the Tokyo rail system, finding the same paths that it took teams of engineers years to plan.

[youtube]http://www.youtube.com/watch?v=GwKuFREOgmo

Researchers have also used slime molds to recreate highways in China, the United States, Canada, the U.K., and Spain, noting that sometimes the mold discovers a slightly more efficient route than the humans did.

Though reports on this research started coming out a few years ago, I haven't seen cities using slime molds in actual transportation planning yet. Who will be first to add slime mold to the urban planning department?

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COMMENTS

Slime Mold Grows Network Just Like Tokyo Rail System
In the experiment, researchers led by Toshiyuki Nakagaki, of Hokkaido University in Sapporo, Japan, placed oat flakes (a slime mold delicacy) in a pattern that mimicked the way cities are...
Slime mould attacks simulates Tokyo rail network
In a Japanese laboratory, a group of scientists is encouraging a rapidly expanding amoeba-like blob to consume Tokyo. Thankfully, the blob in question is a “slime mould” just around 20cm wide...
Brainless Slime Mold Builds a Replica Tokyo Subway
But a team of Japanese researchers found, for a new study in Science, that you don’t even need a brain to be to a traffic genius. Single-celled slime molds, they found, can build networks as complex as the Tokyo subway …
Brainless slime mold grows in pattern like Tokyo’s …
A group of researchers led by Toshiyuki Nakagaki from the Hokkaido University in Japan, placed Physarum polycephalum in a petri-dish scattered with oat flakes. The position of food scraps was deliberately placed …
Slime mold is master network engineer
In the experiment, researchers led by Toshiyuki Nakagaki, of Hokkaido University in Sapporo, Japan, placed oat flakes (a slime mold delicacy) in a pattern that mimicked the way cities are...
Slime Mold Beats Humans at Perfecting Traffic Networks
A team of researchers studied the slime mold species Physarum polycephalum and found that as it grows it connects itself to scattered food crumbs in a design that’s nearly identical to...
How a Brainless Slime Mold Recreated the Tokyo Rail System
Scientists in Japan decided to see how the mold would navigate the Tokyo area, and set up a "map" with oak flakes—slime mold's favorite food—marking local cities.