Tag Archives: simulation

You can now hold the whole (simulated) universe in the palm of your hand

A team of international researchers led by members at the National Institutes of Natural Sciences in Tokyo wants to put the universe in the palm of your hand.

Image credits IAA-CSIC.

The Universe is a really big place, which can make understanding it a bit difficult. What would definitely help in this regard would be a simulation encompassing it in its entirety — which is exactly what the researchers did. Named Uchuu (“Outer Space” in Japanese), this is the largest and most realistic simulation of the Universe to date, consisting of 2.1 trillion particles spread across a simulated cube whose side is 9.63 billion light-years.

A digital new world

The simulated universe is the product of a collaboration between researchers from Japan, Spain, the U.S.A., Argentina, Australia, Chile, France, and Italy. ATERUI II, the most powerful supercomputer dedicated to astronomy in the world, was used to produce Uchuu, an effort that still took a full year.

“To produce Uchuu we have used […] all 40,200 processors (CPU cores) available exclusively for 48 hours each month. Twenty million supercomputer hours were consumed, and 3 Petabytes of data were generated, the equivalent of 894,784,853 pictures from a 12-megapixel cell phone,” explains Tomoaki Ishiyama, an associate professor at Chiba University who developed the code used to generate Uchuu.

The intended purpose behind Uchuu is to give astronomers a new tool to understand the results of Big Data galaxy surveys. This type of research simply generates immense quantities of data and making heads and tails of it all can become quite difficult.

But Uchuu’s sheer scale can, counterintuitively, help researchers parse this data much more easily. The side of the simulated square, of 9.63 billion light-years, is around three-quarters of the estimated distance between the Earth and the farthest galaxies we can currently observe. This provides the context for researchers to study the evolutionary history of the Universe on a scale that was previously impossible.

Obviously, the software isn’t perfect, nor does it simulate an entire Universe in complete detail. It focuses on the large-scale structures that defined its history and evolution. The team explains that they focused on the large-scale structures formed by dark matter (known as ‘halos’) which control processes such as the formation of galaxies, instead of relatively smaller structures such as stars.

This focus on the large scale comes down to technical constraints. Uchuu aims to simulate almost 13.8 billion years of the history of the Universe, roughly from the Big Bang up to today.

“Uchuu is like a time machine: we can go forward, backward and stop in time, we can ‘zoom in’ on a single galaxy or ‘zoom out’ to visualize a whole cluster, we can see what is really happening at every instant and in every place of the Universe from its earliest days to the present, being an essential tool to study the Cosmos,” explains Julia F. Ereza, a Ph.D. student at the Institute of Astrophysics of Andalusia (Instituto de Astrofísica de Andalucía / IAA-CSIC), who uses Uchuu for their research.

The end of this process is, essentially, a recording of all the computations ATERUI II performed during this time. This shows the evolution of dark matter haloes in a 100-terabyte catalog, one which you can download and browse at your own leisure — if you have the disk space to spare, which most of us here don’t.

But fear not! The catalog is also publically available on the cloud thanks to the IAA-CSIC (link at the bottom of the page). Future releases will include catalogues of virtual galaxies and gravitational lensing maps.

‘Dish Life’ lets you play as a stem cell researcher on Android, iPhone, or PC

A team of researchers from the University of Cambridge want to make laboratories and the scientific process more familiar to the public in the best way possible: with video games.

Image credits University of Cambridge.

The game is named “Dish Life” and puts the player in the role of a burgeoning stem cell researcher as they navigate the tough (and sometimes hilarious) journey from undergraduate to cutting-edge expert. Dish Life is available for free on the Apple and Android App Stores, as well as on Steam for PC.

But it’s not all empty fun. The game was designed with the help of Cambridge sociologists and stem cell scientists from the University’s Stem Cell Institute to provide a realistic taste of life inside a biotechnology laboratory.

The game of science

“The route to scientific discovery can feel like a mystery to many of us,” said Dr Karen Jent from the ReproSoc group in Cambridge’s Department of Sociology, who led the game’s development. “A lot of people only encounter the process of science through hyperbolic headlines or cinematic tales of the lone genius.”

“We want to use gaming to have a different kind of conversation about science. Science involves teamwork and care as much as reason and logic. We aimed to create an interactive experience reflecting the nurturing of experiments and building of social relationships at the heart of good science.”

Jent explains that her work allowed her to see the interpersonal dynamics that form in stem labs, but also the bond that forms between researchers and the cells they grow. These require near-constant attention and care, she explains, likening them to microscopic kids. These relationships form the foundation of the game: it’s “part Sims, part Tamagotchi,” she explains, with strategy and dilemma thrown in to spice things up.

In Dish Life, players must manage to strike a balance between caring for their (every-hungrier) cells while helping improve their lab’s wellbeing, reputation, and nurturing their own careers through publications and securing promotions. Players need to feed and monitor cell cultures, eventually splitting cultures up when they outgrow their Petri dishes and start converting them into specific cell types. Each success rewards experience points that players can use to unlock new abilities, colleagues, and equipment. However, players also have to keep tabs on the wellbeing of their avatar (the in-game researcher they play) and colleagues by engaging in social life in the lab, and complete quests that include job interviews and to produce new drugs.

The game draws inspiration from a 2016 short film Jent produced with stem cell researchers Dr. Loriana Vitillo and movie director Chloe Thomas (which was also named Dish Life). The film cast children for the role of stem cells and used a paddling pool in lieu of a petri dish. It also featured a number of researchers explaining the quasi-relationship they developed with the cell cultures they cared for through constant monitoring, feeding, even talking aloud to them for months on end.

“It was an ordinary day in the lab, feeding cells, when it occurred to me that we often talk about what we discover but not how we discover, about our real lives,” said Vitillo, game and film co-producer, and Cambridge Stem Cell Institute alumni. “I wanted to tell a different story.”

“With stem cells set to change healthcare, we want to make biotechnology more accessible by showing how this science is really done.”

The game is surprisingly complex and covers a wide range of commentaries on the life of researchers and broader society. Workplace issues such as bullying and maternity cover make an appearance, as do media controversies, government committees, and ethical choices around animal testing and CRISPR. There’s also great depth to the game, with avatars being given access to new issues as they progress in academia.

“Once you run a successful lab, the game opens up questions of medical ethics, environmental impact, the bioeconomy and equality in science,” said Jent explains. “Although those cells will always need feeding.”

The game was designed by Pocket Sized Hands, a Dundee-based games studio. The Cambridge team plans to continue testing the game with groups of stem cell scientists and update gameplay accordingly after release, so you can be sure to always get a realistic taste of life in the lab.

Don’t forget to feed those cells, though

Physicists perform the most detailed simulation of the Universe yet

Images showing various disk galaxies from the simulated TNG50 universe. Credit: D. Nelson, TNG team.

How did the universe evolve from a point of singularity, known as the Big Bang, into a massive structure whose boundaries seem limitless? New clues and insight into the evolution of the universe have recently been provided by an international team of physicists, who performed the most detailed large-scale simulation of the universe to date.

Formation and evolution of a massive galaxy in the TNG50 simulation. The resulting TNG50 galaxy is similar in mass and shape to the Andromeda galaxy (M31). After a turbulent beginning, the galaxy experiences no major disturbances and can settle down into an equilibrium state. Credit: D. Nelson, TNG team.

The researchers made their own universe in a box — a cube of space spanning more than 230 million light-years across. Previous cosmological simulations were either very detailed but spanned a small volume or less detailed across large volumes. The new simulation, known as TNG50, managed to combine the best of two worlds, producing a large-scale replica of the cosmos while, at the same time, allowing for unprecedented computational resolution.

The level of detail is incredible, matching what was once only possible to do in simulations of individual galaxies. TNG50, in fact, tracks 20 billion particles representing dark matter, stars, cosmic gas, magnetic fields, and supermassive black holes.

However, this kind of fine detail came at a cost. It took more than 16,000 cores on the Hazel Hen supercomputer in Stuttgart operating in tandem, non-stop for a year to perform the required calculations. For reference, it would have taken 15,000 years to complete the simulation on a single processor, making TNG50 one of the most computationally demanding astrophysical simulations to date.

In two recently published studies led by Annalisa Pillepich and Dylan Nelson, from the Max Planck Institute for Astronomy and Max Planck Institute for Astrophysics, respectively, the researchers shared their most important findings.

“Numerical experiments of this kind are particularly successful when you get out more than you put in. In our simulation, we see phenomena that had not been programmed explicitly into the simulation code. These phenomena emerge in a natural fashion, from the complex interplay of the basic physical ingredients of our model universe,” Nelson said in a statement.

One example of such emerging behavior if the formation of “disk” galaxies, like the Milky Way. While disk galaxies seem very ordered and flat, by rewinding their evolution, researchers could see that such structures emerge from chaotic and disorganized turbulent clouds of gas.

“In practice, TNG50 shows that our own Milky Way galaxy with its thin disk is at the height of galaxy fashion: over the past 10 billion years, at least those galaxies that are still forming new stars have become more and more disk-like, and their chaotic internal motions have decreased considerably. The Universe was much more messy when it was just a few billion years old!” Pillepich said in a statement.

The outflow of as gas from a galaxy. Left to right: false-color representations of the velocity, temperature, density, and heavy element content of the galaxy. The galaxy itself is the tiny blue drop in the second frame from the left or the yellow firmament in the third column. Credit: D. Nelson, TNG team.

Another emerging phenomenon captured by the simulation was represented by high-speed outflows and winds of gas emanating from galaxies. These outflows and winds are the result of supernovae and supermassive black hole activity.

These galactic outflows were initially chaotic — just like early galactic structures — but, over time, they became more focused on the paths of least resistance. In the modern universe, these winds slow down as they make their way away from the gravitational well of the dark matter halo, and can eventually stall and fall back onto their parent galaxies. The astronomers liken the process to a galactic fountain of recycled gas.

By this process, gas is redistributed from the center of the galaxy to its outskirts. In time, this contributes to the transformation of the galaxy into a thin disk. But this can also work both ways: galactic structures also shape galactic fountains.

In the future, the astronomers will release all the simulation’s data to the scientific community at large so that new discoveries might come out of the TNG50 universe.

The two studies will be published in the December 2019 issue of the Monthly Notices of the Royal Astronomical Society

The atomic model of an entire human gene. Credit: Los Alamos National Laboratory.

Scientists perform billion-atom simulation of a human gene

The atomic model of an entire human gene. Credit: Los Alamos National Laboratory.

The atomic model of an entire human gene. Credit: Los Alamos National Laboratory.

Researchers have simulated a billion atoms which make up an entire human gene for a split-second. This is the largest simulation of human DNA and an important milestone towards the ultimate goal of digitally reproducing the human genome. 

“It is important to understand DNA at this level of detail because we want to understand precisely how genes turn on and off,” said Karissa Sanbonmatsu, a structural biologist at Los Alamos. “Knowing how this happens could unlock the secrets to how many diseases occur.”

Sanbonmatsu and colleagues performed their study on the Los Alamos’ Trinity supercomputer, the sixth fastest in the world. But even for this behemoth, simulating the intricate complexities of DNA was a huge challenge that required all of its computing resources. The model is quite slow too, simulating just one nanosecond of molecular activity per day.

DNA, or deoxyribonucleic acid, is the hereditary material in humans and almost all other organisms. This incredible molecule contains all the instructions an organism needs to develop, live, and reproduce. Its structure is so neatly compacted and precise that you could string together all the DNA in a human body to wrap around the earth 2.5 million times.

The reason why the blueprint for life is so compact has to do with the way the string-like molecule is wound up in a network of tiny spools. The various ways in which these spools wind and unwind turn genes on and off. In other words, when the DNA is more compacted, genes are turned off and when DNA expands, genes are turned on.

Researchers do not yet fully understand how all of this process pans out, which is why they’ve developed this atomistic model. Solving this mystery could one day lead to novel gene therapies and medical applications.

But before that happens, we need much faster computers. Modeling billions and billions of atoms all moving at the same time requires phenomenal resources. And, if we want to model an entire chromosome (or even the human genome), scientists will have to wait for the next generation of supercomputers, such as exascale computers, which will be many times faster than today’s machines.

Scientific reference: Jaewoon Jung et al. Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations, Journal of Computational Chemistry (2019). DOI: 10.1002/jcc.25840.

Climate change protest sign.

New role-playing game engages people from all backgrounds with climate action

Climate change is no joke — but it can be a game.

Climate change protest sign.

Image via Maxpixel / Public Domain.

More specifically, it can be the subject of an MIT Sloan role-playing video game. Dubbed World Climate Simulation, the game puts players in the shoes of UN members partaking in climate talks. Its developers report that over four-fifths of participants who played the game showed an increased desire to combat climate change, regardless of their political beliefs.

Climate UN-change

“The big question for climate change communication is: how can we build the knowledge and emotions that drive informed action without real-life experience which, in the case of climate change, will only come too late?”, asks Prof. Juliette Rooney Varga, lead researcher of the study and Director of the University of Massachusetts Lowell Climate Change Initiative.

The team’s approach revolved around three elements: “information grounded in solid science, an experience that helps people feel for themselves on their own terms and social interaction arising from conversation with their peers,” explains co-author Andrew Jones of Climate Interactive.

In the game, developed countries pledge money through the Green Climate Fund to help developing nations cut emissions and adapt to climate change. The game’s core mechanics are handled by a real-life climate policy computer model known as C-ROADS. This model has been used to guide UN climate negotiations in the past, as it is a very powerful simulator of expected outcomes. Players’ choices were run through C-ROADS and resulted in immediate feedback on how each would ultimately affect the environment.

The group worked with 2,000 participants of various socioeconomic backgrounds and ages recruited from “eight different countries across four continents”, explains an MIT Sloan press release. Through the game, the team looked at each player’s beliefs regarding climate change, their emotional responses to its effects, and willingness to address the main drivers of climate change. By the conclusion of play trials, participants showed greater urgency in tackling the issue, the team reports.

Post-trial questions.

Post-survey responses to questions regarding (A) how engaging the World Climate simulation was as a learning experience, (B) the effects the simulation had on motivation to address climate change and (C) desire to learn more about climate change science, solutions, politics, economics, and policies.
Image credits J.N. Rooney-Varga et al., 2018, PLOS One.

The idea behind the game was to try and bridge the huge divides that the political spectrum imparts on the discussion, the team explains. By putting people in charge of tackling the issue and letting them see how their lives will be impacted, the game aims to engage those that aren’t very concerned about climate action.

Hands-on experience

The team reports that players go headlong into the first round of climate negotiations, usually being quite lax in the changes they call for. However, after C-ROADS showed the outcome of these talks to their health, prosperity, and welfare, the team adds, they generally went into the following rounds with a much more aggressive approach to achieving emissions cuts.

“The first round of negotiations ends with a plenary session in which a representative from each delegation delivers a short speech describing their pledge and negotiating position, including concessions they seek from the other parties,” the paper explains.

“In our experience, the first round of pledges always falls short of the emissions reductions required to limit expected warming to 2 °C and are often qualitatively similar to the actual pledges that emerged from the Paris Agreement, leading to warming of approximately 3.3 °C by 2100.”

“Participants often express surprise that the impact of their pledges is not greater and ask many questions about the structure and dynamics of the climate system as they seek to understand why the simulation results differ from their expectations.”

Perhaps more importantly, they were also more hopeful in the eventual success of environmental actions, as well as a greater desire to understand climate science and the impact of climate change. Urgency is key to actually undergoing the societal, economic, and political changes required to combat climate change. The other two traits will help keep our eyes on the goal during difficult times and limit the effect of mumbo-jumbo à la ‘clean coal‘.

“It was this increased sense of urgency, not knowledge, that was key to sparking motivation to act,” said Prof. Juliette Rooney Varga, lead researcher of the study and Director of the University of Massachusetts Lowell Climate Change Initiative.

In the end, the team hopes to push environmental talks to the forefront of national and international dialogue and policy-making and to take political interest out of climate action.

“Gains were just as strong among American participants who oppose government regulation of free markets – a political ideology that has been linked to climate change denial in the US – suggesting the simulation’s potential to reach across political divides,” the paper reads.

“Research shows that showing people research doesn’t work,” said John Sterman, co-author of the study and professor at MIT’s Sloan School of Management. “World Climate works because it enables people to express their own views, explore their own proposals and thus learn for themselves what the likely impacts will be.”

Schools in France, Germany, and South Korea have adopted World Climate Simulation as an official educational resource, the team adds.

The paper “Combining role-play with interactive simulation to motivate informed climate action: Evidence from the World Climate simulation” has been published in the journal PLOS One.


NASA releases atmospheric simulation of this year’s hurricane season

A gorgeous new animation published by NASA depicts sea salt, dust, and smoke movements in the atmosphere during this year’s hurricane season.


Because air is so hard to see, NASA uses aerosol particles to track movements in the atmosphere. By combining raw satellite data with mathematical models of atmospheric phenomena, NASA researchers can see how smoke, dust, and sea salt are transported across the globe — allowing the agency a glimpse into weather patterns that would otherwise remain hidden to our view.

For example, tracking how sea salt (blue-white) evaporates from oceans will showcase the evolution of all of 2017’s hurricanes. The animation also captures the massive wildfires in the Pacific Northwest on the smoke layer of the simulation (gray). Particles released in these fires made it all the way from Oregon to Washington, though the south, eventually reaching the UK (in early September).

Dust (brown) also makes an appearance, most notably piggybacking on storm systems out of the Sahara and towards the Americas. Unlike sea salt, however, it doesn’t last too long in the eye of the storm. Here, dust particles are captured by cloud droplets and rain down on the ocean.

Advances in computing speed allow scientists to include more details of these physical processes in their simulations than ever before. So in time, they’re only going to become more complex and will more closely reflect reality.


Musk’s argument that we live in a simulation doesn’t hold water, quantum physicists say

The chance of us living inside a computer simulation is virtually nil, according to scientists at the University of Oxford and the Hebrew University. Their findings suggest that it’s mathematically impossible for the known universe to be computer generated by some advanced civilization living in a base reality.


Credit: The Matrix.

When the now classic sci-fi The Matrix premiered, its premise of a fabricated reality inside a world-sized computer mainframe blew everyone’s minds. Upon leaving movie theaters, many would ask themselves for a moment: is this world even real? Philosophers have actually been tackling this subject for ages. Indeed, The Matrix itself is heavily influenced by philosophical themes, such as those of 17th Century French philosopher and mathematician René Descartes. In many of his theses, Descartes questions the nature, limits, and validity of human knowledge.

Most recently, level-headed individuals like Neil DeGrasse Tyson or Elon Musk have revitalized this notion that we’re all Sims somehow. Musk, for instance, argues that given the exponential growth with which computing technology advances, it’s reasonable to assume that one day, virtual reality will become indistinguishable from reality. If that’s the case, we might already be trapped in the simulation of some other advanced civilization who is living in a genuine, base reality.

“So given that we’re clearly on a trajectory to have games that are indistinguishable from reality, and those games could be played on any set-top box or on a PC or whatever, and there would probably be billions of such computers or set-top boxes, it would seem to follow that the odds that we’re in base reality is one in billions,” Musk explains in the video above.

“Tell me what’s wrong with that argument. Is there a flaw in that argument?”

Ok, in that case, let’s cue theoretical physicists Zohar Ringel and Dmitry Kovrizhin. The duo checked what kind of computing power would be required to exhibit quantum effects. It didn’t take them long to realize that in order to simulate certain quantum phenomena occurring in metals, such a machine is simply unworkable. The math simply doesn’t add up.

For instance, to store information for only a few hundred electrons, a computer’s memory would require more atoms than those available in the known universe. Simulating not just a whole rocky planet and its trillions of conscious beings, but the whole freaking universe too, the physicists argue, is just impossible given what we know today. At least, it’s impossible in a scenario like the one Musk alludes to. At the end of the day, the machines that construct a virtual reality need to be physically rooted somewhere. The flaw in Musk’s argument is that you eventually hit a brick wall.

Now, the authors’ proof outlined in Science Advances employs extremely complex physics and mathematics, such as the quantum Monte Carlo — a body of computational methods that use random sampling to analyze many-body quantum problems where the equations involved cannot be solved directly. I won’t pretend I understand any of the quantum physics involved in this paper but the two scientists seem to have a point.

Is this the last word, though? Probably not. To be fair, this paper proves that the universe can’t be simulated using any algorithms or computers imaginable by these physicists. It would be hubris to believe that all that’s out there has already been discovered or even imagined.


Wobbly Winners: The Link Between Motion Sickness and Mobile Gaming


It’s common sense why some ailments correlate with gaming. Repetitive motion and long periods of holding a controller or mobile device lend themselves to carpal tunnel syndrome, while excessive sitting can lead to everything from stiff muscles to heart strain. But now some games for mobile platforms are turning up a new medical concern for hardcore gamers — motion sickness. With more powerful graphics processing and more immersive game play, mobile game designers have started running into the motion sickness problem in their elaborate virtual worlds. Thankfully, they’re also researching ways to limit or eliminate the problem.

What is Motion Sickness?

Motion sickness is a feeling of nausea resulting from different sensory organs getting conflicting information about the state of the body. Classic occurrences of motion sickness are seasickness, car sickness, and nausea following a fast-moving amusement park ride. In all these cases, sensory organs like the eyes and inner ear see or feel motion, but the body itself isn’t the source of the motion. This means that the brain receives two different signals from different sources that usually work together: one source says the body’s moving, the other says it’s standing still. The natural response to this conflicting info is nausea.

How Do Games Cause Motion Sickness?

Like with car sickness, game-related nausea also known as “simulation sickness,” is the result of the eyes receiving motion stimuli that the inner ear doesn’t feel. This is most common in games that put players in a first-person perspective and that include a lot of sharp, sudden movement. An early example of simulation sickness came from the game Mirror’s Edge, a first-person parkour simulator that included a lot of “realistic” body movement, including the camera bobbing up and down like the player character’s head, wobbling and rolling with the character’s body, and motion blur when the character was moving quick.

Do Mobile Games Cause Motion Sickness More Often?

It’s hard to say if mobile games are more likely to cause simulation sickness, but there are some factors of mobile devices that contribute to the seemingly greater prevalence of the condition. Simulation sickness is more common in players whose eyes are closer to their screens, likely because this means the motion on the screen takes up more of their field of vision. Because mobile devices have smaller screens than personal computers or console-connected televisions, mobile gamers tend to keep their screens closer to their eyes so they can see more details.

Studies have also shown than mobile gamers who use stands for their devices are more likely to experience simulation sickness than players who hold their devices, likely because stands reduce the amount of actual body motion required to play the game.

What are Developers Doing About Simulation Sickness?

With console-level games on the horizon for mobile devices, more gamers are going to migrate to mobile. There are many ways that game developers and mobile device designers can reduce the likelihood of inducing simulation sickness during mobile gaming. For instance, sharper, less natural motion like 90-degree turns and excessive bobbing are greater contributors to motion sickness than smooth motion, so developers can be aware of how their games move.

Device designers can also create mobile screens that are larger and provide higher-definition images that allow users to see more detail without having to hold the device too close to their eyes. Triple-A gamers will have better luck opting for a device with a high-def screen like the HTC One.

Easing Motion Sickness

Until game designers develop a surefire method to prevent simulation sickness, players who are susceptible to the condition should be aware of how to mitigate their symptoms. Playing for shorter periods, pausing to reorient the eyes to a still surface like a wall or horizon, and opting for gyroscope controls instead of touch controls can all ease the woozy feeling of simulation sickness.

In a way, simulation sickness is an indicator of how far gaming has come. We’ve reached a level where games are realistic enough to trick real sensory organs. Now it’s just a matter of making sure games don’t fool the eye or inner ear too well.