Computers Math

Researchers are using computer models to simulate COVID-19 infections on a cellular level — the basic structural level of the human body.
The models allow for virtual trials of drugs and vaccines, opening the possibility of pre-assessment for drug and vaccine efficacy against the virus.
The research team at the University of Waterloo includes Anita Layton, professor of applied mathematics and Canada 150 Research Chair in mathematical biology and medicine, and Mehrshad Sadria, an applied mathematics PhD student.
The team uses “in silico” experiments to replicate how the human immune system deals with the COVID-19 virus. In silico refers to trials situated in the silicon of computer chips, as opposed to “in vitro” or “in vivo” experiments, situated in test tubes or directly in living organisms.
“It’s not that in-silico trials should replace clinical trials,” Layton said. “A model is a simplification, but it can help us whittle down the drugs for clinical trials. Clinical trials are expensive and can cost human lives. Using models helps narrow the drug candidates to the ones that are best for safety and efficacy.”
The researchers, one of the first groups to be working on these models, were able to capture the results of different treatments that were used on COVID-19 patients in clinical trials. Their results are remarkably consistent with live data on COVID infections and treatments.
One example of a treatment used in the model was Remdesivir, a drug that was used in the World Health Organization’s global “solidarity” trials. The simulated model and the live trial both showed the drug to be biologically effective but clinically questionable, unless administered shortly after viral infection.
The model might also work for current and future variants of concern. The researchers anticipate the virus will continue to undergo mutation, which could precipitate new waves of infection.
“As we learn more about different variants of concern, we can change the model’s structure or parameters to simulate the interaction between the immune system and the variants,” Sadria said. “And we can then predict if we should apply the same treatments or even how the vaccines might work as well.”
Layton and Sadria are part of a new team, led by researchers at the University Health Network (UHN), which recently received a rapid response grant from the Canadian Institute of Health Research on COVID variants.
The UHN team will conduct experimental studies and modeling simulations to understand the spread of COVID variants in Canada.
The study, “Modeling within-Host SARS-CoV-2 Infection Dynamics and Potential Treatments,” authored by Sadria and Layton, was recently published in the journal Viruses.
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For thousands of years, people looked into the night sky with their naked eyes — and told stories about the few visible stars. Then we invented telescopes. In 1840, the philosopher Thomas Carlyle claimed that “the history of the world is but the biography of great men.” Then we started posting on Twitter.
Now scientists have invented an instrument to peer deeply into the billions and billions of posts made on Twitter since 2008 — and have begun to uncover the vast galaxy of stories that they contain.
“We call it the Storywrangler,” says Thayer Alshaabi, a doctoral student at the University of Vermont who co-led the new research. “It’s like a telescope to look — in real time — at all this data that people share on social media. We hope people will use it themselves, in the same way you might look up at the stars and ask your own questions.”
The new tool can give an unprecedented, minute-by-minute view of popularity, from rising political movements to box office flops; from the staggering success of K-pop to signals of emerging new diseases.
The story of the Storywrangler — a curation and analysis of over 150 billion tweets — and some of its key findings were published on July 16 in the journal Science Advances.
EXPRESSIONS OF THE MANY
The team of eight scientists who invented Storywrangler — from the University of Vermont, Charles River Analytics, and MassMutual Data Science — gather about ten percent of all the tweets made every day, around the globe. For each day, they break these tweets into single bits, as well as pairs and triplets, generating frequencies from more than a trillion words, hashtags, handles, symbols and emoji, like “Super Bowl,” “Black Lives Matter,” “gravitational waves,” “#metoo,” “coronavirus,” and “keto diet.” More

Imagine an orange cat. Now, imagine the same cat, but with coal-black fur. Now, imagine the cat strutting along the Great Wall of China. Doing this, a quick series of neuron activations in your brain will come up with variations of the picture presented, based on your previous knowledge of the world.
In other words, as humans, it’s easy to envision an object with different attributes. But, despite advances in deep neural networks that match or surpass human performance in certain tasks, computers still struggle with the very human skill of “imagination.”
Now, a USC research team has developed an AI that uses human-like capabilities to imagine a never-before-seen object with different attributes. The paper, titled Zero-Shot Synthesis with Group-Supervised Learning, was published in the 2021 International Conference on Learning Representations on May 7.
“We were inspired by human visual generalization capabilities to try to simulate human imagination in machines,” said the study’s lead author Yunhao Ge, a computer science PhD student working under the supervision of Laurent Itti, a computer science professor.
“Humans can separate their learned knowledge by attributes — for instance, shape, pose, position, color — and then recombine them to imagine a new object. Our paper attempts to simulate this process using neural networks.”
AI’s generalization problem
For instance, say you want to create an AI system that generates images of cars. Ideally, you would provide the algorithm with a few images of a car, and it would be able to generate many types of cars — from Porsches to Pontiacs to pick-up trucks — in any color, from multiple angles. More

Engineers at UC Riverside have unveiled an air-powered computer memory that can be used to control soft robots. The innovation overcomes one of the biggest obstacles to advancing soft robotics: the fundamental mismatch between pneumatics and electronics. The work is published in the open-access journal, PLOS One.
Pneumatic soft robots use pressurized air to move soft, rubbery limbs and grippers and are superior to traditional rigid robots for performing delicate tasks. They are also safer for humans to be around. Baymax, the healthcare companion robot in the 2014 animated Disney film, Big Hero 6, is a pneumatic robot for good reason.
But existing systems for controlling pneumatic soft robots still use electronic valves and computers to maintain the position of the robot’s moving parts. These electronic parts add considerable cost, size, and power demands to soft robots, limiting their feasibility.
To advance soft robotics toward the future, a team led by bioengineering doctoral student Shane Hoang, his advisor, bioengineering professor William Grover, computer science professor Philip Brisk, and mechanical engineering professor Konstantinos Karydis, looked back to the past.
“Pneumatic logic” predates electronic computers and once provided advanced levels of control in a variety of products, from thermostats and other components of climate control systems to player pianos in the early 1900s. In pneumatic logic, air, not electricity, flows through circuits or channels and air pressure is used to represent on/off or true/false. In modern computers, these logical states are represented by 1 and 0 in code to trigger or end electrical charges.
Pneumatic soft robots need a way to remember and maintain the positions of their moving parts. The researchers realized that if they could create a pneumatic logic “memory” for a soft robot, they could eliminate the electronic memory currently used for that purpose.
The researchers made their pneumatic random-access memory, or RAM, chip using microfluidic valves instead of electronic transistors. The microfluidic valves were originally designed to control the flow of liquids on microfluidic chips, but they can also control the flow of air. The valves remain sealed against a pressure differential even when disconnected from an air supply line, creating trapped pressure differentials that function as memories and maintain the states of a robot’s actuators. Dense arrays of these valves can perform advanced operations and reduce the expensive, bulky, and power-consuming electronic hardware typically used to control pneumatic robots.
After modifying the microfluidic valves to handle larger air flow rates, the team produced an 8-bit pneumatic RAM chip able to control larger and faster-moving soft robots, and incorporated it into a pair of 3D-printed rubber hands. The pneumatic RAM uses atmospheric-pressure air to represent a “0” or FALSE value, and vacuum to represent a “1” or TRUE value. The soft robotic fingers are extended when connected to atmospheric pressure and contracted when connected to vacuum.
By varying the combinations of atmospheric pressure and vacuum within the channels on the RAM chip, the researchers were able to make the robot play notes, chords, and even a whole song — “Mary Had a Little Lamb” — on a piano. Click here to view a video of the robot playing piano.
In theory, this system could be used to operate other robots without any electronic hardware and only a battery-powered pump to create a vacuum. The researchers note that without positive pressure anywhere in the system — only normal atmospheric air pressure — there is no risk of accidental overpressurization and violent failure of the robot or its control system. Robots using this technology would be especially safe for delicate use on or around humans, such as wearable devices for infants with motor impairments.
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Materials provided by University of California – Riverside. Original written by Holly Ober. Note: Content may be edited for style and length. More

A team of researchers from the University of Maryland has 3D printed a soft robotic hand that is agile enough to play Nintendo’s Super Mario Bros. — and win!
The feat, highlighted on the front cover of the latest issue of Science Advances, demonstrates a promising innovation in the field of soft robotics, which centers on creating new types of flexible, inflatable robots that are powered using water or air rather than electricity. The inherent safety and adaptability of soft robots has sparked interest in their use for applications like prosthetics and biomedical devices. Unfortunately, controlling the fluids that make these soft robots bend and move has been especially difficult — until now.
The key breakthrough by the team, led by University of Maryland assistant professor of mechanical engineering Ryan D. Sochol, was the ability to 3D print fully assembled soft robots with integrated fluidic circuits in a single step.
“Previously, each finger of a soft robotic hand would typically need its own control line, which can limit portability and usefulness,” explains co-first author Joshua Hubbard, who performed the research during his time as an undergraduate researcher in Sochol’s Bioinspired Advanced Manufacturing (BAM) Laboratory at UMD. “But by 3D printing the soft robotic hand with our integrated fluidic transistors, it can play Nintendo based on just one pressure input.”
As a demonstration, the team designed an integrated fluidic circuit that allowed the hand to operate in response to the strength of a single control pressure. For example, applying a low pressure caused only the first finger to press the Nintendo controller to make Mario walk, while a high pressure led to Mario jumping. Guided by a set program that autonomously switched between off, low, medium, and high pressures, the robotic hand was able to press the buttons on the controller to successfully complete the first level of Super Mario Bros. in less than 90 seconds.
“Recently, several groups have tried to harness fluidic circuits to enhance the autonomy of soft robots,” said recent Ph.D. graduate and co-first author of the study Ruben Acevedo, “but the methods for building and integrating those fluidic circuits with the robots can take days to weeks, with a high degree of manual labor and technical skill.”
To overcome these barriers, the team turned to “PolyJet 3D Printing,” which is like using a color printer, but with many layers of multi-material ‘inks’ stacked on top of one another in 3D. More

Measurements of biomechanical properties inside living cells require minimally invasive methods. Optical tweezers are particularly attractive as a tool. It uses the momentum of light to trap and manipulate micro- or nanoscale particles. A team of researchers led by Prof. Dr. Cornelia Denz from the University of Münster (Germany) has now developed a simplified method to perform the necessary calibration of the optical tweezers in the system under investigation. Scientists from the University of Pavia in Italy were also involved. The results of the study have been published in the journal Scientific Reports.
The calibration ensures that measurements of different samples and with different devices are comparable. One of the most promising techniques for calibrating optical tweezers in a viscoelastic medium is the so-called active-passive calibration. This involves determining the deformability of the sample under investigation and the force of the optical tweezers. The research team has now further improved this method so that the measurement time is reduced to just a few seconds. The optimized method thus offers the possibility of characterizing dynamic processes of living cells. These cannot be studied with longer measurements because the cells reorganize themselves during the measurement and change their properties. In addition, the shortening of the measurement time also helps to reduce the risk of damage to the biological samples due to light-induced heating.
In simplified terms, the underlying procedure to perform the calibration works as follows: The micro- or nanometer-sized particles are embedded in a viscoelastic sample held on the stage of a microscope. Rapid and precise nanometer-scale displacements of the specimen stage cause the optically trapped particle to oscillate. By measuring the refracted laser light, changes in the sample’s position can be recorded, and in this way, conclusions can be drawn about its properties, such as stiffness. This is usually done sequentially at different oscillation frequencies. The team led by Cornelia Denz and Randhir Kumar, a doctoral student in the Münster research group, now performed the measurement at several frequencies simultaneously for a wide frequency range. This multi-frequency method leads to a shortened measurement time of a few seconds. The scientists used solutions of methyl cellulose in water at different concentrations as samples. These have a similar viscoelasticity to living cells.
Background: Biomechanical properties such as stiffness, viscosity and viscoelasticity of living cells and tissues play a crucial role in many vital cellular functions such as cell division, cell migration, cell differentiation and tissue patterning. These properties of living cells could also serve as indicators of disease progression. For example, the onset and development of cancer is typically accompanied by changes in cell stiffness, viscosity, and viscoelasticity.
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The laws of quantum physics rule the microcosm. They determine, for example, how easily electrons move through a crystal and thus whether the material is a metal, a semiconductor or an insulator. Quantum physics may lead to exotic properties in certain materials: In so-called topological insulators, only the electrons that can occupy some specific quantum states are free to move like massless particles on the surface, while this mobility is completely absent for electrons in the bulk. What’s more, the conduction electrons in the “skin” of the material are necessarily spin polarized, and form robust, metallic surface states that could be utilized as channels in which to drive pure spin currents on femtosecond time scales (1 fs= 10-15 s).
These properties open up exciting opportunities to develop new information technologies based on topological materials, such as ultrafast spintronics, by exploiting the spin of the electrons on their surfaces rather than the charge. In particular, optical excitation by femtosecond laser pulses in these materials represents a promising alternative to realize highly efficient, lossless transfer of spin information. Spintronic devices utilizing these properties have the potential of a superior performance, as they would allow to increase the speed of information transport up to frequencies a thousand times faster than in modern electronics.
However, many questions still need to be answered before spintronic devices can be developed. For example, the details of exactly how the bulk and surface electrons from a topological material respond to the external stimulus i.e., the laser pulse, and the degree of overlap in their collective behaviors on ultrashort time scales.
A team led by HZB physicist Dr. Jaime Sánchez-Barriga has now brought new insights into such mechanisms. The team, which has also established a Helmholtz-RSF Joint Research Group in collaboration with colleagues from Lomonosov State University, Moscow, examined single crystals of elemental antimony (Sb), previously suggested to be a topological material. “It is a good strategy to study interesting physics in a simple system, because that’s where we can hope to understand the fundamental principles,” Sánchez-Barriga explains. “The experimental verification of the topological property of this material required us to directly observe its electronic structure in a highly excited state with time, spin, energy and momentum resolutions, and in this way we accessed an unusual electron dynamics,” adds Sánchez-Barriga.
The aim was to understand how fast excited electrons in the bulk and on the surface of Sb react to the external energy input, and to explore the mechanisms governing their response. “By controlling the time delay between the initial laser excitation and the second pulse that allows us to probe the electronic structure, we were able to build up a full time-resolved picture of how excited states leave and return to equilibrium on ultrafast time scales. The unique combination of time and spin-resolved capabilities also allowed us to directly probe the spin-polarization of excited states far out-of-equilibrium,” says Dr. Oliver J. Clark.
The data show a “kink” structure in transiently occupied energy-momentum dispersion of surface states, which can be interpreted as an increase in effective electron mass. The authors were able to show that this mass enhancement plays a decisive role in determining the complex interplay in the dynamical behaviors of electrons from the bulk and the surface, also depending on their spin, following the ultrafast optical excitation.
“Our research reveals which essential properties of this class of materials are the key to systematically control the relevant time scales in which lossless spin-polarised currents could be generated and manipulated,” explains Sánchez-Barriga. These are important steps on the way to spintronic devices which based on topological materials possess advanced functionalities for ultrafast information processing.
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A team of researchers from Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), the University of Liège and the Helmholtz Institute Erlangen-Nürnberg for Renewable Energy have developed a microswimmer that appears to defy the laws of fluid dynamics: their model, consisting of two beads that are connected by a linear spring, is propelled by completely symmetrical oscillations. The Scallop theorem states that this cannot be achieved in fluid microsystems. The findings have now been published in the academic journal Physical Review Letters.
Scallops can swim in water by quickly clapping their shells together. They are large enough to still be able to move forwards through the moment of inertia while the scallop is opening its shell for the next stroke. However, the Scallop theorem applies more or less depending on the density and viscosity of the fluid: A swimmer that makes symmetrical or reciprocal forward or backward motions similar to the opening and closing of the scallop shell will likely not move an inch. ‘Swimming through water is as tough for microscopic organisms as swimming through tar would be for humans,’ says Dr. Maxime Hubert. ‘This is why single-cell organisms have comparatively complex means of propulsion such as vibrating hairs or rotating flagella.’
Swimming at the mesoscale
Dr. Hubert is a postdoctoral researcher in Prof. Dr. Ana-Suncana Smith’s group at the Institute of Theoretical Physics at FAU. Together with researchers at the University of Liège and the Helmholtz Institute Erlangen-Nürnberg for Renewable Energy, the FAU team has developed a swimmer which does not seem to be limited by the Scallop theorem: The simple model consists of a linear spring that connects two beads of different sizes. Although the spring expands and contracts symmetrically under time reversal, the microswimmer is still able to move through the fluid.
‘We originally tested this principle using computer simulations,’ says Maxime Hubert. ‘We then built a functioning model’. In the practical experiment, the scientists placed two steel beads measuring just a few hundred micrometres in diameter on the surface of water contained in a Petri dish. The surface tension of the water represented the contraction of the spring and expansion in the opposite direction was achieved with a magnetic field which caused the microbeads to periodically repel other.
Vision: Swimming robots for transporting drugs
The swimmer is able to propel itself because the beads are of different sizes. Maxime Hubert says, ‘The smaller bead reacts much faster to the spring force than the larger bead. This causes asymmetrical motion and the larger bead is pulled along with the smaller bead. We are therefore using the principle of inertia, with the difference that here we are concerned with the interaction between the bodies rather than the interaction between the bodies and water.’
Although the system won’t win any prizes for speed — it moves forwards about a thousandth of its body length during each oscillation cycle — the sheer simplicity of its construction and mechanism is an important development. ‘The principle that we have discovered could help us to construct tiny swimming robots,’ says Maxime Hubert. ‘One day they might be used to transport drugs through the blood to a precise location.’
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