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Wonderful designs of Venus’s deep-sea flower sponges, suitable for the design of ships, airplanes and skyscrapers



Extreme Flow Simulations Reveal Skeletal Adaptations of Deep-Sea Sponges


Extreme Current Simulation Reveals Skeleton Adaptation of Deep Sea Sponges

Hydrodynamic field inside and outside the skeletal structure of the glass sponge Euplectella aspergillum. The field was reconstructed using CINECA supercomputers. Kinetic techniques and advanced computational codes have made it possible to accurately reconstruct the living conditions of deep sponges, highlighting their remarkable structural and hydrodynamic properties. Credit: J. Falcucci.

The first ever simulation of the deep sea was published in the journal Nature. Venus flower sponge and how it reacts to and affects the flow of nearby water.

The remarkable structural properties of the basket sponge (E. aspergillum) may seem far removed from human-made structures. However, understanding how the lattice structure of the body’s holes and ridges affects the hydrodynamics of seawater in its immediate vicinity could lead to improved designs for buildings, bridges, marine vehicles and aircraft, and anything else that must respond safely to the forces generated by the flow. air or water.

While past research has examined the structure of the sponge, there has been little research into the hydrodynamic fields surrounding and penetrating the body, and whether, in addition to improving its mechanical properties, the skeletal motives of E. Aspergillum lie in optimizing the physics of flow inside and outside its cavity. body.

Hydrodynamic field inside and outside the skeletal structure of the glass sponge Euplectella aspergillum. The field was reconstructed using CINECA supercomputers. Kinetic techniques and advanced computational codes have made it possible to accurately reconstruct the living conditions of deep sponges, highlighting their remarkable structural and hydrodynamic properties. Credit: Tor Vergata University of Rome.

Collaboration on three continents at the intersection of physics, biology and engineering led by Giacomo Falcucci (from the University of Rome Tor Vergata and Harvard University) in collaboration with Sauro Suchci (Italian Institute of Technology) and Maurizio Porfiri (Tandon School). Engineering, New York University) used supercomputing muscles and specialized software to gain a deeper understanding of these interactions, creating the first-ever simulation of a deep-sea sponge and how it reacts to and affects the currents of nearby water.

The journal published the work “Simulation of the extreme current reveals the adaptation of the skeleton of deep-sea sponges.” Nature, revealed a deep connection between the structure and function of the sponge, shedding light on both the ability of the basket sponge to withstand the dynamic forces of the surrounding ocean and its ability to create a nutrient-rich vortex within the “basket” of the body cavity.

“This organism has been studied a lot from a mechanical point of view because of its amazing ability to significantly deform despite its fragile glassine structure,” said first author Giacomo Falcuchi of the Tor Vergata University of Rome and Harvard University. “We were able to investigate aspects of fluid dynamics to understand how the geometry of the sponge provides a functional response to a liquid to create something special about how it interacts with water.”

“By studying the flow of fluid inside and outside the body cavity of the sponge, we found traces of the expected adaptation to the environment. The structure of the sponge not only helps to reduce drag, but also promotes the creation of low-speed vortexes in the body cavity, which are used for feeding and reproduction, ”added Porfiri, co-author of the study.

The structure of E. Aspergillum, reproduced by co-author Pierluigi Fanelli of the University of Tusia, Italy, resembles a thin glass vase in the form of a thin-walled cylindrical tube with a large central atrium, siliceous spicules – hence their commonly used name “glass sponges”. The spicules are made up of three perpendicular rays, giving them six points. Microscopic spicules “intertwine” together, forming a very fine mesh, which gives the sponge’s body a rigidity not inherent in other types of sponges, and allows it to survive at great depths in the water column.

To understand how Venus’s flower basket sponges do this, the team used an Exascale Marconi100-class computer at the CINECA high-performance computing center in Italy, which is capable of creating complex simulations using billions of dynamic space-time data points in three dimensions. …

The researchers also used special software developed by study co-author Giorgio Amati of SCAI (Super Computing Applications and Innovation) at CINECA, Italy. The software allowed for supercomputational modeling based on Boltzmann lattice methods, a class of computational fluid dynamics methods for complex systems that represent a fluid as a collection of particles and track the behavior of each of them.

In-silico experiments involving about 100 billion virtual particles simulated hydrodynamic conditions on the deep sea floor, where E. Aspergillum lives. The results, processed by Veselin K. Krastev of the University of Rome Tor Vergata, allowed the group to investigate how the organization of holes and ridges in a sponge improves its ability to reduce the forces exerted by moving seawater (an engineering question posed by Falcucci and Suchci). , and how its structure affects the flow dynamics in the body cavity of the sponge to optimize selective filter feeding and interaction of gametes for sexual reproduction (a biological question formulated by Porfiri and an expert biologist on ecological adaptation of aquatic creatures, co-author Giovanni Polverino from the Center for Evolutionary Biology of the University of Western Australia, Perth).

“This work exemplifies the application of discrete fluid dynamics in general and the Boltzmann lattice method in particular,” said co-author Sauro Suchci of the Italian Institute of Technology and Harvard University. Sauro Suchci is recognized worldwide as one of the fathers of the Lattice Boltzmann method. “IN accuracy The technique, combined with access to one of the best supercomputers in the world, has allowed us to perform levels of computation never before attempted, shedding light on the role of fluid flows in the adaptation of living organisms in the abyss. “

“Our exploration of the role of sponge geometry in its response to fluid flow is essential for the design of high-rise buildings, or indeed any mechanical structure, from skyscrapers to new low-resistance structures for ships or aircraft fuselages,” Falcucci said. “For example, will there be less aerodynamic drag in high-rise buildings built with a similar grid of ridges and holes? Does this optimize the distribution of the applied forces? Answering these very questions is the key task of the team. “

Ref: “Extreme Flow Simulation Shows Adaptation of the Skeleton of Deep Sea Sponges” Giacomo Falcucci, Giorgio Amati, Pierluigi Fanelli, Veselin K. Krastev, Giovanni Polverino, Maurizio Porfiri and Sauro Succi, July 21, 2021, Nature
DOI: 10.1038 / s41586-021-03658-1

This study was supported by the CINECA Computational Grant (J. Falcucci), the PRIN Projects (J. Falcucci), the Forrest Research Foundation (J. Polverino), the US National Science Foundation (M. Porfiri) and the European Research Council with the ERC Advance Grant of the Horizon 2020 Program (S. Suchci).


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Researchers reconfigure material topology at microscale





Encrypted Harvard Shield

The researchers encoded the patterns and designs in the material, making tiny, invisible changes to the geometry of the triangular lattice. Credit: Image courtesy of Shukong Lee / Bolei Deng / Harvard SEAS.

Reconfigurable materials can do amazing things. Flat sheets turn to faceExtruded cube transforms into dozens of different shapes… But there is one thing that a reconfigurable material cannot change yet: its underlying topology. A 100 cell reconfigurable material will always have 100 cells, even if those cells are stretched or compressed.

Now researchers at the Harvard School of Engineering and Applied Sciences. John A. Paulson (SEAS) developed a method for altering the fundamental topology of cellular material at the microscale. Research published in Nature

“The creation of cellular structures that can dynamically change their topology will open up new possibilities in the development of active materials with information encryption, selective particle capture, and customizable mechanical, chemical and acoustic properties,” said Joanna Eisenberg, professor of materials science Amy Smith Berilson. at SEAS, professor of chemistry and chemical biology and senior article author.

Triangle material topology

Hexagon material topology

Researchers have developed a method for altering the fundamental topology of a cellular material at the microscale, paving the way for active materials with tunable mechanical, chemical and acoustic properties. Credit: Images courtesy of Shukong Lee / Bolei Deng / Harvard SEAS.

The researchers used the same physics that binds our hair when it gets wet – capillary force. Capillary force works well on soft, pliable material like our hair, but it fights tough cellular structures that require bending, stretching, or folding, especially around strong, connected knots. Capillary force is also temporary as materials tend to return to their original configuration after drying.

To develop a durable but reversible method for transforming the topology of rigid cellular microstructures, the researchers developed a two-tier dynamic strategy. They started with a rigid polymer honeycomb microstructure with a triangular lattice topology and exposed it to droplets of a volatile solvent chosen to swell and soften the polymer at the molecular level. This made the material temporarily more flexible, and in this flexible state, the capillary forces created by the evaporating liquid brought the edges of the triangles closer together, changing their bonds with each other and turning them into hexagons. Then, as the solvent quickly evaporated, the material dried out and was trapped in its new configuration, regaining its stiffness. The whole process took a matter of seconds.

“When you think about applications, it is very important not to lose the mechanical properties of the material after the transformation process,” said Shukong Lee, a graduate student at Eisenberg’s lab and co-author of the paper. “Here we have shown that we can start with a hard material and end with a hard material while temporarily softening it during the reconfiguration phase.”

Assembly of microstructures

Microstructure assembly video. A liquid acts on the triangular lattice, which swells and softens the polymer. In this flexible state, the capillary forces created by the evaporating liquid brought the edges of the triangles closer together, changing their bonds with each other and turning them into hexagons. Credit: Video courtesy of Shukong Lee / Bolei Deng / Harvard SEAS

The new material topology is so strong that it can withstand heat or immersion in some fluids for days without disassembly. Its reliability actually posed a problem for researchers who hoped to make the conversion reversible.

To go back to the original topology, the researchers developed a method for combining two fluids. The former temporarily enlarges the lattice, which causes the adhering walls of the hexagons to flake off and allows the lattice to return to its original triangular structure. The second, less volatile liquid delays the emergence of capillary forces until the first liquid evaporates and the material regains its rigidity. Thus, structures can be repeatedly assembled and disassembled and held in any intermediate configuration.

Disassembly of microstructures

Video of disassembly of microstructures. The first one temporarily swells the lattice, which peels off the adhered walls. The second, less volatile liquid delays the emergence of capillary forces until the first liquid evaporates and the material regains its rigidity. Credit: Video courtesy of Shukong Lee / Bolei Deng / Harvard SEAS

“To expand our approach to arbitrary lattices, it was important to develop a generalized theoretical model that links cell geometry, material stiffness, and capillary forces,” said Bolei Deng, paper co-author and graduate student at Katya Bertholdi’s laboratory, William and Ami Kuan Danoff Professor of Applied Mechanics. in SEAS.

Guided by this model, the researchers demonstrated programmed reversible topological transformations of various lattice geometries and reacting materials, including the transformation of a lattice of circles into squares.

Researchers have studied various applications for research. For example, the team encoded the patterns and designs in the material, making tiny invisible changes to the geometry of the triangular lattice.

“You can imagine that this will be used to encrypt information in the future, because you cannot see the pattern in the material when it is disassembled,” Lee said.

The researchers also demonstrated very local transformation, assembly and disassembly of sections of the lattice using a tiny liquid droplet. This method can be used to adjust the friction and wetting properties of a material, change its acoustic properties and mechanical elasticity, and even trap gas particles and bubbles.

“Our strategy can be applied to a variety of applications,” said Bertholdi, who is also a co-author of the article. “We can apply this method to a variety of materials, including sensitive materials, with different geometries and different scales, even at the nanoscale, where topology plays a key role in the development of tunable photonic metasurfaces. The design space for that is huge. “

Reference: “Fluid-Induced Topological Transformations of Cellular Microstructures” by Shukong Lee, Bolei Deng, Alison Grintal, Alisha Schneider-Yamamura, Jinliang Kang, Reese S. Martens, Katie T. Zhang, Jiang Li, Xicin Yu, Katya Bertholdi, and Joanna. Eisenberg, April 14, 2021, Nature
DOI: 10.1038 / s41586-021-03404-7

This study was co-authored by Alison Grintal, Alissha Schneider-Yamamura, Jinliang Kang, Reese S. Martens, Katie T. Zhang, Jian Li, and Xiqing Yu.

It was supported by the National Science Foundation under the Material Design for Revolution and Design for Our Future (DMREF) Program # DMR-1922321, Harvard University Materials Research and Engineering Center (MRSEC), award # DMR-18 2011754 and the Department of Energy USA (DOE), Office of Science, Basic Energy Sciences (BES) under number DE-SC0005247.


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Help clean up space junk with the first of its kind Mission Optimizer



Help clean up space junk with the first of its kind Mission Optimizer


ClearSpace-1 takes over Vespa

Illustration ClearSpace-1, a planned mission for active garbage collection. Credit: ClearSpace SA.

Less than a year after the UK Space Agency pledged £ 1 million to combat space debris, Fujitsu UK has successfully combined quantum computing and artificial intelligence to support the transformation of its debris removal system.

Fujitsu Prototype – Created in collaboration with Glasgow University, Amazon Web Services and Astroscale UK will improve mission planning so that a single spacecraft can efficiently choose which pieces of space debris to remove in a single mission, much faster than is currently possible.

Removing space debris is key to sustainability in space, reducing or even preventing the risk of legacy spacecraft colliding with new and existing satellites.

What’s more, supporting debris removal missions with Fujitsu technology will help reduce the risk of catastrophic collisions in orbit, which could lead to thousands of other new debris that pose a real threat to operational satellites in orbit.

By carefully deciding what debris and when to collect, Digital Annealer’s quantum proposal optimizes a mission plan to determine the minimum fuel and minimum time needed to safely return a failed spacecraft or satellites to disposal orbit. Finding the optimal route for collecting space debris will significantly save time and money during the mission planning phase, as well as, as a result, increase commercial profitability.

Space debris objects in low Earth orbit

The debris objects shown in the images are artist’s impression based on actual density data. However, debris objects are shown zoomed in to make them visible at the specified scale. Credit: ESA.

With 2350 inoperative satellites Currently in orbit and more than 28,000 debris tracked by space surveillance networks, this technology will help the UK increase its market share in the space sector. It will also further support the UK government’s commitment to a more sustainable future overall.

Dr. Matteo Ceriotti, professor of space engineering, and graduate student Julia Viavattene, who led the project for the University of Glasgow, said: “The University of Glasgow was involved in this project from the very beginning – developing the trajectory. the models needed to efficiently remove space debris as well as to estimate the cost of travel.

“The University has a long history of experience in the design and optimization of space trajectories, which is why we have strived to be at the forefront of any government initiative to enhance the UK’s image in the space sector. With the help of Fujitsu, AWS and Astroscale UK, we have helped overcome the challenges of removing space debris to make future projects easier. ”

Ellen Devereux, digital firing consultant for Fujitsu UK and Ireland, said: “All space debris presents a potential risk of collision with operating systems that many of us take for granted, from weather forecasts to telecommunications.

“With the support of the UK Space Agency, Astroscale UK, AWS and the University of Glasgow, we have developed a solution to optimize the planning of a maintenance ship’s mission before it goes into space. This means that organizations like Astroscale UK can choose to collect more trash faster than ever before.

“This not only makes the process much more cost-effective for organizations that need to move and dispose of garbage, but it also leverages artificial intelligence and quantum computing.

“Over the past six months, we have learned that this technology has tremendous value for optimization in space; not only for garbage collection, but also for in-orbit maintenance and more. We now understand its potential better, and we can’t wait to see how the technology will be applied during the future mission. ”

Jacob Gere, head of space surveillance and tracking at the UK space agency, said: “Monitoring dangerous space objects is vital to protect the services we all rely on, from communications devices to satellite navigation. This project is one of the first examples of the use of quantum computing and artificial intelligence to solve space debris problems, but it is unlikely to be the last.

“The UK is committed to making space sustainable, and Fujitsu, working with Astroscale UK, the University of Glasgow and AWS, has demonstrated the real value of keeping space uncluttered by making it accessible to future generations.”

Stephen Vox, CTO at Astroscale UK, said: “Finding the optimal mission plan manually is time consuming and difficult. Astroscale UK is leading the next pioneering move under the End-of-Life Services by Astroscale (ELSA) program to remove not only one piece of debris, but multiple objects of debris with a single serving satellite known as ELSA-M, which is essentially a more economical way to remove debris from orbit. By teaming up with Fujitsu, AWS and the University of Glasgow, we hope to further optimize this for future missions. ”

The study was carried out under a grant from the UK Space Agency “Expanding Space Surveillance and Tracking Research”. The project, which was developed over six months in accordance with government digital services guidelines, uses fast technologies based on an artificial neural network (ANN). Trajectory design algorithms developed by the University of Glasgow, together with Fujitsu Digital Annealer and Quantum Inspired Optimization Services, to address some of the major optimization problems associated with Active Debris Removal (ADR) mission planning.

Amazon Web Services provided Cloud and AI and ML tools and services to support the project. The Amazon Sagemaker toolbox has been used to rapidly develop ANNs that accurately predict the cost of orbital movements in a fraction of the time required to fully calculate them. Astroscale UK, the world’s first commercial company to embark on a debris removal demonstration mission from lower Earth orbit, offers an end-use case as a typical user of multi-mission optimization.

Fujitsu, which spearheaded the project, is one of seven UK companies to receive more than £ 1 million in space debris tracking from the UK Space Agency. The UK Space Agency and the Department of Defense have announced the next step in their joint initiative to raise UK awareness of events in space.


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Scientists use human protein to deliver RNA molecular drugs to cells



SEND Technology Restoring Health


Fully assembled SEND packages

The fully assembled SEND bags are released from the collection cage for gene therapy. Credit: McGovern Institute

A programmable system built from human body components is a step towards safer and more targeted delivery of gene editing and other molecular therapeutics.

Researchers from Massachusetts Institute of TechnologyThe McGovern Institute for Brain Research at MIT, Howard Hughes Medical Institute and the Broad Institute at MIT and Harvard have developed a new way to deliver molecular therapy to cells. A system called SEND can be programmed to encapsulate and deliver various RNA cargo. SEND uses natural proteins in the body that form virus-like particles and bind RNA, and may elicit a smaller immune response than other delivery approaches.

The new delivery platform works effectively in cell models and, with further development, could open up a new class of delivery methods for a wide range of molecular drugs, including gene editing and gene replacement. Existing delivery vehicles for these therapeutic agents may be ineffective and randomly integrate into the genome of cells, and some may stimulate unwanted immune responses. SEND promises to overcome these limitations, which could open up new avenues for the introduction of molecular medicine.

Researchers at MIT, MIT’s McGovern Brain Research Institute, Howard Hughes Medical Institute, and MIT’s Broad Institute and Harvard have developed a new way to deliver molecular therapy to cells. Credit: Created by the McGovern Institute and Opus Design in collaboration with Feng Zhang, Rhiannon Macrae, and the Broad Institute.

“The biomedical community is developing powerful molecular therapeutics, but getting them to cells in an accurate and efficient manner is not an easy task,” said CRISPR pioneer Feng Zhang, senior study author, member of the Broad Institute core institute, researcher at McGovern. Institute, and Professor of Neuroscience James and Patricia Poitras at MIT. “SEND can solve these problems.” Zhang is also a researcher at Howard Hughes Medical Institute and a professor in the Department of Brain, Cognitive Sciences, and Biological Engineering at MIT.

I report The science, the command describes how to SEND (Selective Eendogenous eNcapsidization for cell Delivery) uses molecules produced by human cells. At the center of SEND is a protein called PEG10, which usually binds to its own mRNA and forms a spherical protective capsule around it. In their research, the team developed PEG10 to selectively package and deliver other RNAs. The scientists used SEND to deliver the CRISPR-Cas9 gene editing system to mouse and human cells to edit target genes.

First author Michael Segel, a postdoctoral fellow at Zhang’s lab, and Blake Lash, a second author and graduate student at the lab, said PEG10 is not unique in its ability to carry RNA. “That’s what is so exciting,” Segel said. “This study shows that there are probably other RNA transfer systems in the human body that can also be used for therapeutic purposes. It also raises some really interesting questions about what the natural roles of these proteins might be. “

Inspiration from within

The PEG10 protein exists naturally in the human body and comes from the “retrotransposon” – a virus-like genetic element that was integrated into the genome of human ancestors millions of years ago. Over time, PEG10 was metabolized by the body to become part of the repertoire of proteins essential for life.

Four years ago, researchers showed that another protein derived from the retrotransposon, ARC, forms virus-like structures and is involved in the transfer of RNA between cells. Although these studies have shown that it is possible to create retrotransposon proteins as a delivery platform, scientists have not been able to successfully use these proteins to package and deliver specific RNA shipments into mammalian cells.

SEND Health Recovery Technologies

SEND packages are injected into diseased cells to deliver therapeutic mRNA and restore health. Credit: McGovern Institute

Knowing that some proteins derived from the retrotransposon are capable of binding and packaging molecular loads, Zhang’s team turned to these proteins as possible delivery vehicles. They systematically searched for these proteins in the human genome, looking for those that could form protective capsules. In their initial analysis, the team found 48 human genes encoding proteins that could have this ability. Of these, 19 candidate proteins were present in both mice and humans. In the cell line that the team studied, PEG10 stood out as an efficient shuttle; the cells released significantly more PEG10 particles than any other protein tested. PEG10 particles also predominantly contain their own mRNA, suggesting that PEG10 may be able to package certain RNA molecules.

Development of a modular system

To develop the SEND technology, the team identified molecular sequences or “signals” in PEG10 mRNA that PEG10 recognizes and uses to package its mRNA. The researchers then used these signals to construct both PEG10 and other RNA cargoes so that PEG10 could selectively package those RNAs. The team then adorned the PEG10 capsules with additional proteins called “fusogens” that sit on the surface of cells and help them fuse together.

By creating fusogens on PEG10 capsules, researchers must be able to target the capsule to a specific type of cell, tissue, or organ. As a first step towards this goal, the team used two different fusogens, including one found in the human body, to ensure the delivery of the SEND cargo.

“By mixing and matching the various components in the SEND system, we believe it will provide a modular platform for the development of therapeutic agents for a variety of diseases,” Zhang said.

Progressive gene therapy

SEND is made up of proteins that are naturally produced in the body, which means it cannot trigger an immune response. If demonstrated in further research, the researchers say SEND could open the door to multiple uses of gene therapy with minimal side effects. “SEND technology will augment viral delivery vectors and lipid nanoparticles to further expand the toolbox for gene delivery and therapies into cells,” Lash said.

The team will then test SEND on animals and further develop a system to deliver the cargo to various tissues and cells. They will also continue to explore the natural diversity of these systems in the human body to identify other components that can be added to the SEND platform.

“We are delighted to continue to advance this approach,” Zhang said. “The realization that we can use PEG10 and most likely other proteins to engineer a delivery pathway in the human body to package and deliver new RNA and other potential therapies is a really powerful concept.”

Reference: “The mammalian retrovirus-like protein PEG10 packs its own mRNA and can be pseudotyped to deliver mRNA” Michael Segel, Blake Lash, Jingwei Song, Alim Ladha, Catherine S. Liu, Xin Jin, Sergey L. Mehedov, Rhiannon K. Macrae , Evgeny Kunin and Feng Zhang, August 20, 2021, The science
DOI: 10.1126 / science.abg6155

This work was made possible with the support of the Simons Center for the Social Brain at MIT; Internal Research Program of the National Institutes of Health; National Institutes of Health Grants 1R01-HG009761 and 1DP1-HL141201; Howard Hughes Medical Institute; Open charity; G. Harold and Leila Y. Mathers Charitable Foundation; Edward Mullinkrodt Jr. Foundation; The Poitras Center for Mental Disorders Research at the Massachusetts Institute of Technology; Hock E. Tan and C. Lisa Young, Center for Autism Research, MIT; The Yang Tang Center for Molecular Therapy at the Massachusetts Institute of Technology; Lisa Yang; The Phillips family; R. Metcalfe; and J. and P. Poitras.


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