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Latest news on complex systems in life sciences, engineering, education and government
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Bad sleep 'dramatically' alters body

Bad sleep 'dramatically' alters body | Complex Insight  - Understanding our world | Scoop.it
A run of poor sleep can have a dramatic effect on the internal workings of the human body, say UK researchers.
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Good article on BBC health:Researchers at the University of Surrey analysed the blood of 26 people after they had had plenty of sleep, up to 10 hours each night for a week, and compared the results with samples after a week of fewer than six hours a night. More than 700 genes were altered by the sleep shift. Each contains the instructions for building a protein, so those that became more active produced more proteins - changing body chemistry in response to reduced sleep. These results help indicate the role of sleep in regulating body chemistry and how regular sleep is important to maintain body functions such as replenishing and replacing cells. 

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Laser spotlight reveals machine 'climbing' DNA

Laser spotlight reveals machine 'climbing' DNA | Complex Insight  - Understanding our world | Scoop.it

New imaging technology has revealed how the molecular machines that remodel genetic material inside cells 'grab onto' DNA like a rock climber looking for a handhold.

 

The experiments, reported in this week's Science, use laser light to generate very bright patches close to single cells. When coupled with fluorescent tags this 'spotlight' makes it possible to image the inner workings of cells fast enough to see how the molecular machines inside change size, shape, and composition in the presence of DNA.

 

The Oxford team built their own light microscopy technology for the study, which is a collaboration between the research groups of Mark Leake in Oxford University's Department of Physics and David Sherratt in Oxford University's Department of Biochemistry.

 

The molecular machines in question are called Structural Maintenance of Chromosome (SMC) complexes: they remodel the genetic material inside every living cell and work along similar principles to a large family of molecules that act as very small motors performing functions as diverse as trafficking vital material inside cells to allowing muscles to contract.

 

The researchers studied a particular SMC, MukBEF (which is made from several different protein molecules), inside the bacterium E.coli. David Sheratt and his team found a way to fuse 'fluorescent proteins' directly to the DNA coding for MukBEF, effectively creating a single dye tag for each component of these machines.

 

Up until now conventional techniques of biological physics or biochemistry have not been sufficiently fast or precise to monitor such tiny machines inside living cells at the level of single molecules.

 

'Each machine functions in much the same way as rock-climber clinging to a cliff face,' says Mark Leake of Oxford University’s Department of Physics, 'it has one end anchored to a portion of cellular DNA while the other end opens and closes randomly by using chemical energy stored in a ubiquitous bio-molecule called adenosine triphosphate, or 'ATP': the universal molecular fuel for all living cells.

 

'This opening and closing action of the machine is essentially a process of mechanical 'grabbing', in which it attempts to seize more free DNA, like the rock-climber searching for a new handhold.'

 

It is hoped that pioneering biophysics experiments such as this will give fresh insights into the complex processes which are vital to life, and pave the way for a whole new approach to biomedical research at the very tiny length scale for understanding the causes of many diseases in humans, and how to devise new strategies to combat them. 


Via Dr. Stefan Gruenwald
ComplexInsight's insight:

its turtles all the way down... as we obtain more and more data and insight into cellular molecular mechanisms  their organisation, interactions, spatial and temporal dynamics become increasingly mechanistic with multiscale emergent propertiesarising from local interactions. This pioneering biophysics approach will likely generate a lot more insights into molecular mechanisms as it gets increasingly adopted for other experiments.

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Main culprit behind breast cancers discovered - Daily News & Analysis

Science World Report Main culprit behind breast cancers discovered Daily News & Analysis The findings came from a team of researchers led by Reuben Harris, Ph.D., associate professor of biochemistry, molecular biology and biophysics and also a...
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Mutation is a major problem with treatment of breast cancer. The discovery that an enzyme – called APOBEC3B helps drive multiple mutations – may change the way breast cancer is diagnosed and treated. Article is worth reading though results will need additional confirmation and investigation. Click on title to learn more.

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Biological Computation - Microsoft Research

Biological Computation - Microsoft Research | Complex Insight  - Understanding our world | Scoop.it
Application and development of computational methods and tools for modeling and analyzing complex biological systems.
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AS some one who deeply subscribes to Chris Langton's view that the natural stufy of Computing is to stufy computation as its writ across all of nature, this  research at Microsoft is deeply interesting (and echoes compaies liek Autodesk who come from one discipline and are increasingly looking at life sciences through the view of computing:  The Biological Computation group is conducting research to uncover fundamental principles of biological computation: what cells compute, how and why. We focus primarily on developing computational techniques that enable multiscale modelling, from molecules to cells to systems. Our work currently focuses on fundamentals of Biological Computation, with applications in Immunology and Development, together with principles of Programming Life, with applications in DNA Computing and Synthetic Biology. Click on the image or title to learn more.

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Will 'big data' prevent disease?

Will 'big data' prevent disease? | Complex Insight  - Understanding our world | Scoop.it
How the blistering pace of technological change could have a profound impact on healthcare.
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Good article from the BBC Future health series. Video is worth watching if you want an insight into how new technologies will impact healthcare.

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Metagenomics and its connection to microbial community organization - F1000 Biology Reports - F1000

Metagenomics and its connection to microbial community organization - F1000 Biology Reports - F1000 | Complex Insight  - Understanding our world | Scoop.it

"Microbes dominate most global biogeochemical cycles, and microbial metagenomics (studying the collective microbial genomes) provides invaluable new insights into microbial systems, independent of cultivation. Metagenomic approaches targeting specific genes, e.g. small subunit (ssu) ribosomal RNA (rRNA), can be used to investigate microbial community organization by efficiently showing which taxa of organisms are present, while shotgun approaches show all genes and can indicate what functions the organisms are capable of. But collecting and organizing comprehensive shotgun data is extremely challenging and costly, and, in theory, predicting functionalities from microbial identities alone would save immense effort. However, we don’t yet know to what extent such predictions are applicable."

 

Finally: a population-scale means of studying microbial communities.  The next few years are going to be VERY illuminating.


Via Ed Rybicki
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Proteins made to order

Proteins made to order | Complex Insight  - Understanding our world | Scoop.it

 A key part of synthetic biology and biological engineering will be the ability to create protiens for specific purposes. Researchers from University of Washington in Seattle have done just that -  designed proteins from scratch with predictable structures. Fascinating summary on Nature's blog. Click the image or the title ot learn more.

 

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The Mysterious, Mutant, Civilizing Power of Milk

The Mysterious, Mutant, Civilizing Power of Milk | Complex Insight  - Understanding our world | Scoop.it

Fascinating article on Slate regarding the mutation from lactose intolerant to lactore tolerant in some humans. Two hundred thousand years later, around 10,000 B.C., this began to change. A genetic mutation appeared, somewhere near modern-day Turkey, that jammed the lactase-production gene permanently in the “on” position. The original mutant was probably a male who passed the gene on to his children. People carrying the mutation could drink milk their entire lives. Genomic analyses have shown that within a few thousand years, at a rate that evolutionary biologists had thought impossibly rapid, this mutation spread throughout Eurasia, to Great Britain, Scandinavia, the Mediterranean, India and all points in between, stopping only at the Himalayas. Independently, other mutations for lactose tolerance arose in Africa and the Middle East, though not in the Americas, Australia, or the Far East. Click on the image or title to learn more.

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3D structure of an unmodified G protein-coupled receptor in its natural habitat - Phys.Org

3D structure of an unmodified G protein-coupled receptor in its natural habitat - Phys.Org | Complex Insight  - Understanding our world | Scoop.it

Using NMR spectroscopy, the team mapped the arrangement of atoms in a protein called CXCR1, which detects the inflammatory signal interleukin 8 and, through a G protein located inside the cell, triggers a cascade of events that can mobilize immune cells, for example. Because G protein-coupled receptors are critical for many cellular responses to external signals, they have been a major target for drugs. More precise knowledge of the shapes of these receptors will allow drugmakers to tailor small molecules to better fit specific targets, avoiding collateral hits that can cause detrimental side effects. "This finding will have a major impact on structure-based drug development since for the first time the principal class of drug receptors can be studied in their biologically active forms where they interact with other proteins and potential drugs," said Stanley Opella, professor of chemistry and biochemistry at the University of California, San Diego who led the work, which Nature published online October 21st in advance of the print edition. Read more at: http://phys.org/news/2012-10-3d-unmodified-protein-coupled-receptor-natural.html#jCp or click on the image or title for more info.

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Virus exploitscellular waste disposal system

Virus exploitscellular waste disposal system | Complex Insight  - Understanding our world | Scoop.it

Over the years, researchers in the laboratory of ETH-professor Ari Helenius have elucidated the tricks and tactics viruses use to enter human cells and exploit them for their own multiplication and spread. Jason Mercer, in a collaboration with Berend Snijder and colleagues from the Universtiy of Zürich  have just released a publication which puts forward new insights into how viruses enter human cells. "For the first time we were able to demonstrate a mechanism by which a virus uses the cellular waste-disposal system to facilitate release of the viral DNA, which is subsequently multiplied, and used for the formation of new virus particles" he says. In addition, the researchers were able to block the release of viral DNA – using a drug which is already approved for human use. Complete protein inventory During infection, viruses communicate with the host cell and they "abuse" a specific set of host proteins to assist them during their life-cycle. In collaboration with the group of University Professor Lukas Pelkmans, Jason Mercer set out to identify the cellular proteins which the vaccinia virus requires. The idea being that this knowledge may be helpful when developing new strategies to stop infection

Click on the image, or the title or read more at: http://phys.org/news/2012-10-virus-exploitscellular-disposal.html#jCp

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Drug-Resistant Superbugs Found in Wild Animals | Wired Science | Wired.com

Drug-Resistant Superbugs Found in Wild Animals | Wired Science | Wired.com | Complex Insight  - Understanding our world | Scoop.it

One of the most notorious and hard-to-treat bacteria in humans has been found in wildlife, according to a new study in the Journal of Wildlife Diseases. The researchers isolated methicillin-resistant Staphylococcus aureus (MRSA) in two rabbits and a shorebird. Wild animals may act as an environmental reservoir for the disease from which humans could get infected. S. aureus can cause skin infections or, if it gets into the bloodstream, life-threatening illness. Most infections are easy to manage with penicillin and related antibiotics, but MRSA, the resistant variety, is on the rise; also known as a “superbug,” it kills an estimated 18,000 Americans a year. In most cases, people contract the bacterium from a hospital stay. Hospitals are breeding grounds for antibiotic-resistant organisms, because patients are treated with a wide variety of antimicrobial drugs, prompting pathogens to develop defenses. Learn more by clicking on the image or the title.

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Paging Dr. Watson: Artificial Intelligence As a Prescription for Health Care | Wired Science | Wired.com

Paging Dr. Watson: Artificial Intelligence As a Prescription for Health Care | Wired Science | Wired.com | Complex Insight  - Understanding our world | Scoop.it

Health care in the United States certainly needs an overhaul. The question is whether that overhaul will come from artificially intelligent doctors. IBM  has launched partnerships with insurance giant WellPoint and the Sloan-Kettering Cancer Center in New York and is expected offer Watson commercially to hospitals within the next few years. Wired article discusses the approach and pros and cons as seen by some doctors. Worth a read for a quick intro to modern AI comprising data mining and big data topics as an approach to treatment diagnostics in healthcare. Click on the image or the title to learn more.

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DNA Viruses: The Really Big Ones (Giruses)

DNA Viruses: The Really Big Ones (Giruses) | Complex Insight  - Understanding our world | Scoop.it

Viruses with genomes greater than 300 kb and up to 1200 kb are being discovered with increasing frequency. These large viruses (often called giruses) can encode up to 900 proteins and also many tRNAs. Consequently, these viruses have more protein-encoding genes than many bacteria, and the concept of small particle/small genome that once defined viruses is no longer valid. Giruses infect bacteria and animals although most of the recently discovered ones infect protists. Thus, genome gigantism is not restricted to a specific host or phylogenetic clade.


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Stanford scientists fit light-emitting bioprobe in a single cell

Stanford scientists fit light-emitting bioprobe in a single cell | Complex Insight  - Understanding our world | Scoop.it

Via Gerd Moe-Behrens
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Gerd Moe-Behrens's curator insight, February 20, 2013 12:43 PM

BY ANDREW MYERS

"Stanford researchers are the first to demonstrate that sophisticated light resonators can be inserted inside living cells without damage to the cell. The development marks a new age in which tiny lasers and light-emitting diodes yield new avenues in the study of living cells.If engineers at Stanford have their way, biological research may soon be transformed by a new class of light-emitting probes small enough to be injected into individual cells without harm to the host.

 Welcome to biophotonics, a discipline at the confluence of engineering, biology and medicine in which light-based devices – lasers and light-emitting diodes (LEDs) – are opening up new avenues in the study and influence of living cells. The team described their probe in a paper published online Feb. 13 by the journal Nano Letters. It is the first study to demonstrate that tiny, sophisticated devices known as light resonators can be inserted inside cells without damaging the cell. Even with a resonator embedded inside, a cell is able to function, migrate and reproduce as normal."



http://stanford.io/13gA8P8

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Unique Microscope Captures Motion of DNA Structures in Space, Time

Unique Microscope Captures Motion of DNA Structures in Space, Time | Complex Insight  - Understanding our world | Scoop.it
Pasadena, CA (Scicasts) – Every great structure, from the Empire State Building to the Golden Gate Bridge, depends on specific mechanical properties to remain strong and reliable.
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Scientists at the California Institute of Technology (Caltech) have recently developed techniques for visualizing the behaviour of biological nanostructures in both space and time, allowing them to directly measure stiffness and map its variation throughout the network. Given that the behaviour of biological materials are partly determined by their structure (the arrangement of atoms in three dimensional space and how the structure changes over time) this type of visualization holds a huge amount of promise for revealing insights into biomaterials that were previously hidden. Knowing the mechanical properties of DNA structures is crucial to building sturdy biological networks and understanding subcellular structural formation. The researchers say that this type of visualization of biomechanics in space and time should be applicable to the study of other biological nanomaterials, including the abnormal protein assemblies that underlie diseases like Alzheimer's and Parkinson's disease.  Click on the image or title to read the full article.


 

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UAB researchers cure type 1 diabetes in dogs - EurekAlert (press release)

UAB researchers cure type 1 diabetes in dogs - EurekAlert (press release) | Complex Insight  - Understanding our world | Scoop.it
UAB researchers cure type 1 diabetes in dogs EurekAlert (press release) The study was led by the head of the UAB's Centre for Animal Biotechnology and Gene Therapy (CBATEG) Fàtima Bosch, and involved the Department of Biochemistry and Molecular...
ComplexInsight's insight:

As a dog lover this is an awesome piece of research (plus the fact that traditionally research in diabetes in dogs has led to improved treatments in humans). Researchers from the Universitat Autònoma de Barcelona (UAB), led by Fàtima Bosch, have shown for the first time that it is possible to cure diabetes in large animals with a single session of gene therapy. As published this week in Diabetes, the principal journal for research on the disease, after a single gene therapy session, the dogs recover their health and no longer show symptoms of the disease. In some cases, monitoring continued for over four years, with no recurrence of symptoms. The therapy is minimally invasive. It consists of a single session of various injections in the animal's rear legs using simple needles that are commonly used in cosmetic treatments. These injections introduce gene therapy vectors, with a dual objective: to express the insulin gene, on the one hand, and that of glucokinase, on the other. Glucokinase is an enzyme that regulates the uptake of glucose from the blood. When both genes act simultaneously they function as a "glucose sensor", which automatically regulates the uptake of glucose from the blood, thus reducing diabetic hyperglycemia (the excess of blood sugar associated with the disease). To learn more click on the headline or image.

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New nerve cells found in the brain

New nerve cells found in the brain | Complex Insight  - Understanding our world | Scoop.it
Scientists have identified a previously unknown group of never cells in the brain which regulate cardiovascular functions.
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Scientists at Karolinska Institutet in Sweden, in collaboration with colleagues in Germany and the Netherlands, have identified a previously unknown group of nerve cells in the brain. The nerve cells regulate cardiovascular functions such as heart rhythm and blood pressure. It is hoped that the discovery, which is published in theJournal of Clinical Investigation, will be significant in the long term in the treatment of cardiovascular diseases in humans

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Interactome3D

Interactome3D | Complex Insight  - Understanding our world | Scoop.it
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Researchers have developed a platform that compiles all the atomic data, previously stored in diverse databases, on protein structures and protein interactions for eight organisms of relevance. They apply a singular homology-based modelling procedure.The scientists Roberto Mosca, Arnaud Ceol and Patrick Aloy provide the international biomedical community with Interactome3D, an open-access and free web platform developed entirely by the Institute for Research in Biomedicine (IRB Barcelona). Interactome 3D offers for the first time the possibility to anonymously access and add molecular details of protein interactions and to obtain the information in 3D models. A great article describing the services is available here:  http://www.nanowerk.com/news2/biotech/newsid=28103.php#ixzz2FLF10eRq ; or click on the image or title to explore the service directly.

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Single-celled amoebae can remember, make decisions and anticipate change - slime molds redefine intelligence

Single-celled amoebae can remember, make decisions and anticipate change - slime molds redefine intelligence | Complex Insight  - Understanding our world | Scoop.it

Something scientists have come to understand is that slime molds are much smarter than they look. One species in particular, the SpongeBob SquarePants–yellow Physarum polycephalum, can solve mazes, mimic the layout of man-made transportation networks and choose the healthiest food from a diverse menu—and all this without a brain or nervous system. "Slime molds are redefining what you need to have to qualify as intelligent," Reid says.


Via Dr. Stefan Gruenwald, Complexity Digest
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Will we ever… reveal all the secrets of life from DNA?

Will we ever… reveal all the secrets of life from DNA? | Complex Insight  - Understanding our world | Scoop.it

Good article on the BBC Future website : As our technologies and understanding advance, will we eventually be able to look at a pile of raw DNA sequence and glean all the workings of the organism it belongs to? Just as physicists can use the laws of mechanics to predict the motion of an object, can biologists use fundamental ideas in genetics and molecular biology to predict the traits and flaws of a body based solely on its genes? Could we pop a genome into a black box, and print out the image of a human? Or a fly? Or a mouse?

Not easily... Click on the image or the title to learn more.

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Bacterial genes energy-sensing switch discovery could have broad implications

Biochemists at The Scripps Research Institute (TSRI) have discovered a genetic sequence that can alter its host gene's activity in response to cellular energy levels. The scientists have found this particular energy-sensing switch in bacterial genes, which could make it a target for a powerful new class of antibiotics. If similar energy-sensing switches are also identified for human genes, they may be useful for treating metabolism-related disorders such as type 2 diabetes and heart disease. Read more at: http://phys.org/news/2012-10-bacterial-genes-energy-sensing-discovery-broad.html#jCp or click on the title to learn more information.

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Where Will The Next Pandemic Come From? And How Can We Stop It?

Where Will The Next Pandemic Come From? And How Can We Stop It? | Complex Insight  - Understanding our world | Scoop.it

Very interesting article on filoviruses in Popular Science from David Quammen's new book, Spillover  . Style of the article reminded me a lot of Richard Preston's  excellent The Hot Zone (1994) and covers similar territory with more upto date insight, information and examples including the background to the 2008 CCD, WHO amd NICD paper on discovery of Marbug virus reservour n a large fruit bat Colony in Uganda. 

 

The dangers presented by zoonoses (transferance of animal disease to humans) are real and severe, but the degree of uncertainties is also high. Too many factors vary randomly, or almost randomly, in that system. Prediction, in general, so far as all these diseases are concerned, is a tenuous proposition, more likely to yield false confidence than actionable intelligence. The practical alternative to soothsaying, as one expert put it, is “improving the scientific basis to improve readiness.” By “the scientific basis” he meant the understanding of which virus groups to watch, the field capabilities to detect spillovers in remote places before they become regional outbreaks, the organizational capacities to control outbreaks before they become pandemics, plus the laboratory tools and skills to recognize known viruses speedily, to characterize new viruses almost as fast, and to create vaccines and therapies without much delay. If we can’t predict a forthcoming influenza pandemic or any other newly emergent virus, we can at least be vigilant; we can be well prepared and quick to respond; we can be ingenious and scientifically sophisticated in the forms of our response. Good article and Quammen's book is on the must read list for this year. Learn more by clicking on the image or the title for more information.

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Combating cancer’s conversations

Combating cancer’s conversations | Complex Insight  - Understanding our world | Scoop.it

Scientists believe we have a better chance of tackling the disease by knowing what tumour cells are saying to one another and then cutting off communications. One of the authors, physicist Eshel Ben-Jacob of Tel Aviv University in Israel, has argued for some time that many single-celled organisms, whether they are tumour cells or gut bacteria, show a rudimentary form of social intelligence – an ability to act collectively in ways that adapt to the prevailing conditions, learn from experience and solve problems, all with the “aim” of improving their chances of survival. He even believes there is evidence that they can modify their own genomes in beneficial ways. Many bacteria can engage in similar feats of communication and coordination, which can produce complex colony shapes such as vortex-like circulating blobs or exotic branching patterns. These displays of “social intelligence” help the colonies survive adversity, sometimes to our cost. Biofilms, for example – robust, slimy surface coatings that harbour bacteria and can spread infection in hospitals – are manufactured through the co-operation of several different species. Click on the image or title to learn more.

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DNA folded into shapes offers alternative gene delivery vehicle

DNA folded into shapes offers alternative gene delivery vehicle | Complex Insight  - Understanding our world | Scoop.it

Researchers from Johns Hopkins and Northwestern universities have discovered how to control the shape of nanoparticles that move DNA through the body and have shown that the shapes of these carriers may make a big difference in how well they work in treating cancer and other diseases.  The use of computer models allowed Luijten’s team to mimic traditional lab experiments at a far faster pace. These molecular dynamic simulations were performed on Quest, Northwestern’s high-performance computing system. The computations were so complex that some of them required 96 computer processors working simultaneously for one month.  “Our computer simulations and theoretical model have provided a mechanistic understanding, identifying what is responsible for this shape change,” Associate Professor Eric Luijten said. “We now can predict precisely how to choose the nanoparticle components if one wants to obtain a certain shape.”. Click on the image or the title to learn more.

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Craig Venter Imagines a World with Printable Life Forms | Wired Science | Wired.com

Craig Venter Imagines a World with Printable Life Forms | Wired Science | Wired.com | Complex Insight  - Understanding our world | Scoop.it
Craig Venter imagines a future where you can download software, print a vaccine, inject it, and presto! Contagion averted.
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