Posts belonging to Category Computational chemistry

How To Remove Air Pollution Inside Cars

You might think sitting in your car with your windows closed keeps you safe from air pollution. The makers of a new pollution-busting filter say you’d be wrong.


When you’re in your car you’re directly in the lanes of traffic and you’re actually taking air into the car. That’s coming from the exhaust of the cars in front of you. This means that there are greatly elevated levels of air pollution inside of a vehicle. This is both for nitrogen dioxide and for particulate matter“,  says Matthew Johnson,  Professor of Chemistry at the University of Copenhagen (Denmark).

Toxic air pollution passes through air inlets inside cars. Emissions from diesel vehicles are worst. The team from University of Copenhagen and start-up Airlabs has created Airbubbl, which contains two filters.
We have a chemical filter that’s removing nitrogen dioxide and ozone and odour from the air stream. We also have a high performance particle filter that’s removing soot and road dust and brake dust and these other components. We combine that inside this case. This plugs into the cigarette lighter. We have some quiet fans at the two ends of the device and we’ve used computational fluid dynamics in order to direct the airflow towards the passengers,” explains Johnson.
Independent tests in London saw nitrogen dioxide concentrations inside cars fall by 95 percent in 10 minutes. The Airbubbl is lightweight and easily attachable. A Kickstarter campaign has been launched to market the device.



How To Trap DNA molecules With Your Smartphone

Researchers from the University of Minnesota College of Science and Engineering have found yet another remarkable use for the wonder material graphenetiny electronictweezers” that can grab biomolecules floating in water with incredible efficiency. This capability could lead to a revolutionary handheld disease diagnostic system that could be run on a smart phoneGraphene, a material made of a single layer of carbon atoms, was discovered more than a decade ago and has enthralled researchers with its range of amazing properties that have found uses in many new applications from microelectronics to solar cells. The graphene tweezers developed at the University of Minnesota are vastly more effective at trapping particles compared to other techniques used in the past due to the fact that graphene is a single atom thick, less than 1 billionth of a meter.

The physical principle of tweezing or trapping nanometer-scale objects, known as dielectrophoresis, has been known for a long time and is typically practiced by using a pair of metal electrodes. From the viewpoint of grabbing molecules, however, metal electrodes are very blunt. They simply lack the “sharpness” to pick up and control nanometer-scale objects.

Graphene is the thinnest material ever discovered, and it is this property that allows us to make these tweezers so efficient. No other material can come close,” said research team leader Sang-Hyun Oh, a Professor at the University of Minnesota. “To build efficient electronic tweezers to grab biomolecules, basically we need to create miniaturized lightning rods and concentrate huge amount of electrical flux on the sharp tip. The edges of graphene are the sharpest lightning rods.

The team also showed that the graphene tweezers could be used for a wide range of physical and biological applications by trapping semiconductor nanocrystals, nanodiamond particles, and even DNA molecules. Normally this type of trapping would require high voltages, restricting it to a laboratory environment, but graphene tweezers can trap small DNA molecules at around 1 Volt, meaning that this could work on portable devices such as mobile phones.

The research study has been published  in Nature Communications.


Artificial Intelligence Chip Analyzes Molecular-level Data In Real Time

Nano Global, an Austin-based molecular data company, today announced that it is developing a chip using intellectual property (IP) from Arm, the world’s leading semiconductor IP company. The technology will help redefine how global health challenges – from superbugs to infectious diseases, and cancer are conquered.

The pioneering system-on-chip (SoC) will yield highly-secure molecular data that can be used in the recognition and analysis of health threats caused by pathogens and other living organisms. Combined with the company’s scientific technology platform, the chip leverages advances in nanotechnology, optics, artificial intelligence (AI), blockchain authentication, and edge computing to access and analyze molecular-level data in real time.

In partnership with Arm, we’re tackling the vast frontier of molecular data to unlock the unlimited potential of this universe,” said Steve Papermaster, Chairman and CEO of Nano Global. “The data our technology can acquire and process will enable us to create a safer and healthier world.”

We believe the technology Nano Global is delivering will be an important step forward in the collective pursuit of care that improves lives through the application of technology,” explained Rene Haas, executive vice president and president of IPG, Arm. “By collaborating with Nano Global, Arm is taking an active role in developing and deploying the technologies that will move us one step closer to solving complex health challenges.”

Additionally, Nano Global will be partnering with several leading institutions, including Baylor College of Medicine and National University of Singapore, on broad research initiatives in clinical, laboratory, and population health environments to accelerate data collection, analysis, and product development.
The initial development of the chip is in process with first delivery expected by 2020. The company is already adding new partners to their platform.


Polymeric Materials Outperform Natural Antibodies

Experts from the Biotechnology Group led by Professor Sergey Piletsky at the University of Leicester (UK) in collaboration with the spin-off company MIP Diagnostics Ltd, have announced the development of polymeric materials with molecular recognition capabilities which hold the potential to outperform natural antibodies in various diagnostic applications.

chemical background

 In a newly released article ‘A comparison of the performance of molecularly imprinted polymer nanoparticles for small molecule targets and antibodies in the ELISA format’ the researchers successfully demonstrated that polymer nanoparticles produced by the molecular imprinting technique (MIP nanoparticles) can bind to the target molecule with the same or higher affinity and specificity than widely used commercially available antibodies and against challenging targets.

Additionally, their ease of manufacture, short lead time, high affinity and the lack of requirement for cold chain logistics make them an attractive alternative to traditional antibodies for use in immunoassays.

Professor Piletsky, from our Department of Chemistry, explained: “It is now well over twenty years since the first demonstration that molecularly imprinted polymers can be used as the recognition material in assays for clinically significant drugs“. 


New Genetic And Stem-Cell Technology To Grow Sheets Of Skin

Somewhere in Germany’s Ruhr valley, a nine-year-old boy is doing what children do: playing football, joking around with friends and going to school. Two years ago, he was confined to a hospital bed, dying of a rare and cruel genetic skin disease. The boy had junctional epidermolysis bullosa, or JEB. He, like other people with the disease, carried a mutation in a gene that controls the integrity of the skin. Doctors could only try to ease his suffering as some 80% of his skin simply fell away.

A team of Italian researchers came to his aid by combining stem-cell techniques with gene therapy. As a young scientist at Harvard Medical School in Boston, Massachusetts, in the 1980s, Michele De Luca — the lead author of the new study — watched pioneers in skin regeneration learn to grow small sheets of skin from cells taken from burns patients, and to use them in grafts. He extended the work in Italy, applying new genetic and stem-cell technologies. He developed ways to generate stem cells from human skin, replace disease-causing genes in them and grow sheets of healthy skin on scaffolds in the lab.

He chose JEB for his first clinical trial, which he registered with the Italian Medicines Agency in 2002. Four years later, he reported his first success, in which he created healthy skin patches from biopsies to replace small areas of sloughed-off skin on the legs of a patient with a form of JEB (F. Mavilio et al. Nature Med. 12, 1397–1402; 2006). New European Commission regulations introduced in 2007 required him to pause the project while he created facilities adhering to ‘good manufacturing practices’ (GMPs) and a spin-off company to meet the demands for strengthened oversight of cell-based therapies.

Having a company refocused his team’s attention on a different type of stem-cell therapy, one likely to yield a product for the market faster. Holoclar, a treatment that replaces the eye’s cornea in a form of blindness, became the world’s first commercial stem-cell therapy in 2015.

A few months later, at the University of Modena, De Luca got a call out of the blue from doctors in Germany who were trying to treat the little boy. Because the therapy had been in a clinical trial, albeit one on hold at the time, and because De Luca could provide GMP services, German regulatory authorities quickly approved the one-off compassionate use of the JEB therapy. Surgeons in Germany sent a skin biopsy to Modena, and two major skin transplants followed. Six months after the initial biopsy, the boy returned to school. During the many months since, he has not had so much as a blister, and loves to show off his ‘new skin’. By their nature, highly personalized treatments using gene therapies and products derived from an individual’s stem cells are likely to be applicable to only a subset of patients.

Scientists and clinicians have presented the details of the recovery in Nature (T. Hirsch et al.Nature; 2017). This major clinical development was based on decades of basic research. The clinical data gathered during 21 months of follow-up after the boy’s treatment have also led to major insights into human skin biology, as discussed in an accompanying News & Views (M. Aragona and C. Blanpain Nature; 2017). For example, normal regeneration of the epidermis is directed by only a few stem-cell clones that can self-renew.


Smart Paper Conducts Electricity, Detects Water

In cities and large-scale manufacturing plants, a water leak in a complicated network of pipes can take tremendous time and effort to detect, as technicians must disassemble many pieces to locate the problem. The American Water Works Association indicates that nearly a quarter-million water line breaks occur each year in the U.S., costing public water utilities about $2.8 billion annually.

A University of Washington (UW) team wants to simplify the process for discovering detrimental leaks by developing “smartpaper that can sense the presence of water. The paper, laced with conductive nanomaterials, can be employed as a switch, turning on or off an LED light or an alarm system indicating the absence or presence of water.

Water sensing is very challenging to do due to the polar nature of water, and what is used now is very expensive and not practical to implement,” said lead author Anthony Dichiara, a UW assistant professor of bioresource science and engineering in the School of Environment and Forest Sciences. “That led to the reason to pursue this work.”

Along with Dichiara, a team of UW undergraduate students in the Bioresource Science and Engineering program successfully embedded nanomaterials in paper that can conduct electricity and sense the presence of water. Starting with pulp, they manipulated the wood fibers and carefully mixed in nanomaterials using a standard process for papermaking, but never before used to make sensing papers.

Discovering that the paper could detect the presence of water came by way of a fortuitous accident. Water droplets fell onto the conductive paper the team had created, causing the LED light indicating conductivity to turn off. Though at first they thought they had ruined the paper, the researchers realized they had instead created a paper that was sensitive to water.
The researchers described their discovery in a paper appearing in the Journal of Materials Chemistry A.


Nanocompounds Enhance Microbial Activity On Soil, Enrich Crops

We live in a world where day to day objects seems to be getting smaller and better. The advent of nanotechnology is a major contributing factor to this phenomenon. Defined as the “engineered construction of matter at the molecular level”, nanotechnology has applications and uses in a multitude of fields. From medicine, electronics, food, clothing, batteries and environment, nanotechnology seems to be pushing the limits of all these fields. Now, scientist have discovered yet another novel application of nanotechnologyfacilitating soil microbial growth.

Indian scientists from the G. B. Pant University of Agriculture and Technology, Pantnangar, Indian Veterinary Research Institute, Izatnagar, and State Council for Science & Technology, Dehradun, studied the impact of three nanocompounds on soil microbial activity and the health of plants being cultivated.

The scientists found that supplementing agricultural soils with nanocompounds like nanoclay, nanochitosan and nanozeolite led to a higher growth of microbial populations in the soil. And such an increased microbial population further led to increased levels of phosphorus, organic carbon and nitrogen in the soils, all of which are known to improve the health of crops being cultivated. Additionally, the scientists also observed increased levels of microbial enzyme activity in the soil, as well as a 50% rise in the total protein content of the soil.

Although nanoclay had the least effect on the soil’s pH, nanozeolite was found to best facilitate the growth of soil microbes. An increase in soil microbial activity along with all the other downstream benefits, caused by these nanocompounds, are all an indicator of enhanced soil health. Therefore, supplementing soils with such nanocompounds could go a long way in improving the agricultural soils, plant health and ultimately, the crop yields of the country.


Editing Genes In Human Embryos

Two new CRISPR tools overcome the scariest parts of gene editing.The ability to edit RNA and individual DNA base pairs will make gene editing much more precise. Several years ago, scientists discovered a technique known as CRISPR/Cas9, which allowed them to edit DNA more efficiently than ever before.
Since then, CRISPR science has exploded; it’s become one of the most exciting and fast-moving areas of research, transforming everything from medicine to agriculture and energy. In 2017 alone, more than 14,000 CRISPR studies were published.

But here’s the thing: CRISPR, while a major leap forward in gene editing, can still be a blunt instrument. There have been problems with CRISPR modifying unintended gene targets and making worrisome, and permanent, edits to an organism’s genome. These changes could be passed down through generations, which has raised the stakes of CRISPR experiments — and the twin specters of “designer babies” and genetic performance enhancers — particularly when it comes to editing genes in human embryos.
So while CRISPR science is advancing quickly, scientists are still very much in the throes of tweaking and refining their toolkit. And on Wednesday, researchers at the Broad Institute of MIT and Harvard launched a coordinated blitz with two big reports that move CRISPR in that safer and more precise direction.
In a paper published in Science, researchers described an entirely new CRISPR-based gene editing tool that targets RNA, DNA’s sister, allowing for transient changes to genetic material. In Nature, scientists described how a more refined type of CRISPR gene editing can alter a single bit of DNA without cutting it — increasing the tool’s precision and efficiency.

The first paper, out Wednesday in Science, describes a new gene editing system. This one, from researchers at MIT and Harvard, focuses on tweaking human RNA instead of DNA.

Our cells contain chromosomes made up of chemical strands called DNA, which carry genetic information. Those genes have recipes for proteins that lead to a bunch of different traits. But to carry out the instructions in any one recipe, DNA needs another type of genetic material called RNA to get involved.

RNA is ephemeral: It acts like a middleman, or a messenger. For a gene to become a protein, that gene has to be transcribed into RNA in the cell, and the RNA is then read to make the protein. If the DNA is permanent — the family recipe book passed down through generations — the RNA is like your aunt’s scribbled-out recipe on a Post-It note, turning up only when it’s needed and disappearing again.

With the CRISPR/Cas9 system, researchers are focused on editing DNA. (For more on how that system works, read this Vox explainer.) But the new Science paper describes a novel gene editing tool called REPAIR that’s focused on using a different enzyme, Cas13, to edit that transient genetic material, the RNA, in cells. REPAIR can target specific RNA letters, or nucleosides, that are involved in single-base changes that regularly cause disease in humans.

This is hugely appealing for one big reason: With CRISPR/Cas9, the changes to the genome, or the cell’s recipe book, are permanent. You can’t undo them. With REPAIR, since researchers can target single bits of ephemeral RNA, the changes they make are transient, even reversible. So this system could fix genetic mutations without actually touching the genome (like throwing away your aunt’s Post-It note recipe without adding it to the family recipe book).


How To Detect Lead In Water

Gitanjali Rao, 11-year-old girl, is “America’s Top Young Scientist” of this year, with her invention of Tethys, a device that detects lead in water.


Tethys, the Greek goddess of fresh water, is a lead detection tool. What you do is first dip a disposable cartridge, which can easily be removed and attached to the core device in the water you wish to test. Once you do that, that’s basically the manual part. Then you just pull out an app on your phone and check your status and it looks like the water in this container is safe. So that’s just very simple, about like a 10 to 15 second process,” says Gitanjali Rao . The young girl was affected by the Flint, Michigan water catastrophe when the city started using the Flint River for water in 2014, sparking a crisis that was linked to an outbreak of Legionnaires’ disease, at least 12 deaths and dangerously high lead levels in children.

I was most affected about Flint, Michigan because of the amount of people that were getting affected by the lead in water. And I also realized that it wasn’t just in Flint, Michigan and there were over 5,000 water systems in the U.S. alone. In the beginning of my final presentation at the event, I talked about a little boy named Opemipo, he’s 10 years old and lives in Flint, Michigan. And he has 1 percent elevated lead levels in his blood. And he’s among the thousands of adults and children exposed to the harmful effects of lead in water. So it’s a pretty big deal out there today,” remembers Rao. The seventh-grader said it took her five months to make Tethys from start to finish.

My first couple of times when I was doing my experimentation and test, I did fail so many times and it was frustrating, but I knew that it was just a learning experience and I could definitely develop my device further by doing even more tests and getting advice from my mentor as well. So, never be afraid to try,” explains Rao, who  won the 2017 Discovery Education 3M Young Scientist Challenge, along with a $25,000 prize.


Self-regulating Nanoparticles Treat Cancer

Scientists from the University of Surrey have developed ‘intelligentnanoparticles which heat up to a temperature high enough to kill cancerous cells – but which then self-regulate and lose heat before they get hot enough to harm healthy tissue. The self-stopping nanoparticles could soon be used as part of hyperthermic-thermotherapy to treat patients with cancer, according to an exciting new study reported in NanoscaleThermotherapy has long been used as a treatment method for cancer, but it is difficult to treat patients without damaging healthy cells. However, tumour cells can be weakened or killed without affecting normal tissue if temperatures can be controlled accurately within a range of 42°C to 45°C.

Scientists from Surrey’s Advanced Technology Institute have worked with colleagues from the Dalian University of Technology in China to create nanoparticles which, when implanted and used in a thermotherapy session, can induce temperatures of up to 45°C. The Zn-Co-Cr ferrite nanoparticles produced for this study are self-regulating, meaning that they self-stop heating when they reach temperatures over 45°C. Importantly, the nanoparticles are also low in toxicity and are unlikely to cause permanent damage to the body.

This could potentially be a game changer in the way we treat people who have cancer. If we can keep cancer treatment sat at a temperature level high enough to kill the cancer, while low enough to stop harming healthy tissue, it will prevent some of the serious side effects of vital treatment. It’s a very exciting development which, once again, shows that the University of Surrey research is at the forefront of nanotechnologies – whether in the field of energy materials or, in this case, healthcare,” said Professor Ravi Silva, Head of the Advanced Technology Institute at the University of Surrey.

Dr. Wei Zhang, Associate Professor from Dalian University of Technology explains: “Magnetic induced hyperthermia is a traditional route of treating malignant tumours. However, the difficulties in temperature control has significantly restricted its usage If we can modulate the magnetic properties of the nanoparticles, the therapeutic temperature can be self-regulated, eliminating the use of clumsy temperature monitoring and controlling systems.

“By making magnetic materials with the Curie temperature falling in the range of hyperthermia temperatures, the self-regulation of therapeutics can be achieved. For the most magnetic materials, however, the Curie temperature is much higher than the human body can endure. By adjusting the components as we have, we have synthesized the nanoparticles with the Curie temperature as low as 34oC. This is a major nanomaterials breakthrough.”


Lab-grown Diamonds

This shiny, sparkly diamond was made inside a laboratory – but it has the same chemical makeup as its counterpart found deep inside the earth.


All the composition is exactly the same. It is a real diamond. What we’ve done is we’ve just taken what’s happened in nature and just put it in a lab,” said  Kelly Good, Director of Marketing of Pure Grown Diamonds.

Essentially, all diamonds are carbon. And inside a laboratory, scientists are using a method called microwave plasma chemical vapour deposition to grow the stones from a diamond seed. They do it by creating a plasma ball made of hydrogen inside a growth chamber. Methane, which is a carbon source, is added. The carbon mix rains down on the diamond seeds, layer by layer, creating a large, rough diamond that is cut and polished. The process takes about 10 to 12 weeks. Marketers tout the lab-grown diamonds as an eco-friendly, conflict-free alternative to mined diamonds. “Our consumer is millennials, anybody who is getting engaged are really buying the lab-grown diamonds. They also like the fact of the environmental aspect of it. That it’s grown in a greenhouse. There is less soil being moved. We have a less carbon footprint,” explains Kelly Good.

While similar in appearance, there are differences. David Weinstein, Executive Director of the International  Gemological Institute (New York), comments: “I have a crystal, a diamond and I’m looking at it and I see a peridot crystal, a green peridot crystal, I know right away, this wasn’t created in a machine. So the inclusions can really be very telling as to what the origins of the material is. And that’s what our gemologists look for.”
While lab-grown gems have been around for decades, but it’s only recently that the science and technology have made it possible to grow large, gem quality stones. And according to a report by Morgan Stanley, the lab-grown diamond market could grow by about 15 percent by the year 2020.


How To Clean Nuclear Waste

Cleaning up radioactive waste is a dangerous job for a human. That’s why researchers at the University of  Manchester are developing robots that could do the job for us. Five years ago, in 2011, a major earthquake and tsunami devastated the east coast of Japan, leading to explosions and subsequent radiation release at the Fukushima Daiichi Nuclear Power Station. The fuel in three of the reactors is believed to have melted, causing a large amount of contaminated water on site.

This is still to be dealt with today – which isn’t too surprising, given that the clean-up of Chernobyl is still underway 30 years after the infamous nuclear accident took place. After the accident at Chernobyl, where an extremely high level of radiation was released, workers had to be sent into areas to which you wouldn’t want to send a human being. For the safety of others, they entered the plant to survey its condition, extinguish fires and manually operate equipment and machinery – all in an environment that endangered their lives. The challenge in dismantling the site at Fukushima is the residual radiation level. In the surrounding areas levels have fallen significantly; in some places (still off limits to former residents) radiation levels actually aren’t very different from natural background levels in certain other parts of the world. But in the reactor itself a person would receive a lethal dose of radiation almost instantly.


At Fukushima, many of the instrumentation systems, such as reactor-water level and reactor pressure, were lost in the incident. This made assessing the integrity of the plant extremely difficult as you couldn’t send people to go and look at it,” explains Professor Barry Lennox, who, alongside Dr Simon Watson at The University of Manchester, is working to find another way of getting access to such dangerous places: by using robots. Professor Lennox and Dr Watson are part of a team working to adapt robots to help clean up Fukushima. They’re developing an underwater remote-operated vehicle – the AVEXIS – to help identify highly radioactive nuclear fuel that is believed to be dispersed underwater in the damaged reactor. The robot is already aiding decommissioning efforts at Sellafield, where it will swim around the ponds storing legacy waste to map and monitor the conditions within them.