June 1, 2017 by Linda Vu This image shows the structure of berkelium in oxidation state +IV. Researchers used the new Berkeley Lab algorithm to calculate the absorption spectrum and confirm what what several experimental results have been hintingthat the element berkelium breaks form with its heavy element peers by taking on an extra positive charge when bound to a synthetic organic molecule. This property could help scientists develop better methods for handling and purifying nuclear materials. Credit: Bert de Jong, Berkeley Lab

Glow-in-the-dark objects seem magical when you're a kidthey can brighten up a dark room without the need for electricity, batteries or a light bulb. Then at some point you learn the science behind this phenomenon. Chemical compounds called chromophores become energized, or excited, when they absorb visible light. As they return to their normal state, the stored energy is released as light, which we perceive as a glow. In materials science, researchers rely on a similar phenomenon to study the structures of materials that will eventually be used in chemical catalysis, batteries, solar applications and more.

When a molecule absorbs a photonthe fundamental particle of lightelectrons in the molecular system are promoted from a low-energy (ground) state to a higher-energy (excited) state. These responses resonate at specific light frequencies, leaving "spectral fingerprints" that illuminate the atomic and electronic structures of the system being studied.

In experiments, the "spectral fingerprints" or absorption spectrum, are measured with state-of-the-art facilities like the Advanced Light Source (ALS) at the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab). In computer simulations, these measurements are typically captured with a quantum mechanical method called Time Dependent Density Functional Theory (TDDFT). The computational models are critical in helping researchers make the most of their experiments by predicting and validating results.

Yet despite its usefulness, there are times when TDDFT cannot not be used to calculate the absorption spectrum of a system because it would require too much time and computer resources. This is where a new mathematical "shortcut" developed by researchers in Berkeley Lab's Computational Research Division (CRD) comes in handy. Their algorithm speeds up absorption calculations by a factor of five, so simulations that used to take 10 to 15 hours to compute can now be done in approximately 2.5 hours.

A paper describing this method was published in the Journal of Chemical Theory and Computation (JCTC). And the new approach for computing the absorption spectrum will be incorporated in an upcoming release of the widely used NWChem computational chemistry software suite later this year.

New Algorithms Lead to Computational Savings

To study the chemical structure of new molecules and materials, scientists typically probe the system with an external stimulustypically a laserthen look for small electronic changes. Mathematically, this electronic change can be expressed as an eigenvalue problem. By solving this eigenvalue problem, researchers can get a good approximation of the absorption spectrum, which in turn reveals the resonant frequencies of the system being studied. Meanwhile, the corresponding eigenvector is used to calculate how intensely the system responded to the stimulus. This is essentially the principle behind the TDDFT approach, which has been implemented in several quantum chemistry software packages, including the open-source NWChem software suite.

While this approach has proven to be successful, it does have limitations for large systems. The wider the energy range of electronic responses a researcher tries to capture in a system, the more eigenvalues and eigenvectors need to be computed, which also means more computing resources are necessary. Ultimately, the absorption spectrum of a molecular system with more than 100 atoms becomes prohibitively expensive to compute with this method.

To overcome these limitations, mathematicians in CRD developed a technique to compute the absorption spectrum directly without explicitly computing the eigenvalues of the matrix.

"Traditionally, researchers have had to compute the eigenvalues and eigenvectors of very large matrices in order to generate the absorption spectrum, but we realized that you don't have to compute every single eigenvalue to get an accurate view of the absorption spectrum," says Chao Yang, a CRD mathematician who led the development of the new approach.

By reformulating the problem as a matrix function approximation, making use of a special transformation and taking advantage of the underlying symmetry with respect to a non-Euclidean metric, Yang and his colleagues were able to apply the Lanczos algorithm and a Kernal Polynomial Method (KPM) to approximate the absorption spectrum of several molecules. Both of these algorithms require relatively low-memory compared to non-symmetrical alternatives, which is the key to the computational savings.

Because this method requires less computing power to achieve a result, researchers can also easily calculate the absorption spectrum for molecular systems with several hundreds of atoms.

"This method is a significant step forward because it allows us to model the absorption spectrum of molecular systems of hundreds of atoms at lower computational cost." says Niranjan Govind, a computational chemist at the Pacific Northwest National Laboratory who collaborated with the Berkeley Lab team on the development of the method in the NWChem computational chemistry program.

Recently Berkeley Lab scientists used this method to calculate the absorption spectrum and confirm what several experimental results have been hintingthat the element berkelium breaks form with its heavy element peers by taking on an extra positive charge when bound to a synthetic organic molecule. This property could help scientists develop better methods for handling and purifying nuclear materials. A paper highlighting this result appeared April 10 in the journal Nature Chemistry.

"The experimental results were hinting at this unusual behavior in berkelium, but there wasn't enough experimental evidence to say yes, 100 percent, this is what we're seeing," says study co-author Wibe Albert de Jong, a CRD scientist. "To be 100 percent sure, we did large computational simulations and compared them to the experimental data and determined that they were, indeed, seeing berkelium in an unusual oxidation state."

This new algorithm was developed through a DOE Office of Science-supported Scientific Discovery through Advanced Computing (SciDAC) project focused on advancing software and algorithms for photochemical reactions. SciDAC projects typically bring together an interdisciplinary team of researchers to develop new and novel computational methods for tackling some of the most challenging scientific problems.

"The interdisciplinary nature of SciDAC is a very effective way to facilitate breakthrough science, as each team member brings a different perspective to problem solving," says Yang. "In this dynamical environment, mathematicians, like me, team up with domain scientists to identify computational bottlenecks, then we use cutting-edge mathematical techniques to address and overcome those challenges."

Explore further: Supercomputing mimics berkelium experiments to validate new find

More information: Jiri Brabec et al. Efficient Algorithms for Estimating the Absorption Spectrum within Linear Response TDDFT, Journal of Chemical Theory and Computation (2015). DOI: 10.1021/acs.jctc.5b00887

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Gene therapy and a range of biological research rely on the efficient delivery of nucleic acids into cells through the process known as transfection. Most widely-used transfection approaches for mammalian cells rely on electrostatic forces, usually taking advantage of cationic reagents to bind to negatively-charged nucleic acids and form strong ionic complexes. Cells then grab these complexes and internalize them through a process called endocytosis. However, the concentration of positive charge in the reagents can kill cells, and some cellssuch as embryonic cells, neurons, or cells directly isolated from tissuedont incorporate the nucleic acids successfully.

Now researchers report a novel transfection technique, SnapFect, that relies on bio-orthogonal moleculesa class of chemically-reactive molecules that dont interfere with biological systems (ACS Cent. Sci. 2017, DOI: 10.1021/acscentsci.7b00132). The team designed nanoparticle liposomes carrying a bio-orthogonal ligand. When they add those fatty particles to cell culture, they fuse into the cell membrane within seconds, leaving the ketone ligand exposed on the surface. The team then packages the nucleic acids to be delivered in complementary lipid complexes decorated with oxyamines. When the oxyamine particles are added to the cells, these functional groups react quickly with the cell surface ketones. The membrane-bound nucleic-acid complex is then pulled into the cell via endocytosis, and the nucleic acid can be expressed. Its not based on electrostatics but on click chemistry, says Muhammad N. Yousaf, a chemical biologist at York University. Thats why basically every cell is transfected with the nucleic acid.

Commercial transfection reagents already bring in about $1.5 billion per year. Yousafs team compared SnapFect to two widely-used kits: Lipofectamine (Life Technologies) and ViaFect (Promega). SnapFect transfected cells with a 68% overall efficiency while the other two transfected 19% and 29%, respectively.

Yousaf launched a company called OrganoLinX that this month began selling SnapFect ($350 for 20-25 transfections). We focused on making [the kit] just as easy to use as other commercial products out there, he says.

Besides improving efficiency, researchers could also pre-treat one batch of cells to decorate them with ketones and then mix them with other cell types before adding nucleic acids. Just the pre-treated ones will be transfected, Yousaf explains. Its like precision transfection. Because the team can create a variety of complexes using the oxyamine particles, the technique can also deliver other molecules such as proteins into cells.

I think its an interesting step forward, says James H. Eberwine, a molecular neurobiologist at the University of Pennsylvaniaparticularly the techniques universal applicability to DNA, RNA, and proteins, as well as the specificity conferred by the click chemistry approach.

Eberwine adds that while the study compares SnapFect to two widely-used techniques, researchers often optimize those techniques for their particular applications and achieve much higher efficiencies than those noted in this study. I would certainly try it, he says, and if it really does have the higher efficiency then I could see value in doing this.

Currently cell surface modification with ketones must occur shortly before addition of the oxyamine-bundled cargo. But SnapFect would be especially powerful if the ketone modification was more permanent, Eberwine says. That way, researchers could pre-engineer the surface of immature cells, then allow those cells to develop, migrate, and find their place in the local microenvironment of an experimental system before they get transfected. This would be a real boon, he says.

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Genetic engineering through click chemistry - The Biological SCENE

Michael Leggett has been a member of his local astronomical society for several years. He tells us how he has been drawing on his chemistry background to deliver lectures on astrochemistry to astronomers.

My local astronomical society ran a survey to find out what subjects members might want covered. One member requested something about chemistry and I decided to prepare an introduction to astrochemistry as a series of short talks looking at one element at a time, its basic chemistry and aspects of interest to astronomers.

The series began in 2016 with the first short talk on hydrogen, and this was followed by a second short talk on the heavy hydrogen isotopes deuterium and tritium. The final short talk in 2016 was about helium and the noble gases.

The series will continue well into 2017 (possibly beyond) with the next short talk provisionally about lithium and the alkali metals. This will be followed by talks on beryllium, boron, carbon, nitrogen, oxygen, fluorine and their corresponding groups, with subsequent talks on selected transition metals, lanthanides and actinides.

I also regularly present talks for astronomical societies on chemical, biological and historical aspects of astronomy and astronautics.

The Orion Nebula, taken by a member of the Milton Keynes Astronomical Society, John Bell Picture: John Bell

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Chemistry of the stars - Royal Society of Chemistry

MetroHealth has an acute care hospital with a Level I trauma and burn center and more than 25 locations throughout Cuyahoga County. MetroHealth is currently in the planning phase of building a new state-of-the-art hospital on the near west side of Cleveland, a massive $1billion project that is expected to open in 2022. The new facility will be the centerpiece of the system's 52-acre campus that will undergo a complete transformation over the next five years.

"We are developing an integrated strategy to help MetroHealth evolve its brand and increase primary care services throughout Cuyahoga County," said Ned Show, CEO of Chemistry. "MetroHealth is focused on keeping people well and becoming the leading health system for preventative care. We're excited to help MetroHealth accomplish that goal."

About ChemistryWith offices in Atlanta and Pittsburgh, Chemistry combines the best elements of traditional and digital marketing to create positive reactions. As a full-service agency with more than 100 employees, it is constantly experimenting with new technologies and new media in the worlds of advertising, online marketing, media planning/buying, web design/development, mobile marketing and public relations. Chemistry provides solutions to a broad range of clients including the most respected brands in hospitality, healthcare and financial services. To learn more, visit createareaction.com.

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Chemistry is one of the big winners when it comes to EU research funding securing almost 55 million in 201415 alone. This is according to an analysis for the national academies, which found that chemistry was one of the top five disciplines when it came to attracting European research grants behind only clinical medicine, biosciences and physics. It also relies heavily on that funding: on average, EU grants accounted for 23% of departmental research income in the same year. This funding is now under threat with Britains planned exit from the EU.

Jason Love, head of inorganic chemistry at Edinburgh University isnt surprised: Its a broad subject so its able to get funding from medical research, biological research, more fundamental physical sciences research and materials. The breadth [] means we will collaborate widely. Moreover, there are a lot of challenges in chemistry that cant be solved in isolation. On average, over the past six years, 16% of his departments research funding has come from EU programmes.

Overall, higher education has taken the lions share of Horizon 2020 funding coming into the UK: over 1.93 billion (1.69 billion) by the end of 2016, equating to 63% of the total. Higher education institutions (HEI) arent so successful in other countries. To put the scale of EU investment in context, in 201415 HEIs reported 725 million in EU funding, which was 12% of their total income from grants and contracts, or around 25% of the 2.75 billion in research grants provided through UK government bodies.

The sector also attracts significant support from the European Regional Development Fund, and loans from the European Investment Bank which, according to the reports authors, Technopolis, have enabled research institutes to move forward earlier with more ambitious development plans. These endorsements from the bank can also be key in attracting other investors.

Amer Gaffar, director of the Manchester Fuel Cell Innovation Centre, says a 1.6 million award allowed Manchester Metropolitan University to get the centre off the ground quickly. Its doors will open at the end of the year and provide SMEs with equipment to develop hydrogen fuel cells. EU funding has also allowed his team to build partnerships across Europe that will be vital to the success of the centre.

EU research programmes provide unique personal grants and fellowships. During the Seventh Framework Programme (FP7) the predecessor to Horizon 2020 the UK won over 22% of European Research Council (ERC) grants. These not only provide science funding but enable us to attract international staff, which is incredibly important, says Claire Carmalt, head of chemistry at University College London. 1520% of her departments funding portfolio comes from the EU.

Last year one of its researchers won an ERC consolidator grant, which backs ground-breaking, risky research. The department, she adds, will leverage off the exciting science it supports. Edinburghs chemistry department also has two starting grants that help cement early stage careers. Love questions whether the UK government will offer more funds for early career researchers. These can really kick start a career or push on to important innovations, he notes.

Those grants also provide a flexibility not offered by UK funding sources. A lot of UK research council grants have an industrial or manufacturing focus [] whereas EU funding can have projects for fundamental science, says Carmalt. We need the fundamental research to get us to the applied.

Schemes such as the Marie Skodowska-Curie Actions, which support mobility between countries, are fantastic for bringing across really top people to the UK and help diversify talent, Carmalt adds. The UK has been very successful in winning these awards. But both Carmalt and Love are concerned that Brexit will mean losing academic staff from across the EU: How will we plug the gap? asks Carmalt. Edinburgh has already lost EU colleagues.

UK industry also gets substantial funding for research from the EU. In the first two years of Horizon 2020, companies received an average of 189 million a year. SMEs have been particularly successful, attracting more funding from Horizon 2020 and FP7, than any other country. It also accounts for a much higher proportion of R&D spend by SMEs than for the UK business sector as a whole. SMEs did particularly well in thematic funding such as ICT, nanosciences and materials.

Companies that took part in projects in FP7 report improved access to markets. Large companies also report significant benefits. The reports authors notes that the framework programmes facilitates strategic collaboration across Europe and helps underpin the innovation ecosystem by supporting the pipeline of ideas and talent from universities. They also point to the unique scale and reach of Horizon 2020 joint technology initiatives such as those on innovative medicines and hydrogen fuel cells, dwarf anything being done on a national scale.

Analysis suggests that public R&D expenditure like Horizon 2020 has a significant crowding-in effect, encouraging further private investment in R&D outside the programme. Studies suggest that for every 1 spent on R&D by the European commission, a further 0.74 will be invested by companies or other organisations in the wider EU economy. Technopolis argues that the effect could be stronger in an advanced economy like the UKs.

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Value of EU to UK chemistry revealed - Chemistry World (subscription)

The last time Tom Savage entered a season as the presumptive starting quarterback was four years ago, when, as a senior, he guided the Pitt Panthers to a 6-6 record that culminated in a 30-27 victory in the Little CaesarsPizza Bowl.

Nearly five months after that game, which Savage was knocked out of early, the Houston Texans selected Savage in the fourth round of the 2014 NFL Draft. After waiting in the wings three seasons, the now 27-year-old signal caller will finally get his chance to become an NFL starter.

After three long years watching and learning head coach Bill OBriens complex offensive scheme, Savage entered OTAs as Houstons starting quarterback. Despite the acquisition of Deshaun Watson via the 2017NFL Draft, Savage plans on finishing 2017 as the starter.

To do that, Savage will need to build chemistry and rapport with his teammates on both sides of the ball. Accordingto Savage, getting the chance to practice against the leagues top defense is invaluable.

Its a good bonding experience obviously within the team, but the challenges are they are the Houston Texans defense, said Savage. Im realizing you have to get this ball out quick, especially with that front and those guys covering.

As difficult as its been, Savage seems to be enjoying the challenge.I love this because were all out there competing and were all kind of if you heard it were all yapping at each other. Its a good bonding experience.

Even more important for Savage and the rest of the Texans offense in OTAs is to work on timing, chemistry and getting the offense functioning as a unit much better than they did in 2016.

By opening OTAs as the starter, Savage is now receiving important first-team reps, which give him that opportunity to build a rapport with his lineman, backs and receivers.

Its helping a lot, Savage said about playing with the starters. We get a limited time, and we all have to meet extra a little bit after if we want to get better. Thats what it comes down to.

But Savage knows that while staying after practice with his pass catchers is important, lining up with the entire offense, going over cadences and learning to work as a cohesive unit is the most important take away from Mays OTAs.

Just repetition and stuff were doing after practice and extra meetings. We get a limited time, and we all have to meet extra a little bit after if we want to get better, said Savage. Thats what it comes down to.

Despite this being his first season as a starter, Savage isnt preparing differently than he has in his previous three seasons, but he understands he is now being counted on as a leader.

I think a little more of it is in the communication, obviously, with some of the guys. When youre a third-string quarterback, youre not really going up to DeAndre Hopkins and telling him how you want a bow route or something. Now communication comes in and you have to be on the same page with all of them. Thats what were working on now.

Entering his fourth season as a pro, Savage knows the spotlight will be on him. Its a great opportunity. I hate to say its special because I have to go out there and I have to earn it every day, said Savage.

Savage also knows in the NFL you must constantly earn playing time, so hes not necessarily ready to celebrate his new role. Perhaps with veteran savvy, Savage thinks there will be time to celebrate later.

Itll be special at the end of the season.

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Tom Savage building chemistry with teammates | Texans Wire - Texans Wire

Building chemistry with his new teammates remains the primary goal for Green Bay Packers quarterback Aaron Rodgers during organized team activities, which continue into the second phase this week.

I think at this point, when youre adding new guys to the mix, its about chemistry, Rodgers said last week. Thats the on the field chemistry. Its reading body language when theyre running routes, its getting on the same page with the verbiage when you have new players. And starting to figure out how guys like to run routes, where they like the ball in certain situations, how they use their body. Its about timing, and getting that chemistry with the new skill players.

The Packers have added a number of new pieces to the offense this offseason, including veteran tight ends Martellus Bennett and Lance Kendricks. Green Bay also drafted two young receivers (DeAngelo Yancey, Malachi Dupre) and rebuilt the running back position.

Building a rapport and understanding each new individuals wants and needs is necessary for keeping a high-octane offense running smoothly. The connection between Rodgers and Bennett the versatile tight end and teams replacement for playoff hero Jared Cook is especially important for ensuring the Packers hit the ground running to start 2017.

The two have already been working overtime to establish the on-field relationship.

Im always talking to him on the field, too, trying to see what he wants, Bennett said, according to Jason Wilde of the Wisconsin State Journal. (Ill say), Hey, how did that look? or hell give me the thumbs up. Or if Im in another group, I always look back at him, Hey, is that what you want? Is there something different you want on this? Always trying to figure out, just trying to have those conversations on and off the field, trying to get know each other as players, and as people.

Kendricks,who spent his first six years with the Rams, is also using OTAs to find his footing in a new environment.

New organization, new offense, new verbiage, new schemes and stuff, Kendricks said. Its going to take a little bit of time, I just gotta take it day-by-day. But Ill catch on.

The new tight ends still have ample opportunity to get on the same page with Rodgers and comfortable within the offense, especially considering the Packers emphasis on the passing game during OTAs.

Chemistry is really important, Rodgers said. Its about learning those guys, and their body movements, and what routes they feel good about and what routes they struggle with. Well have plenty of time, in these OTAs, a lot of individual time. Were not doing a lot of run plays, by design. It gives us a lot of time to work on the passing gameIm confident well be ready to go once the season starts.

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Aaron Rodgers: OTAs are for building on-field chemistry - Packers Wire