Tag Archives: Harvard University

Nucleic acid-based memory storage

We’re running out of memory. To be more specific, there are two problems: the supply of silicon and a limit to how much silicon-based memory can store. An April 27, 2016 news item on Nanowerk announces a nucleic acid-based approach to solving the memory problem,

A group of Boise State [Boise State University in Idaho, US] researchers, led by associate professor of materials science and engineering and associate dean of the College of Innovation and Design Will Hughes, is working toward a better way to store digital information using nucleic acid memory (NAM).

An April 25, 2016 Boise State University news release, which originated the news item, expands on the theme of computer memory and provides more details about the approach,

It’s no secret that as a society we generate vast amounts of data each year. So much so that the 30 billion watts of electricity used annually by server farms today is roughly equivalent to the output of 30 nuclear power plants.

And the demand keeps growing. The global flash memory market is predicted to reach $30.2 billion this year, potentially growing to $80.3 billion by 2025. Experts estimate that by 2040, the demand for global memory will exceed the projected supply of silicon (the raw material used to store flash memory). Furthermore, electronic memory is rapidly approaching its fundamental size limits because of the difficulty in storing electrons in small dimensions.

Hughes, with post-doctoral researcher Reza Zadegan and colleagues Victor Zhirnov (Semiconductor Research Corporation), Gurtej Sandhun (Micron Technology Inc.) and George Church (Harvard University), is looking to DNA molecules to solve the problem. Nucleic acid — the “NA” in “DNA” — far surpasses electronic memory in retention time, according to the researchers, while also providing greater information density and energy of operation.

Their conclusions are outlined in an invited commentary in the prestigious journal Nature Materials published earlier this month.

“DNA is the data storage material of life in general,” said Hughes. “Because of its physical and chemical properties, it also may become the data storage material of our lives.” It may sound like science fiction, but Hughes will participate in an invitation-only workshop this month at the Intelligence Advanced Research Projects Activity (IARPA) Agency to envision a portable DNA hard drive that would have 500 Terabytes of searchable data – that’s about the the size of the Library of Congress Web Archive.

“When information bits are encoded into polymer strings, researchers and manufacturers can manage and manipulate physical, chemical and biological information with standard molecular biology techniques,” the paper [in Nature Materials?] states.

Cost-competitive technologies to read and write DNA could lead to real-world applications ranging from artificial chromosomes, digital hard drives and information-management systems, to a platform for watermarking and tracking genetic content or next-generation encryption tools that necessitate physical rather than electronic embodiment.

Here’s how it works. Current binary code uses 0’s and 1’s to represent bits of information. A computer program then accesses a specific decoder to turn the numbers back into usable data. With nucleic acid memory, 0’s and 1’s are replaced with the nucleotides A, T, C and G. Known as monomers, they are covalently bonded to form longer polymer chains, also known as information strings.

Because of DNA’s superior ability to store data, DNA can contain all the information in the world in a small box measuring 10 x 10 x 10 centimeters cubed. NAM could thus be used as a sustainable time capsule for massive, scientific, financial, governmental, historical, genealogical, personal and genetic records.

Better yet, DNA can store digital information for a very long time – thousands to millions of years. Currently, usable information has been extracted from DNA in bones that are 700,000 years old, making nucleic acid memory a promising archival material. And nucleic acid memory uses 100 million times less energy than storing data electronically in flash, and the data can live on for generations.

At Boise State, Hughes and Zadegan are examining DNA’s stability under extreme conditions. DNA strands are subjected to temperatures varying from negative 20 degrees Celsius to 100 degrees Celsius, and to a variety of UV exposures to see if they can still retain their information. What they’re finding is that much less information is lost with NAM than with the current state of the industry.

Here’s a link to and a citation for the Nature Materials paper,

Nucleic acid memory by Victor Zhirnov, Reza M. Zadegan, Gurtej S. Sandhu, George M. Church, & William L. Hughes. Nature Materials 15, 366–370 (2016)  doi:10.1038/nmat4594 Published online 23 March 2016

This paper is behind a paywall.

Tune your windows for privacy

Caption: With an applied voltage, the nanowires on either side of the glass become attracted to each other and move toward each other, squeezing and deforming the soft elastomer. Because the nanowires are scattered unevenly across the surface, the elastomer deforms unevenly. That uneven roughness causes light to scatter, turning the glass opaque. Credit: David Clarke/Harvard SEAS [School of Engineering and Applied Sciences]

Right now, this is my favourite science illustration. A March 14, 2016 news item on Nanowerk announces Harvard’s new technology that can turn a clear window into an opaque one at the touch of a switch,

Say goodbye to blinds.

Researchers at the Harvard John A. Paulson School of Engineering and Applied Sciences have developed a technique that can quickly change the opacity of a window, turning it cloudy, clear or somewhere in between with the flick of a switch.

Tunable windows aren’t new but most previous technologies have relied on electrochemical reactions achieved through expensive manufacturing. This technology, developed by David Clarke, the Extended Tarr Family Professor of Materials, and postdoctoral fellow Samuel Shian, uses geometry [to] adjust the transparency of a window.

A March 14, 2016 Harvard University news release (also on EurekAlert) by Leah Burrows, which originated the news item, describes the technology in more detail,

The tunable window is comprised of a sheet of glass or plastic, sandwiched between transparent, soft elastomers sprayed with a coating of silver nanowires, too small to scatter light on their own.

But apply an electric voltage and things change quickly.

With an applied voltage, the nanowires on either side of the glass are energized to move toward each other, squeezing and deforming the soft elastomer. Because the nanowires are distributed unevenly across the surface, the elastomer deforms unevenly. The resulting uneven roughness causes light to scatter, turning the glass opaque.

The change happens in less than a second.

It’s like a frozen pond, said Shian.

“If the frozen pond is smooth, you can see through the ice. But if the ice is heavily scratched, you can’t see through,” said Shian.

Clarke and Shian found that the roughness of the elastomer surface depended on the voltage, so if you wanted a window that is only light clouded, you would apply less voltage than if you wanted a totally opaque window.

“Because this is a physical phenomenon rather than based on a chemical reaction, it is a simpler and potentially cheaper way to achieve commercial tunable windows,” said Clarke.

Current chemical-based controllable windows use vacuum deposition to coat the glass, a process that deposits layers of a material molecule by molecule. It’s expensive and painstaking. In Clarke and Shian’s method, the nanowire layer can be sprayed or peeled onto the elastomer, making the technology scalable for larger architectural projects.

Next the team is working on incorporating thinner elastomers, which would require lower voltages, more suited for standard electronical supplies.

Here’s a link to and a citation for the paper,

Electrically tunable window device by Samuel Shian and David R. Clarke. Optics Letters Vol. 41, Issue 6, pp. 1289-1292 (2016) •doi: 10.1364/OL.41.001289

This is an open access paper.

Namib beetles, cacti, and pitcher plants teach scientists at Harvard University (US)

In this latest work from Harvard University’s Wyss Institute for Biologically Inspired Engineering, scientists have looked at three desert dwellers for survival strategies in water-poor areas. From a Feb. 25, 2015 news item on Nanowerk,

Organisms such as cacti and desert beetles can survive in arid environments because they’ve evolved mechanisms to collect water from thin air. The Namib desert beetle, for example, collects water droplets on the bumps of its shell while V-shaped cactus spines guide droplets to the plant’s body.

As the planet grows drier, researchers are looking to nature for more effective ways to pull water from air. Now, a team of researchers from the Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS) and the Wyss Institute for Biologically Inspired Engineering at Harvard University have drawn inspiration from these organisms to develop a better way to promote and transport condensed water droplets.

A Feb. 24, 2016 Harvard University press release by Leah Burrows (also on EurekAlert), which originated the news item, expands on the theme,

“Everybody is excited about bioinspired materials research,” said Joanna Aizenberg, the Amy Smith Berylson Professor of Materials Science at SEAS and core faculty member of the Wyss Institute. “However, so far, we tend to mimic one inspirational natural system at a time. Our research shows that a complex bio-inspired approach, in which we marry multiple biological species to come up with non-trivial designs for highly efficient materials with unprecedented properties, is a new, promising direction in biomimetics.”

The new system, described in Nature, is inspired by the bumpy shell of desert beetles, the asymmetric structure of cactus spines and slippery surfaces of pitcher plants. The material harnesses the power of these natural systems, plus Slippery Liquid-Infused Porous Surfaces technology (SLIPS) developed in Aizenberg’s lab, to collect and direct the flow of condensed water droplets.

This approach is promising not only for harvesting water but also for industrial heat exchangers.

“Thermal power plants, for example, rely on condensers to quickly convert steam to liquid water,” said Philseok Kim, co-author of the paper and co-founder and vice president of technology at SEAS spin-off SLIPS Technologies, Inc. “This design could help speed up that process and even allow for operation at a higher temperature, significantly improving the overall energy efficiency.”

The major challenges in harvesting atmospheric water are controlling the size of the droplets, speed in which they form and the direction in which they flow.

For years, researchers focused on the hybrid chemistry of the beetle’s bumps — a hydrophilic top with hydrophobic surroundings — to explain how the beetle attracted water. However, Aizenberg and her team took inspiration from a different possibility – that convex bumps themselves also might be able to harvest water.

“We experimentally found that the geometry of bumps alone could facilitate condensation,” said Kyoo-Chul Park, a postdoctoral researcher and the first author of the paper. “By optimizing that bump shape through detailed theoretical modeling and combining it with the asymmetry of cactus spines and the nearly friction-free coatings of pitcher plants, we were able to design a material that can collect and transport a greater volume of water in a short time compared to other surfaces.”

“Without one of those parameters, the whole system would not work synergistically to promote both the growth and accelerated directional transport of even small, fast condensing droplets,” said Park.

“This research is an exciting first step towards developing a passive system that can efficiently collect water and guide it to a reservoir,” said Kim.

Here’s a link to and a citation for the paper,

Condensation on slippery asymmetric bumps by Kyoo-Chul Park, Philseok Kim, Alison Grinthal, Neil He, David Fox, James C. Weaver, & Joanna Aizenberg. Nature (2016) doi:10.1038/nature16956 Published online 24 February 2016

This paper is behind a paywall.

I have featured the Namib beetle and its water harvesting capabilities most recently in a July 29, 2014 posting and the most recent story I have about SLIPS is in an Oct. 14, 2014 posting.

Using copyright to shut down easy access to scientific research

This started out as a simple post on copyright and publishers vis à vis Sci-Hub but then John Dupuis wrote a think piece (with which I disagree somewhat) on the situation in a Feb. 22, 2016 posting on his blog, Confessions of a Science Librarian. More on Dupuis and my take on it after a description of the situation.

Sci-Hub

Before getting to the controversy and legal suit, here’s a preamble about the purpose for copyright as per the US constitution from Mike Masnick’s Feb. 17, 2016 posting on Techdirt,

Lots of people are aware of the Constitutional underpinnings of our copyright system. Article 1, Section 8, Clause 8 famously says that Congress has the following power:

To promote the progress of science and useful arts, by securing for limited times to authors and inventors the exclusive right to their respective writings and discoveries.

We’ve argued at great length over the importance of the preamble of that section, “to promote the progress,” but many people are confused about the terms “science” and “useful arts.” In fact, many people not well-versed in the issue often get the two backwards and think that “science” refers to inventions, and thus enables a patent system, while “useful arts” refers to “artistic works” and thus enables the copyright system. The opposite is actually the case. “Science” at the time the Constitution was written was actually synonymous with “learning” and “education” (while “useful arts” was a term meaning invention and new productivity tools).

While over the centuries, many who stood to benefit from an aggressive system of copyright control have tried to rewrite, whitewash or simply ignore this history, turning the copyright system falsely into a “property” regime, the fact is that it was always intended as a system to encourage the wider dissemination of ideas for the purpose of education and learning. The (potentially misguided) intent appeared to be that by granting exclusive rights to a certain limited class of works, it would encourage the creation of those works, which would then be useful in educating the public (and within a few decades enter the public domain).

Masnick’s preamble leads to a case where Elsevier (Publishers) has attempted to halt the very successful Sci-Hub, which bills itself as “the first pirate website in the world to provide mass and public access to tens of millions of research papers.” From Masnick’s Feb. 17, 2016 posting,

Rightfully, this is being celebrated as a massive boon to science and learning, making these otherwise hidden nuggets of knowledge and science that were previously locked up and hidden away available to just about anyone. And, to be clear, this absolutely fits with the original intent of copyright law — which was to encourage such learning. In a very large number of cases, it is not the creators of this content and knowledge who want the information to be locked up. Many researchers and academics know that their research has much more of an impact the wider it is seen, read, shared and built upon. But the gatekeepers — such as Elsveier and other large academic publishers — have stepped in and demanded copyright, basically for doing very little.

They do not pay the researchers for their work. Often, in fact, that work is funded by taxpayer funds. In some cases, in certain fields, the publishers actually demand that the authors of these papers pay to submit them. The journals do not pay to review the papers either. They outsource that work to other academics for “peer review” — which again, is unpaid. Finally, these publishers profit massively, having convinced many universities that they need to subscribe, often paying many tens or even hundreds of thousands of dollars for subscriptions to journals that very few actually read.

Simon Oxenham of the Neurobonkers blog on the big think website wrote a Feb. 9 (?), 2016 post about Sci-Hub, its originator, and its current legal fight (Note: Links have been removed),

On September 5th, 2011, Alexandra Elbakyan, a researcher from Kazakhstan, created Sci-Hub, a website that bypasses journal paywalls, illegally providing access to nearly every scientific paper ever published immediately to anyone who wants it. …

This was a game changer. Before September 2011, there was no way for people to freely access paywalled research en masse; researchers like Elbakyan were out in the cold. Sci-Hub is the first website to offer this service and now makes the process as simple as the click of a single button.

As the number of papers in the LibGen database expands, the frequency with which Sci-Hub has to dip into publishers’ repositories falls and consequently the risk of Sci-Hub triggering its alarm bells becomes ever smaller. Elbakyan explains, “We have already downloaded most paywalled articles to the library … we have almost everything!” This may well be no exaggeration. Elsevier, one of the most prolific and controversial scientific publishers in the world, recently alleged in court that Sci-Hub is currently harvesting Elsevier content at a rate of thousands of papers per day. Elbakyan puts the number of papers downloaded from various publishers through Sci-Hub in the range of hundreds of thousands per day, delivered to a running total of over 19 million visitors.

In one fell swoop, a network has been created that likely has a greater level of access to science than any individual university, or even government for that matter, anywhere in the world. Sci-Hub represents the sum of countless different universities’ institutional access — literally a world of knowledge. This is important now more than ever in a world where even Harvard University can no longer afford to pay skyrocketing academic journal subscription fees, while Cornell axed many of its Elsevier subscriptions over a decade ago. For researchers outside the US’ and Western Europe’s richest institutions, routine piracy has long been the only way to conduct science, but increasingly the problem of unaffordable journals is coming closer to home.

… This was the experience of Elbakyan herself, who studied in Kazakhstan University and just like other students in countries where journal subscriptions are unaffordable for institutions, was forced to pirate research in order to complete her studies. Elbakyan told me, “Prices are very high, and that made it impossible to obtain papers by purchasing. You need to read many papers for research, and when each paper costs about 30 dollars, that is impossible.”

While Sci-Hub is not expected to win its case in the US, where one judge has already ordered a preliminary injunction making its former domain unavailable. (Sci-Hub moved.) Should you be sympathetic to Elsevier, you may want to take this into account (Note: Links have been removed),

Elsevier is the world’s largest academic publisher and by far the most controversial. Over 15,000 researchers have vowed to boycott the publisher for charging “exorbitantly high prices” and bundling expensive, unwanted journals with essential journals, a practice that allegedly is bankrupting university libraries. Elsevier also supports SOPA and PIPA, which the researchers claim threatens to restrict the free exchange of information. Elsevier is perhaps most notorious for delivering takedown notices to academics, demanding them to take their own research published with Elsevier off websites like Academia.edu.

The movement against Elsevier has only gathered speed over the course of the last year with the resignation of 31 editorial board members from the Elsevier journal Lingua, who left in protest to set up their own open-access journal, Glossa. Now the battleground has moved from the comparatively niche field of linguistics to the far larger field of cognitive sciences. Last month, a petition of over 1,500 cognitive science researchers called on the editors of the Elsevier journal Cognition to demand Elsevier offer “fair open access”. Elsevier currently charges researchers $2,150 per article if researchers wish their work published in Cognition to be accessible by the public, a sum far higher than the charges that led to the Lingua mutiny.

In her letter to Sweet [New York District Court Judge Robert W. Sweet], Elbakyan made a point that will likely come as a shock to many outside the academic community: Researchers and universities don’t earn a single penny from the fees charged by publishers [emphasis mine] such as Elsevier for accepting their work, while Elsevier has an annual income over a billion U.S. dollars.

As Masnick noted, much of this research is done on the public dime (i. e., funded by taxpayers). For her part, Elbakyan has written a letter defending her actions on ethical rather than legal grounds.

I recommend reading the Oxenham article as it provides details about how the site works and includes text from the letter Elbakyan wrote.  For those who don’t have much time, Masnick’s post offers a good précis.

Sci-Hub suit as a distraction from the real issues?

Getting to Dupuis’ Feb. 22, 2016 posting and his perspective on the situation,

My take? Mostly that it’s a sideshow.

One aspect that I have ranted about on Twitter which I think is worth mentioning explicitly is that I think Elsevier and all the other big publishers are actually quite happy to feed the social media rage machine with these whack-a-mole controversies. The controversies act as a sideshow, distracting from the real issues and solutions that they would prefer all of us not to think about.

By whack-a-mole controversies I mean this recurring story of some person or company or group that wants to “free” scholarly articles and then gets sued or harassed by the big publishers or their proxies to force them to shut down. This provokes wide outrage and condemnation aimed at the publishers, especially Elsevier who is reserved a special place in hell according to most advocates of openness (myself included).

In other words: Elsevier and its ilk are thrilled to be the target of all the outrage. Focusing on the whack-a-mole game distracts us from fixing the real problem: the entrenched systems of prestige, incentive and funding in academia. As long as researchers are channelled into “high impact” journals, as long as tenure committees reward publishing in closed rather than open venues, nothing will really change. Until funders get serious about mandating true open access publishing and are willing to put their money where their intentions are, nothing will change. Or at least, progress will be mostly limited to surface victories rather than systemic change.

I think Dupuis is referencing a conflict theory (I can’t remember what it’s called) which suggests that certain types of conflicts help to keep systems in place while apparently attacking those systems. His point is well made but I disagree somewhat in that I think these conflicts can also raise awareness and activate people who might otherwise ignore or mindlessly comply with those systems. So, if Elsevier and the other publishers are using these legal suits as diversionary tactics, they may find they’ve made a strategic error.

ETA April 29, 2016: Sci-Hub does seem to move around so I’ve updated the links so it can be accessed but Sci-Hub’s situation can change at any moment.

Graphene like water

This is graphene research from Harvard University and Raytheon according to a Feb. 11, 2016 news item on phys.org (Note: Links have been removed),

It’s one atom thick [i.e., two-dimensional], stronger than steel, harder than diamond and one of the most conductive materials on earth.

But, several challenges must be overcome before graphene products are brought to market. Scientists are still trying to understand the basic physics of this unique material. Also, it’s very challenging to make and even harder to make without impurities.

In a new paper published in Science, researchers at the [sic] Harvard and Raytheon BBN Technology have advanced our understanding of graphene’s basic properties, observing for the first time electrons in a metal behaving like a fluid.

A Feb. 11, 2016 Harvard University press release by Leah Burrows (also on EurekAlert), which originated the news item, provides more detail,

In order to make this observation, the team improved methods to create ultra-clean graphene and developed a new way measure its thermal conductivity. This research could lead to novel thermoelectric devices as well as provide a model system to explore exotic phenomena like black holes and high-energy plasmas.

An electron super highway

In ordinary, three-dimensional metals, electrons hardly interact with each other. But graphene’s two-dimensional, honeycomb structure acts like an electron superhighway in which all the particles have to travel in the same lane. The electrons in graphene act like massless relativistic objects, some with positive charge and some with negative charge. They move at incredible speed — 1/300 of the speed of light — and have been predicted to collide with each other ten trillion times a second at room temperature.  These intense interactions between charge particles have never been observed in an ordinary metal before.

The team created an ultra-clean sample by sandwiching the one-atom thick graphene sheet between tens of layers of an electrically insulating perfect transparent crystal with a similar atomic structure of graphene.

“If you have a material that’s one atom thick, it’s going to be really affected by its environment,” said Jesse Crossno, a graduate student in the Kim Lab [Philip Kim, professor of physics and applied physics] and first author of the paper.  “If the graphene is on top of something that’s rough and disordered, it’s going to interfere with how the electrons move. It’s really important to create graphene with no interference from its environment.”

The technique was developed by Kim and his collaborators at Columbia University before he moved to Harvard in 2014 and now have been perfected in his lab at SEAS [Harvard School of Engineering and Applied Sciences].

Next, the team set up a kind of thermal soup of positively charged and negatively charged particles on the surface of the graphene, and observed how those particles flowed as thermal and electric currents.

What they observed flew in the face of everything they knew about metals.

A black hole on a chip

Most of our world — how water flows or how a curve ball curves —  is described by classical physics. Very small things, like electrons, are described by quantum mechanics while very large and very fast things, like galaxies, are described by relativistic physics, pioneered by Albert Einstein.

Combining these laws of physics is notoriously difficult but there are extreme examples where they overlap. High-energy systems like supernovas and black holes can be described by linking classical theories of hydrodynamics with Einstein’s theories of relativity.

But it’s difficult to run an experiment on a black hole. Enter graphene.

When the strongly interacting particles in graphene were driven by an electric field, they behaved not like individual particles but like a fluid that could be described by hydrodynamics.

“Instead of watching how a single particle was affected by an electric or thermal force, we could see the conserved energy as it flowed across many particles, like a wave through water,” said Crossno.

“Physics we discovered by studying black holes and string theory, we’re seeing in graphene,” said Andrew Lucas, co-author and graduate student with Subir Sachdev, the Herchel Smith Professor of Physics at Harvard. “This is the first model system of relativistic hydrodynamics in a metal.”

Moving forward, a small chip of graphene could be used to model the fluid-like behavior of other high-energy systems.

Industrial implications

So we now know that strongly interacting electrons in graphene behave like a liquid — how does that advance the industrial applications of graphene?

First, in order to observe the hydrodynamic system, the team needed to develop a precise way to measure how well electrons in the system carry heat.  It’s very difficult to do, said co-PI Kin Chung Fong, scientist with Raytheon BBN Technology.

Materials conduct heat in two ways: through vibrations in the atomic structure or lattice; and carried by the electrons themselves.

“We needed to find a clever way to ignore the heat transfer from the lattice and focus only on how much heat is carried by the electrons,” Fong said.

To do so, the team turned to noise. At finite temperature, the electrons move about randomly:  the higher the temperature, the noisier the electrons. By measuring the temperature of the electrons to three decimal points, the team was able to precisely measure the thermal conductivity of the electrons.

“This work provides a new way to control the rate of heat transduction in graphene’s electron system, and as such will be key for energy and sensing-related applications,” said Leonid Levitov, professor of physics at MIT [Massachusetts Institute of Technology].

“Converting thermal energy into electric currents and vice versa is notoriously hard with ordinary materials,” said Lucas. “But in principle, with a clean sample of graphene there may be no limit to how good a device you could make.”

Here’s a link to and a citation for the paper,

Observation of the Dirac fluid and the breakdown of the Wiedemann-Franz law in graphene by Jesse Crossno, Jing K. Shi, Ke Wang, Xiaomeng Liu, Achim Harzheim, Andrew Lucas, Subir Sachdev, Philip Kim, Takashi Taniguchi, Kenji Watanabe, Thomas A. Ohki, Kin Chung Fong.Science  11 Feb 2016: pp. DOI: 10.1126/science.aad0343

This paper is behind a paywall.

Here’s an image illustrating the research,

Caption: In a new paper published in Science, researchers at the Harvard and Raytheon BBN Technology have advanced our understanding of graphene's basic properties, observing for the first time electrons in a metal behaving like a fluid. Credit: Peter Allen/Harvard SEAS

Caption: In a new paper published in Science, researchers at the Harvard and Raytheon BBN Technology have advanced our understanding of graphene’s basic properties, observing for the first time electrons in a metal behaving like a fluid. Credit: Peter Allen/Harvard SEAS

Harvard University’s Engineered Water Nanostructures (EWNS)

I last wrote about this research in a March 19, 2015 posting, which focused on work proving that a water-engineered nanostructure platform had microbial properties useful for decontaminating food and allowing manufacturers to avoid using chemicals for the task. This latest research focuses on finetuning the platform’s ability. Here’s more from the latest research paper’s abstract,

A chemical free, nanotechnology-based, antimicrobial platform using Engineered Water Nanostructures (EWNS) was recently developed. EWNS have high surface charge, are loaded with reactive oxygen species (ROS), and can interact-with, and inactivate an array of microorganisms, including foodborne pathogens. Here, it was demonstrated that their properties during synthesis can be fine tuned and optimized to further enhance their antimicrobial potential. A lab based EWNS platform was developed to enable fine-tuning of EWNS properties by modifying synthesis parameters. Characterization of EWNS properties (charge, size and ROS content) was performed using state-of-the art analytical methods. Further their microbial inactivation potential was evaluated with food related microorganisms such as Escherichia coli, Salmonella enterica, Listeria innocua, Mycobacterium parafortuitum, and Saccharomyces cerevisiae inoculated onto the surface of organic grape tomatoes. The results presented here indicate that EWNS properties can be fine-tuned during synthesis resulting in a multifold increase of the inactivation efficacy. More specifically, the surface charge quadrupled and the ROS content increased. Microbial removal rates were microorganism dependent and ranged between 1.0 to 3.8 logs after 45 mins of exposure to an EWNS aerosol dose of 40,000 #/cm3.

Here’s a link to and a citation for the paper,

Optimization of a nanotechnology based antimicrobial platform for food safety applications using Engineered Water Nanostructures (EWNS) by Georgios Pyrgiotakis, Pallavi Vedantam, Caroline Cirenza, James McDevitt, Mary Eleftheriadou, Stephen S. Leonard, & Philip Demokritou. Scientific Reports 6, Article number: 21073 (2016) doi:10.1038/srep21073 Published online: 15 February 2016

This is an open access paper.

Constructing a liver

Chinese researchers have taken a step closer to constructing complex (lifelike) liver tissue according to a Jan. 27, 2016 American Chemical Society (ACS) news release (also on EurekAlert),

Engineered liver tissue could have a range of important uses, from transplants in patients suffering from the organ’s failure to pharmaceutical testing [this usage is sometimes known as liver-on-a-chip]. Now scientists report in ACS’ journal Analytical Chemistry the development of such a tissue, which closely mimics the liver’s complicated microstructure and function more effectively than existing models.

The liver serves a critical role in digesting food and detoxifying the body. But due to a variety of factors, including viral infections, alcoholism and drug reactions, the organ can develop chronic or acute problems. When it doesn’t work well, a person can suffer abdominal pain, swelling, nausea and other symptoms. Complete liver failure can be life-threatening and can require a transplant, a procedure that currently depends on human donors. To curtail this reliance and provide an improved model for predicting drugs’ side effects, scientists have been engineering liver tissue in the lab. But so far, they haven’t achieved the complex architecture of the real thing. Jinyi Wang and colleagues came up with a new approach.

Wang’s team built a microfluidics-based tissue that copies the liver’s complex lobules, the organ’s tiny structures that resemble wheels with spokes. They did this with human cells from a liver and an aorta, the body’s main artery. In the lab, the engineered tissue had a metabolic rate that was closer to real-life levels than other liver models, and it successfully simulated how a real liver would react to various drug combinations. The researchers conclude their approach could lead to the development of functional liver tissue for clinical applications and screening drugs for side effects and potentially harmful interactions.

Here’s a link to and a citation for the paper,

On-Chip Construction of Liver Lobule-like Microtissue and Its Application for Adverse Drug Reaction Assay by Chao Ma, Lei Zhao, En-Min Zhou, Juan Xu, Shaofei Shen, and Jinyi Wang. Northwest A&F University, China Anal. Chem., Article ASAP DOI: 10.1021/acs.analchem.5b03869 Publication Date (Web): January 7, 2016

Copyright © 2016 American Chemical Society

This paper is behind a paywall.

In a teleconference earlier this month (January 2016), I spoke to researchers at the University of Malaya, Universiti Teknologi Malaysia (UTM), and Harvard University about a joint lung and nanomedicine research project where I asked researcher Joseph Brain (Harvard) about using lung-on-a-chip testing in place of in vivo (animal) testing and he indicated more confidence in the ‘precision cut lung slices’ technique. (You can find out more about the Malaysian project in my Jan. 12, 2016 posting but there’s only a brief mention of Brain’s preferred alternative animal testing technique.)

Origami and our pop-up future

They should have declared Jan. 25, 2016 ‘L. Mahadevan Day’ at Harvard University. The researcher was listed as an author on two major papers. I covered the first piece of research, 4D printed hydrogels, in this Jan. 26, 2016 posting. Now for Mahadevan’s other work, from a Jan. 27, 2016 news item on Nanotechnology Now,

What if you could make any object out of a flat sheet of paper?

That future is on the horizon thanks to new research by L. Mahadevan, the Lola England de Valpine Professor of Applied Mathematics, Organismic and Evolutionary Biology, and Physics at the Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS). He is also a core faculty member of the Wyss Institute for Biologically Inspired Engineering, and member of the Kavli Institute for Bionano Science and Technology, at Harvard University.

Mahadevan and his team have characterized a fundamental origami fold, or tessellation, that could be used as a building block to create almost any three-dimensional shape, from nanostructures to buildings. …

A Jan. 26, 2016 Harvard University news release by Leah Burrows, which originated the news item, provides more detail about the specific fold the team has been investigating,

The folding pattern, known as the Miura-ori, is a periodic way to tile the plane using the simplest mountain-valley fold in origami. It was used as a decorative item in clothing at least as long ago as the 15th century. A folded Miura can be packed into a flat, compact shape and unfolded in one continuous motion, making it ideal for packing rigid structures like solar panels.  It also occurs in nature in a variety of situations, such as in insect wings and certain leaves.

“Could this simple folding pattern serve as a template for more complicated shapes, such as saddles, spheres, cylinders, and helices?” asked Mahadevan.

“We found an incredible amount of flexibility hidden inside the geometry of the Miura-ori,” said Levi Dudte, graduate student in the Mahadevan lab and first author of the paper. “As it turns out, this fold is capable of creating many more shapes than we imagined.”

Think surgical stents that can be packed flat and pop-up into three-dimensional structures once inside the body or dining room tables that can lean flat against the wall until they are ready to be used.

“The collapsibility, transportability and deployability of Miura-ori folded objects makes it a potentially attractive design for everything from space-bound payloads to small-space living to laparoscopic surgery and soft robotics,” said Dudte.

Here’s a .gif demonstrating the fold,

This spiral folds rigidly from flat pattern through the target surface and onto the flat-folded plane (Image courtesy of Mahadevan Lab) Harvard University

This spiral folds rigidly from flat pattern through the target surface and onto the flat-folded plane (Image courtesy of Mahadevan Lab) Harvard University

The news release offers some details about the research,

To explore the potential of the tessellation, the team developed an algorithm that can create certain shapes using the Miura-ori fold, repeated with small variations. Given the specifications of the target shape, the program lays out the folds needed to create the design, which can then be laser printed for folding.

The program takes into account several factors, including the stiffness of the folded material and the trade-off between the accuracy of the pattern and the effort associated with creating finer folds – an important characterization because, as of now, these shapes are all folded by hand.

“Essentially, we would like to be able to tailor any shape by using an appropriate folding pattern,” said Mahadevan. “Starting with the basic mountain-valley fold, our algorithm determines how to vary it by gently tweaking it from one location to the other to make a vase, a hat, a saddle, or to stitch them together to make more and more complex structures.”

“This is a step in the direction of being able to solve the inverse problem – given a functional shape, how can we design the folds on a sheet to achieve it,” Dudte said.

“The really exciting thing about this fold is it is completely scalable,” said Mahadevan. “You can do this with graphene, which is one atom thick, or you can do it on the architectural scale.”

Co-authors on the study include Etienne Vouga, currently at the University of Texas at Austin, and Tomohiro Tachi from the University of Tokyo. …

Here’s a link to and a citation for the paper,

Programming curvature using origami tessellations by Levi H. Dudte, Etienne Vouga, Tomohiro Tachi, & L. Mahadevan. Nature Materials (2016) doi:10.1038/nmat4540 Published online 25 January 2016

This paper is behind a paywall.

University of Malaya (Malaysia) and Harvard University (US) partner on nanomedicine/prevention projects

Unusually for a ‘nanomedicine’ project, the talk turned to prevention during a Jan. 10, 2016 teleconference featuring Dr. Noor Hayaty Abu Kasim of the University of Malaya and Dr. Wong Tin Wui of the Universiti Teknologi Malaysia and Dr. Joseph Brain of  Harvard University in a discussion about Malaysia’s major investment in nanomedicine treatment for lung diseases.

A Jan. 11, 2016 Malaysian Industry-Government Group for High Technology (MIGHT) news release on EurekAlert announces both the lung project (University of Malaya/Harvard University) and others under Malaysia’s NanoMITe (Malaysia Institute for Innovative Nanotechnology) banner,

Malaysian scientists are joining forces with Harvard University experts to help revolutionize the treatment of lung diseases — the delivery of nanomedicine deep into places otherwise impossible to reach.

Under a five-year memorandum of understanding between Harvard and the University of Malaya, Malaysian scientists will join a distinguished team seeking a safe, more effective way of tackling lung problems including chronic obstructive pulmonary disease (COPD), the progressive, irreversible obstruction of airways causing almost 1 in 10 deaths today.

Treatment of COPD and lung cancer commonly involves chemotherapeutics and corticosteroids misted into a fine spray and inhaled, enabling direct delivery to the lungs and quick medicinal effect. However, because the particles produced by today’s inhalers are large, most of the medicine is deposited in the upper respiratory tract.

The Harvard team, within the university’s T.H. Chan School of Public Health, is working on “smart” nanoparticles that deliver appropriate levels of diagnostic and therapeutic agents to the deepest, tiniest sacs of the lung, a process potentially assisted by the use of magnetic fields.

Malaysia’s role within the international collaboration: help ensure the safety and improve the effectiveness of nanomedicine, assessing how nanomedicine particles behave in the body, what attaches to them to form a coating, where the drug accumulates and how it interacts with target and non-target cells.

Led by Joseph Brain, the Cecil K. and Philip Drinker Professor of Environmental Physiology, the research draws on extensive expertise at Harvard in biokinetics — determining how to administer medicine to achieve the proper dosage to impact target cells and assessing the extent to which drug-loaded nanoparticles pass through biological barriers to different organs.

The studies also build on decades of experience studying the biology of macrophages — large, specialized cells that recognize, engulf and destroy target cells as part of the human immune system.

Manipulating immune cells represents an important strategy for treating lung diseases like COPD and lung cancer, as well as infectious diseases including tuberculosis and listeriosis.

Dr. Brain notes that every day humans breathe 20,000 litres of air loaded with bacteria and viruses, and that the world’s deadliest epidemic — an outbreak of airborne influenza in the 1920s — killed tens of millions.

Inhaled nanomedicine holds the promise of helping doctors prevent and treat such problems in future, reaching the target area more swiftly than if administered orally or even intravenously.

This is particularly true for lung cancer, says Dr. Brain. “Experiments have demonstrated that a drug dose administered directly to the respiratory tract achieves much higher local drug concentrations at the target site.”

COPD meanwhile affects over 235 million people worldwide and is on the rise, with 80% of cases caused by cigarette smoking. Exacerbated by poor air quality, COPD is expected to rise from 5th to 3rd place among humanity’s most lethal health problems by 2030.

“Nanotechnology is making a significant impact on healthcare by delivering improvements in disease diagnosis and monitoring, as well as enabling new approaches to regenerative medicine and drug delivery,” says Prof. Zakri Abdul Hamid, Science Advisor to the Prime Minister of Malaysia.

“Malaysia, through NanoMITe, is proud and excited to join the Harvard team and contribute to the creation of these life-giving innovations.”

While neither Dr. Abu Kasim nor Dr. Wong are included in the news release both are key members of the Malaysian team tasked to work on nanomedicines for lung disease. Dr. Abu Kasim is a professor of restorative dentistry at the University of Malaya and familiar with nanotechnology-enabled materials and nanoparticles through her work in that field. She is also the project lead for NanoMITe’s Project 4: Consequences of Smoking among the Malaysian Population. From the project webpage,

Smoking is a prevalent problem worldwide but especially so in Asia where nearly more than half of the world population reside. Smoking kills half of its users and despite the many documented harm to health is still a major problem. Globally six million lives are lost each year because of this addiction. This number is estimated to increase to ten million within the next two decades. Apart from the mortality, smokers are at increased risk of health morbidities of smoking which is a major risk factor for many non-communicable diseases (NCD) such as heart diseases, respiratory conditions and even mental health. Together, smoking reduces life expectancy 10-15 years compared to a non-smoker. Those with mental health lose double the years, 20 -25 years of their life as a result of their smoking. The current Malaysia death toll is at 10,000 lives per year due to smoking related health complications.

Although the health impact of smoking has been reported at length, this information is limited nationally. Lung cancer for example is closely linked to smoking, however, the study of the link between the two is lacking in Malaysia. Lung cancer particularly in Malaysia is also often diagnosed late, usually at stages 3 and 4. These stages of cancer are linked with a poorer prognosis. As a result to the harms to health either directly or indirectly, the World Health Organization (WHO) has introduced a legal treaty, the first, called the Framework Convention for Tobacco Control (FCTC). This treaty currently ratified by 174 countries was introduced in 2005 and consists of 38 FCTC Articles which are evidence based policies, known to assist member countries to reduce their smoking prevalence. Malaysia is an early signatory and early adopter of the MPOWER strategy which are major articles of the FCTC. Among them are education and information dissemination informing the dangers of smoking which can be done through awareness campaigns of advocacy using civil society groups. Most campaigns have focused on health harms with little mention non-health or environmental harm as a result of smoking. Therefore there is an opportunity to further develop this idea as a strong advocacy point towards a smoke-free generation in the near future

It is difficult impossible to recall any other nanomedicine initiative that has so thoroughly embedded prevention as part of its mandate. As Dr. Brain puts it, “Malaysia’s commitment to better health for everyone—sometimes, I’m jealous.”

Getting back to nanomedicine, it’s Dr. Wong, an associate professor in the school of pharmaceutics at Universiti Teknologi Malaysia (UTM), who is developing polymeric nanoparticles designed to carry medications into the lungs and Brain who will work on the best method of transport. From Dr. Brain’s webpage,

Dr. Brain’s research emphasizes responses to inhaled gases, particulates, and microbes. His studies extend from the deposition of inhaled particles in the respiratory tract to their clearance by respiratory defense mechanisms. Of particular interest is the role of lung macrophages; this resident cell keeps lung surfaces clean and sterile. Moreover, the lung macrophage is also a critical regulator of inflammatory and immune responses. The context of these studies on macrophages is the prevention and pathogenesis of environmental lung disease as well as respiratory infection.

His research has utilized magnetic particles in macrophages throughout the body as a non-invasive tool for measuring cell motility and the response of macrophages to various mediators and toxins. …

It was difficult to get any specifics about the proposed lung nanomedicine effort as it seems to be at a very early stage.

  • Malaysia through the Ministry of Higher Education with matching funds from the University of Malaya is funding this effort with 1M Ringgits ($300,00 USD) per year over five years for a total of 5M Ringgits ($1.5M USD)
  • A Malaysian researcher will be going to Harvard to collaborate directly with Dr. Brain and others on his team. The first will be Dr. Wong who will come to Harvard in June 2016 where he will work with his polymeric nanoparticles (vehicles for medications) and where Brain will examine transport strategies (aerosol, intrathecal administration, etc.) for those nanoparticle-bearing medications.
  • There will be a series of comparative studies of smoking in Malaysia and the US and other information efforts designed to support prevention strategies.

One last tidbit about research, Dr. Brain will be testing the nanoparticle-bearing medication once it has entered the lung using the ‘precision cut lung slices’ technique, as an alternative to some, if not all, in vivo testing.

Final comments

Nanomedicine is highly competitive and the Malaysians are interested in commercializing their efforts which according to Dr. Abu Kasim is one of the reasons they approached Harvard and Dr. Brain.

Should you find any errors please do let me know.

A bioinspired approach to self-healing materials

Scientists have been working to develop self-healing materials for a while now and a Jan. 8, 2016 news item on Nanowerk chronicles a relatively recent attempt,

Inspired by healing wounds in skin, a new approach protects and heals surfaces using a fluid secretion process. In response to damage, dispersed liquid-storage droplets are controllably secreted. The stored liquid replenishes the surface and completes the repair of the polymer in seconds to hours …

The fluid secretion approach to repair the material has also been demonstrated in fibers and microbeads. This bioinspired approach could be extended to create highly desired adaptive, resilient materials with possible uses in heat transfer, humidity control, slippery surfaces, and fluid delivery.

A December ??, 2015 US Department of Energy (DOE) news release, which originated the news item, expands on the theme,

A polymer that secretes stored liquid in response to damage has been designed and created to function as a self-healing material. While human-made material systems can trigger the release of stored contents, the ability to continuously self-adjust and monitor liquid supply in these compartments is a challenge. In contrast, biological systems manage complex protection and healing functions by having individual components work in concert to initiate and self-regulate a coordinated response. Inspired by biological wound-healing, this new process, developed by researchers at Harvard University, involves trapping and dispersing liquid-storage droplets within a reversibly crosslinked polymer gel network topped with a thin liquid overlayer. This novel approach allows storage of the liquid, yet is reconfigurable to induce finely controlled secretion in response to polymer damage. When the gel was damaged by slicing, the ruptured droplets in the immediate vicinity of the damage released oil and the gel network was squeezed. This squeezing allowed oil to be pushed out from neighboring droplets and the polymer network linkages to unzip and rezip rapidly, allowing just enough oil to flow to the damaged region. Healing occurred at ambient temperature within seconds to hours as fluid was secreted into the crack, severed polymer ends diffused across the gap, and new network linkages were created. Droplet-embedded polymers repaired faster or at lower temperatures than polymers without oil droplets. Also, the repaired droplet-embedded materials were much stronger than the repaired networks that did not contain the droplets. This dynamic liquid exchange to repair the material has also been demonstrated in other forms, showing the potential to extend this bioinspired approach for fabricating highly desired adaptive, resilient materials to a wide range of polymeric structures.

Here’s a link to and a citation for the paper,

Dynamic polymer systems with self-regulated secretion for the control of surface properties and material healing by Jiaxi Cui, Daniel Daniel, Alison Grinthal, Kaixiang Lin, & Joanna Aizenberg. Nature Materials 14,  790–795 (2015) doi:10.1038/nmat4325 Published online 22 June 2015

I’m not sure what occasioned a late push to promote this particular piece of research but if you are interested, the paper is behind a paywall.