Tag Archives: New York University

Do your physical therapy and act as a citizen scientist at the same time

I gather that recovering from a serious injury and/or surgery can require exercise regimens which help strengthen you but can be mind-numbingly boring. According to a Feb. 23, 30217 New York University Tandon School of Engineering news release (also on EurekAlert), scientists have found a way to make the physical rehabilitation process more meaningful,

Researchers at the NYU Tandon School of Engineering have devised a method by which patients requiring repetitive rehabilitative exercises, such as those prescribed by physical therapists, can voluntarily contribute to scientific projects in which massive data collection and analysis is needed.

Citizen science empowers people with little to no scientific training to participate in research led by professional scientists in different ways. The benefit of such an activity is often bidirectional, whereby professional scientists leverage the effort of a large number of volunteers in data collection or analysis, while the volunteers increase their knowledge on the topic of the scientific endeavor. Tandon researchers added the benefit of performing what can sometimes be boring or painful exercise regimes in a more appealing yet still therapeutic manner.

The citizen science activity they employed entailed the environmental mapping of a polluted body of water (in this case Brooklyn’s Gowanus Canal) with a miniature instrumented boat, which was remotely controlled by the participants through their physical gestures, as tracked by a low-cost motion capture system that does not require the subject to don special equipment. The researchers demonstrated that the natural user interface offers an engaging and effective means for performing environmental monitoring tasks. At the same time, the citizen science activity increased the commitment of the participants, leading to a better motion performance, quantified through an array of objective indices.

Visiting Researcher Eduardo Palermo (of Sapienza University of Rome), Post-doctoral Researcher Jeffrey Laut, Professor of Technology Management and Innovation Oded Nov, late Research Professor Paolo Cappa, and Professor of Mechanical and Aerospace Engineering Maurizio Porfiri provided subjects with a Microsoft Kinect sensor, a markerless human motion tracker capable of estimating three-dimensional coordinates of human joints that was initially designed for gaming but has since been widely repurposed as an input device for natural user interfaces. They asked participants to pilot the boat, controlling thruster speed and steering angle, by lifting one arm away from the trunk and using wrist motions, in effect, mimicking one widely adopted type of rehabilitative exercises based on repetitively performing simple movements with the affected arm. Their results suggest that an inexpensive, off-the-shelf device can offer an engaging means to contribute to important scientific tasks while delivering relevant and efficient physical exercises.

“The study constitutes a first and necessary step toward rehabilitative treatments of the upper limb through citizen science and low-cost markerless optical systems,” Porfiri explains. “Our methodology expands behavioral rehabilitation by providing an engaging and fun natural user interface, a tangible scientific contribution, and an attractive low-cost markerless technology for human motion capture.”

Caption: NYU Tandon researchers reported that volunteers who performed repetitive exercises while contributing as citizen scientists were more effective in their physical therapy motions. In the experiment, the volunteers controlled a small boat monitoring the polluted Gowanus Canal by performing hand and arm motions using the Microsoft Kinect motion capture system. Credit: NYU Tandon, PLoS ONE

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

A Natural User Interface to Integrate Citizen Science and Physical Exercise by Eduardo Palermo, Jeffrey Laut, Oded Nov, Paolo Cappa, Maurizio Porfiri. Public Library of Science (PLoS) http://dx.doi.org/10.1371/journal.pone.0172587 Published: February 23, 2017

This paper is open access.

Scientific evidence and certainty: a controversy in the US Justice system

It seems that forensic evidence does not deliver the certainty that television and US prosecutors (I wonder if Canadian Crown Attorneys or Crown Counsels concur with their US colleagues?) would have us believe. The US President’s Council of Advisors on Science and Technology (PCAST) released a report (‘Forensic Science in Criminal Courts: Ensuring Scientific Validity of Feature-Comparison Methods‘ 174 pp PDF) on Sept. 20, 2016 that amongst other findings, notes that more scientific rigour needs to be applied to the field of forensic science.

Here’s more from the Sept. 20, 2016 posting by Eric Lander, William Press, S. James Gates, Jr., Susan L. Graham, J. Michael McQuade, and Daniel Schrag, on the White House blog,

The study that led to the report was a response to the President’s question to his PCAST in 2015, as to whether there are additional steps on the scientific side, beyond those already taken by the Administration in the aftermath of a highly critical 2009 National Research Council report on the state of the forensic sciences, that could help ensure the validity of forensic evidence used in the Nation’s legal system.

PCAST concluded that two important gaps warranted the group’s attention: (1) the need for clarity about the scientific standards for the validity and reliability of forensic methods and (2) the need to evaluate specific forensic methods to determine whether they have been scientifically established to be valid and reliable. The study aimed to help close these gaps for a number of forensic “feature-comparison” methods—specifically, methods for comparing DNA samples, bitemarks, latent fingerprints, firearm marks, footwear, and hair.

In the course of its year-long study, PCAST compiled and reviewed a set of more than 2,000 papers from various sources, educated itself on factual matters relating to the interaction between science and the law, and obtained input from forensic scientists and practitioners, judges, prosecutors, defense attorneys, academic researchers, criminal-justice-reform advocates, and representatives of Federal agencies.

A Sept. 23, 2016 article by Daniel Denvir for Salon.com sums up the responses from some of the institutions affected by this report,

Under fire yet again, law enforcement is fighting back. Facing heavy criticism for misconduct and abuse, prosecutors are protesting a new report from President Obama’s top scientific advisors that documents what has long been clear: much of the forensic evidence used to win convictions, including complex DNA samples and bite mark analysis, is not backed up by credible scientific research.

Although the evidence of this is clear, many in law enforcement seem terrified that keeping pseudoscience out of prosecutions will make them unwinnable. Attorney General Loretta Lynch declined to accept the report’s recommendations on the admissibility of evidence and the FBI accused the advisors of making “broad, unsupported assertions.” But the National District Attorneys Association, which represents roughly 2,5000 top prosecutors nationwide, went the furthest, taking it upon itself to, in its own words, “slam” the report.

Prosecutors’ actual problem with the report, produced by some of the nation’s leading scientists on the President’s Council of Advisors on Science and Technology, seems to be unrelated to science. Reached by phone NDAA president-elect Michael O. Freeman could not point to any specific problem with the research and accused the scientists of having an agenda against law enforcement.

“I’m a prosecutor and not a scientist,” Freeman, the County Attorney in Hennepin County, Minnesota, which encompasses Minneapolis, told Salon. “We think that there’s particular bias that exists in the folks who worked on this, and they were being highly critical of the forensic disciplines that we use in investigating and prosecuting cases.”

That response, devoid of any reference to hard science, has prompted some mockery, including from Robert Smith, Senior Research Fellow and Director of the Fair Punishment Project at Harvard Law School, who accused the NDAA of “fighting to turn America’s prosecutors into the Anti-Vaxxers, the Phrenologists, the Earth-Is-Flat Evangelists of the criminal justice world.”

It has also, however, also lent credence to a longstanding criticism that American prosecutors are more concerned with winning than in establishing a defendant’s guilt beyond a reasonable doubt.

“Prosecutors should not be concerned principally with convictions; they should be concerned with justice,” said Daniel S. Medwed, author of “Prosecution Complex: America’s Race to Convict and Its Impact on the Innocent” and a professor at Northern University School of Law, told Salon. “Using dodgy science to obtain convictions does not advance justice.”

Denvir’s article is lengthier and worth reading in its entirety.

Assuming there’s an association of forensic scientists, I find it interesting they don’t appear to have responded.

Finally, if there’s one thing you learn while writing about science it’s that there is no real certainty. For example, if you read about the Higgs boson discovery, you’ll note that the scientists involved the research never stated with absolute certainty that it exists but rather they ‘were pretty darn sure’ it does (I believe the scientific term is 5-sigma). There’s more about the Higgs boson and 5-sigma in this July 17, 2012 article by Evelyn Lamb for Scientific American,

In short, five-sigma corresponds to a p-value, or probability, of 3×10-7, or about 1 in 3.5 million. This is not the probability that the Higgs boson does or doesn’t exist; rather, it is the probability that if the particle does not exist, the data that CERN [European Particle Physics Laboratory] scientists collected in Geneva, Switzerland, would be at least as extreme as what they observed. “The reason that it’s so annoying is that people want to hear declarative statements, like ‘The probability that there’s a Higgs is 99.9 percent,’ but the real statement has an ‘if’ in there. There’s a conditional. There’s no way to remove the conditional,” says Kyle Cranmer, a physicist at New York University and member of the ATLAS team, one of the two groups that announced the new particle results in Geneva on July 4 [2012].

For the interested, there’s a lot more to Lamb’s article.

Getting back to forensic science, this PCAST report looks like an attempt to bring forensics back into line with the rest of the science world.

Minimalist DNA nanodevices perform bio-analytical chemistry inside live cells

A comparison of minimalist versus baroque architecture is one of the more startling elements in this March 24, 2016 news item on Nanowerk about a scientist working with DNA (deoxyribonucleic acid) nanodevices,

Some biochemistry laboratories fashion proteins into complex shapes, constructing the DNA nanotechnological equivalent of Baroque or Rococo architecture. Yamuna Krishnan, however, prefers structurally minimalist devices.

“Our lab’s philosophy is one of minimalist design,” said Krishnan, a professor of chemistry at the University of Chicago. “It borders on brutalist. Functional with zero bells and whistles. There are several labs that design DNA into wonderful shapes, but inside a living system, you need as little DNA as possible to get the job done.”

That job is to act as drug-delivery capsules or as biomedical diagnostic tools.

A March 24, 2016 University of Chicago news release by Steve Koppes, which originated the news item, provides some background information before launching into the latest news,

In 2011, Krishnan and her group, then at the National Centre for Biological Sciences in Bangalore, India, became the first to demonstrate the functioning of a DNA nanomachine inside a living organism. This nanomachine, called I-switch, measured subcellular pH with a high degree of accuracy. Since 2011, Krishnan and her team have developed a palette of pH sensors, each keyed to the pH of the target organelle.

Last summer, the team reported another achievement: the development of a DNA nanosensor that can measure the physiological concentration of chloride with a high degree of accuracy.

“Yamuna Krishnan is one of the leading practitioners of biologically oriented DNA nanotechnology,” said Nadrian Seeman, the father of the field and the Margaret and Herman Sokol Professor of Chemistry at New York University. “These types of intracellular sensors are unique to my knowledge, and represent a major advance for the field of DNA nanotechnology.”

Chloride sensor

Chloride is the single most abundant, soluble, negatively charged molecule in the body. And yet until the Krishnan group introduced its chloride sensor—called Clensor—there was no effective and practical way to measure intracellular stores of chloride.

“What is especially interesting about this sensor is that it is completely pH independent,” Seeman said, a significant departure from Krishnan’s previous scheme. “She spent a number of years developing pH sensors that work intra-cellularly and provide a fluorescent signal as a consequence of a shift in pH.”

The ability to record chloride concentrations is important for many reasons. Chloride plays an important role in neurobiology, for example. But calcium and sodium—both positively charged ions—tend to grab most of the neurobiological glory because of their role in neuron excitation.

“But if you want your neuron to fire again, you have to bring it back to its normal state. You have to stop it firing,” Krishnan said. This is called “neuronal inhibition,” which chloride does.

“It’s important in order to reset your neuron for a second round of firing, otherwise we would all be able to use our brains only once,” she said.

Under normal circumstances, the transport of chloride ions helps the body produce thin, freely flowing mucus. But a genetic defect results in a life-threatening disease: cystic fibrosis. Clensor’s capacity to measure and visualize protein activity of molecules like the one related to cystic fibrosis transmembrane could lead to high-throughput assays to screen for chemicals that would restore normal functioning of the chloride channel.

Nine diseases

“One could use this to look at chloride ion channel activity in a variety of diseases,” Krishnan said. “Humans have nine chloride ion channels, and the mutation of each of these channels results in nine different diseases.” Among them are osteopetrosis, deafness, muscular dystrophy and Best’s macular dystrophy.

The pH-sensing capabilities of the I-switch, meanwhile, are important because cells contain multiple organelles that maintain specific values of acidity. Cells need these different microenvironments to carry out specialized chemical reactions.

“Each subcellular organelle has a specific resting value of acidity, and that acidity is crucial to its function,” Krishnan said. “When the pH is not the value that it’s meant to be, it results in a range of different diseases.”

There are 70 rare diseases called lysosomal storage disorders, which are progressive and often fatal. Each one—including Batten disease, Niemann-Pick disease, Pompe disease and Tay-Sachs disease—represents a different way a lysosome can go bad. She likened a defective lysosome to a garbage bin that never gets emptied.

“The lysosome is basically responsible for chewing up all the garbage and making sure it’s either reused or got rid of. It’s the most acidic organelle in the cell.” And that acidity is crucial for the degradation process.

Although there are 70 lysosomal storage diseases, small molecule drugs are available for only a few of them. These existing treatments—enzyme-replacement therapies—are expensive and are only palliative treatments. One goal of Krishnan’s group is to demonstrate the utility of their pH sensors to discover new biological insights into these diseases. Developing small molecule drugs—which are structurally simpler and easier to manufacture than traditional biological drugs—could help significantly.

“If we can do this for one or two lysosomal diseases, there’ll be hope for the other 68,” Krishnan said.

Here are links to and citations for the 2015 and 2011 papers,

A pH-independent DNA nanodevice for quantifying chloride transport in organelles of living cells by Sonali Saha, Ved Prakash, Saheli Halder, Kasturi Chakraborty, & Yamuna Krishnan. Nature Nanotechnology 10, 645–651 (2015)  doi:10.1038/nnano.2015.130 Published online 22 June 2015

An autonomous DNA nanomachine maps spatiotemporal pH changes in a multicellular living organism by Sunaina Surana, Jaffar M. Bhat, Sandhya P. Koushika, & Yamuna Krishnan. Nature Communications 2, Article number: 340  doi:10.1038/ncomms1340 Published 07 June 2011

The 2015 paper is behind a paywall but the 2011 paper is open access.

Mathematicians, political scientists, and cake cutting

If you have a sibling, you’ve likely fought at least once over who got the biggest or ‘best’ piece of cake.  (I do and I did.) In any event, it seems that mathematicians and political scientists have been working on a scheme to avoid disputes over cake.

[downloaded from http://link.springer.com/article/10.1007%2Fs00283-013-9442-0#page-1]

A July 16, 2014 Springer news release (also on EurekAlert) describes the quest for fairly sized cake slices and how that might apply to real life issues such as sharing property,

The next time your children quibble about who gets to eat which part of a cake, call in some experts on the art of sharing. Mathematician Julius Barbanel of Union College, and political scientist Steven Brams of New York University, both in the US, published an algorithm in Springer’s The Mathematical Intelligencer by which they show how to optimally share cake between two people efficiently, in equal pieces and in such a way that no one feels robbed.

The cut-and-choose method to share divisible goods has been regarded as fair and envy-free since Biblical times, when Abraham divided land equally, and Lot could choose the part he wanted. But being free of envy is not the only consideration when sharing something. What happens when more than two cuts can be made, or when people prefer different, specific sections of whatever is to be divided? Barbanel and Brams believe that with a giveback procedure it is possible to make a perfect division between two people that is efficient, equitable and void of jealousy.

An objective referee (such as a Mom or a computer) is essential to the plan. The potential cake eaters first tell the referee which parts of the delicacy they value most. In mathematical terms these are called someone’s probability density functions, or pdfs. The referee then marks out the cake at all points were the pdfs of the disgruntled would-be cake eaters cross, and assigns portions. If at this point the two parties receive the same size of cake, the task is over. If not, the giveback process starts.

The party who received the larger part of the cake during the first round must give a part of it back to the other person, starting with those parts in which the ratio of their pdfs is the smallest. This goes on until the parties value their portions equally, and have the same volume of cake to eat. This method only works with a finite number of cuts if the players’ pdfs are straight-lined, or are so-called piecewise linear sections.

The researchers believe the method can be used to share cake and other divisible goods such as land. In the case of beachfront property being co-owned by two developers, for example, it can help to determine who gets what strips of land to build on based on the pieces of land they value most.

“This allocation is not only equitable but also envy-free and efficient – that is, perfect,” says Barbanel.

“This approach focuses on proving the existence of efficient and envy-free divisions, not on providing algorithms to finding them,” emphasizes Brams.

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

Two-Person Cake Cutting: The Optimal Number of Cuts by Julius B. Barbanel and Steven J. Brams. The Mathematical Intelligencer March 2014 DOI 10.1007/s00283-013-9442.

This paper is behind a paywall although there is a free preview available and a special summer discount (30%) on the purchase price until July 31, 2014.

Dental implants with a surface that affects genetic cellular expression

Intra-Lock International is trumpeting in triumph in the wake  of a study noting their OSSEAN-surfaced dental implants promote better bone-healing than an alternative used for comparison. From the June 10, 2014 news item on Azonano,

As reported in the internationally renowned scientific journal, Bone [in press for Aug. 2014], a research team from New York University [NYU] has confirmed what scientific developers at Intra-Lock® International, Inc. have known for several years: the fractal, nano-rough OSSEAN® surface developed for their dental implants actually changes the cellular genetic expression – or the fate of stem cells – at the nano-level, which in turn induces faster healing of implants.

A June 9, 2014 Intra-Lock news release, which originated the new item, describes what usually occurs when an implant is first situated in the tissue (cellular confusion) and how the OSSEAN surface affects the ‘confusion’,

Typically, when an implant is surgically placed, there is a period of cellular “confusion” and chaos around the implant, and usually a little bone resorbs before being formed again. The implant is then at risk from the moment it is inserted through the time when the bone is healed around it – a time period Giorno [Thierry M. Giorno, DDS, director of research and development, and CEO of Intra-Lock®, International] refers to as “the window of negative opportunity.”

However, the NYU researchers found that bone cells immediately start clustering around the OSSEAN implants and begin accelerated healing, with little confusion whatsoever.

This occurs primarily due to the biomimetic structure of the OSSEAN surface, designed and classified as nanorough and fractalii. Mimicking nature at the nano-level, the OSSEAN surface repeats a similar structural pattern to that of natural bone over and over, essentially “tricking” the body into accepting the implant as a natural substance and igniting the healing process far sooner than would occur with an artificial substance, which is smooth at the nano-level and without natural-seeming pattern repetition.

Typically, with an implant of any sort, whether it’s a dental implant in your jaw or a titanium rod in your leg, several weeks will pass before the bone begins to grow around it. During this time lapse, known as the “catabolic phase,” there can be great risk and instability with the implant.

Naturally, compressing the healing time and accelerating the degree of osseointegration – the merging of implant and bone – are highly desirable outcomes, and implants with an OSSEAN can provide a faster healing process, which thereby reduces patient discomfort and provides a higher potential for successful long-term results with the implant.

“If you’ve ever had dental implants, you can appreciate the outcomes the OSSEAN surface provides,” said Giorno. “The healing process has changed forever, and future patients with an OSSEAN surface implant can look forward to reduced complications, overall.”

Looking further into the future, Giorno said, “I believe the effects of OSSEAN can potentially revolutionize the implant industry beyond dentistry and into all types of orthopedics where patients must wait for their bodies to accept a foreign substance. With OSSEAN, the wait is over.”

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

Nanometer-scale features on micrometer-scale surface texturing: A bone histological, gene expression, and nanomechanical study by Paulo G. Coelho, Tadahiro Takayama, Daniel Yoo, Ryo Jimboemail, Sanjay Karunagaran, Nick Tovar, Malvin N. Janal, and Seiichi Yamano. Bone, Issue 65, Aug. 2014. Bone (2014) DOI: http://dx.doi.org/10.1016/j.bone.2014.05.004 Published Online: May 07, 2014

This article is behind a paywall. You can find out more about Intra-Lock and OSSEAN here.

New York University/Caltech grant is part of the NSF’s Origami Design for Integration of Self-assembling Systems for Engineering Innovation (ODISSEI) program

The US National Science Foundation (NSF) has an origami program,  Origami Design for Integration of Self-assembling Systems for Engineering Innovation (ODISSEI), which recently announced a $2M grant to New York University (NYU) and the California Institute of Technology (Caltech) to create new nanomaterials according to an Aug. 6, 2013 news item on Nanowerk,

The National Science Foundation (NSF) has awarded New York University researchers and their colleagues at the California Institute of Technology (Caltech) a $2 million grant to develop cutting-edge nanomaterials that hold promise for improving the manufacturing of advanced materials, biofuels, and other industrial products.

Under the grant, the scientists will develop biomimetic materials with revolutionary properties—these molecules will self-replicate, evolve, and adopt three-dimensional structures a billionth of a meter in size by combining DNA-guided self-assembly with the centuries-old art of origami folding.

The Aug. 5, 2013 NYU press release, which originated the news item,  provides details about the researchers and the project,

The four-year grant is part of the NSF’s Origami Design for Integration of Self-assembling Systems for Engineering Innovation (ODISSEI) program and includes NYU Chemistry Professors Nadrian Seeman and James Canary and NYU Physics Professor Paul Chaikin. They will team up with Caltech’s William A. Goddard, III and Si-ping Han.

Others involved in the project are molecular biologists John Rossi and Lisa Scherer of City of Hope Medical Center and mathematicians Joanna Ellis-Monaghan and Greta Pangborn of Saint Michael’s College in Vermont.

The work will build upon recent breakthroughs in the field of structural DNA nanotechnology, which Seeman founded more than three decades ago and is now pursued by laboratories across the globe. His creations allow him to arrange pieces and form specific molecules with precision—similar to the way a robotic automobile factory can be told what kind of car to make.

Previously, Seeman has created three-dimensional DNA structures, a scientific advance bridging the molecular world to the world where we live. To do this, he and his colleagues created DNA crystals by making synthetic sequences of DNA that have the ability to self-assemble into a series of 3D triangle-like motifs. The creation of the crystals was dependent on putting “sticky ends”—small cohesive sequences on each end of the motif—that attach to other molecules and place them in a set order and orientation. The make-up of these sticky ends allows the motifs to attach to each other in a programmed fashion.

Recently, the Seeman and Chaikin labs teamed up to develop artificial structures that can self-replicate, a process that has the potential to yield new types of materials. In the natural world, self-replication is ubiquitous in all living entities, but artificial self-replication had previously been elusive. Their work marked the first steps toward a general process for self-replication of a wide variety of arbitrarily designed “seeds”. The seeds are made from DNA tile motifs that serve as letters arranged to spell out a particular word. The replication process preserves the letter sequence and the shape of the seed and hence the information required to produce further generations. Self-replication enables the evolution of molecules to optimize particular properties via selection processes.

Under the NSF grant, the researchers will aim to take these innovations to the next level: the creation of self-replicating 3D arrays. To do so, the collaborators will aim to fold replicating 1D and 2D arrays into 3D shapes in a manner similar to paper origami—a complex and delicate process.

In meeting this challenge, they will adopt tools from graph theory and origami mathematics to develop algorithms to direct self-assembling DNA nanostructures and their origami folds. The mathematical component of the endeavor will be supplemented by the artistic expertise of Portland, Ore.-based sculptor Julian Voss-Andreae, who will advise the team on issues related to design and will use his skills to develop life-size physical models of the nanoscopic structures the scientists are seeking to build. [emphasis mine]

I wasn’t expecting to see a sculptor included in the team and I wonder if there might be plans to use his sculptures not only as models but also in exhibitions and art shows to fulfill any science outreach requirements that the NSF might have for its grantees.

I did a little further digging into the NSF’s ‘origami’ program and found this webpage explaining that ‘origami’ is part of a still larger program,

The Emerging Frontiers in Research and Innovation (EFRI) office awarded 15 grants in FY 2012, including the following 8 on the topic of Origami Design for Integration of Self-assembling Systems for Engineering Innovation (ODISSEI): …

As there wasn’t any information about grants for FY 2013, I gather they haven’t had time to update the page or add any recent news releases to the website.

Looking at glass on the molecular scale

Glass isn’t transparent (at the molecular scale) as it’s cooling and scientists have been curious about this transition from liquid to glass state. According to an Oct. 15, 2012 posting by Carol Clark for Emory University’s eScienceCommons, a team from Emory University (and New York University)  has cracked this mystery. First, here’s more about the mystery (from Clark’s article)

Scientists fully understand the process of water turning to ice. As the temperature cools, the movement of the water molecules slows. At 32 F, the molecules lock into crystal lattices, solidifying into ice. In contrast, the molecules of glasses do not crystallize.The movement of the glass molecules slows as the temperature cools, but they never lock into crystal patterns. Instead, they jumble up and gradually become glassier, or more viscous. No one understands exactly why.

The phenomenon leaves physicists to ponder the molecular question of whether glass is a solid, or merely an extremely slow-moving liquid.

This purely technical physics question has stoked a popular misconception: That the glass in the windowpanes of some centuries-old buildings is thicker at the bottom because the glass flowed downward over time.

“The real reason the bottom is thicker is because they hadn’t yet learned how to make perfectly flat panes of glass,” Weeks says [Emory physicist Eric Weeks]. “For practical purposes, glass is a solid and it will not flow, even over centuries. But there is a kernel of truth in this urban legend: Glasses are different than other solid materials.”

Speaking more technically about the transition,

“Cooling a glass from a liquid into a highly viscous state fundamentally changes the nature of particle diffusion,” says Emory physicist Eric Weeks, whose lab conducted the research. “We have provided the first direct observation of how the particles move and tumble through space during this transition, a key piece to a major puzzle in condensed matter physics.”

Weeks specializes in “soft condensed materials,” substances that cannot be pinned down on the molecular level as a solid or liquid, including everyday substances such as toothpaste, peanut butter, shaving cream, plastic and glass.

The scientists have prepared a video animation of what they believing is occurring as glass cools (no sound),

Here’s what the movie depicts (from the Clark article),

The movie and data from the experiment provide the first clear picture of the particle dynamics for glass formation. As the liquid grows slightly more viscous, both rotational and directional particle motion slows. The amount of rotation and the directional movements of the particles remain correlated.

“Normally, these two types of motion are highly coupled,” Weeks says. “This remains true until the system reaches a viscosity on the verge of being glass. Then the rotation and directional movements become decoupled: The rotation starts slowing down more.”

He uses a gridlocked parking lot as an analogy for how the particles are behaving. “You can’t turn your car around, because it’s not a sphere shape and you would bump into your neighbors. You have to wait until a car in front of you moves, and then you can drive a bit in that direction. This is directional movement, and if you can make a bunch of these, you may eventually be able to turn your car. But turning in a crowded parking lot is still much harder than moving in a straight line.”

There’s more about the work and team in Clark’s article. H/T to the Oct. 16, 2012 news item on Nanowerk for alerting me to this work. You can find the article the researchers have written at the Proceedings of the National Academy of Sciences (PNAS),

Decoupling of rotational and translational diffusion in supercooled colloidal fluids by Kazem V. Edmond, Mark T. Elsesser, Gary L. Hunter, David J. Pine, and Eric R. Weeks. Published online before print October 15, 2012, doi: 10.1073/pnas.1203328109 PNAS October 15, 2012

The article is behind a paywall.