March 09, 2010
How the human genome folds in 3-D![]() Erez Lieberman-Aiden G invented a way to find out how the genome folds.
By Ana Lyons
Until recently, the process of how genomic DNA neatly folds itself into the nucleus of a cell — twisting and contorting into a work of astonishingly compact molecular origami — had perplexed biologists. How Hi-C Works
To develop the “Hi-C” method — which constructs three-dimensional maps of entire genomes — Lieberman-Aiden worked with postdoctoral student Nynke van Berkum of UMass Medical School, and their advisors Eric S. Lander and Job Dekker. The team also collaborated with Leonid Mirny’s group (in the MIT Department of Physics and Harvard-MIT Division of Health Sciences and Technology) as well as graduate student Maksim V. Imakaev to simulate of the dynamic behavior of the fractal globule. Local biochemical vs. global spatial modifications
“A very interesting idea at the core [of this research] is that all cells have the same genome, but perform very different functions,” Lieberman-Aiden said. “There’s an incredible variety of functions among cells, despite them all having the same information.” Human genome is organized like a library…made of ramen Lieberman-Aiden’s and his team also zoomed in further, examining how the genome folds at the scale of a megabase, or one million of the genome’s biochemical ‘letters’. The question was: “How does this megabase fold up?” Peano curves appear in genome
Lieberman-Aiden’s research showed that the human genome likely forms fractal-like structures, but that’s only the half of it. Influence of cross-training in math and physics Before coming to MIT as a graduate student, Lieberman-Aiden studied mathematics, physics, and philosophy at Princeton as an undergrad. |
March 09, 2010
Charles P. Thacker Named Recipient of 2009 ACM A.M. Turing Award![]() Photo Courtesy of the NAE ACM has named Charles P. Thacker the recipient of the 2009 ACM A.M. Turing Award for his pioneering design and realization of the Alto, the first modern personal computer, and the prototype for networked personal computers. Alto incorporated bitmap (TV-like) displays, which enable modern graphical user interfaces (GUIs), including What You See Is What You Get (WYSIWYG) editors. Thacker's design, which he built while at Xerox PARC (Palo Alto Research Center), reflected a new vision of a self-sufficient, networked computer on every desk, equipped with innovations that are standard in today's models. Dr. Thacker is also recognized for his contributions to the Ethernet local area network, the "interconnection fabric" that allows multiple digital devices such as workstations, printers, scanners, file servers, and modems to communicate with each other. Today's Ethernets, which are thousands of times faster than the original version, have become the dominant local area networking technology. He also designed the first multiprocessor workstation, and the prototype for today's most used tablet PC, with its capabilities for direct user interaction. The ACM A.M. Turing Award is ACM's most prestigious technical award. It recognizes contributions of lasting and major technical importance, and honors individuals whose work has advanced the field of computing. First presented in 1966, and named for British mathematician Alan M. Turing, the Turing Award is widely considered to be the "Nobel Prize in Computing." It carries a $250,000 prize, with financial support provided by Intel Corporation and Google Inc. Learn more, read the ACM Press Release or visit the ACM A.M. Turing Award site. Charles P. Thacker Named Recipient of 2009 ACM A.M. Turing Award |
March 09, 2010
Model Offers Better Understanding Of Embryonic DevelopmentPosted on: Tuesday, 9 March 2010, 10:52 CST A mathematical model developed at Purdue University can predict complex signaling patterns that could help scientists determine how stem cells in an embryo later become specific tissues, knowledge that could be used to understand and treat developmental disorders and some diseases. During embryonic development, proteins attach to cell receptors and start a cascade of reactions. Understanding those reactions is difficult, however, because feedback signals go back out to the proteins or other molecules along the cascade, constantly changing the reaction pattern. The outcomes of those reactions and the feedback mechanisms - or inputs - are known because they can be observed, but how the inputs lead to the outputs isn't understood. "We want to understand how stem cells become tissue-specific so that we can manipulate that process to create cells that could be used to treat injuries and diseases," said David Umulis, a Purdue assistant professor of agricultural and biological engineering. "Using a model approach, we can simulate these complex signaling patterns to get a better handle on the process." Umulis created a model that predicted accurate outcomes when different feedback mechanisms were inserted. His results were published in the current issue of the journal Developmental Cell. "Fruit fly embryos are a fantastic system to peer into early development since input/output relationships are easy to observe. You have a mutation and an output, but we don't typically know what happens in the middle," he said. "Realistic model embryos proved an additional tool that can be used to aid in that understanding. Models can link that cause and effect." The study looked at fruit fly, or drosophila, embryos during very early development to decipher what controls the differentiation of these stem cells at their proper locations. During the process, cells take on identities that later specify tissue types in the adult organism. Before directional cues dictate development, the stem cells are capable of becoming many different tissues. Using models to analyze the dynamic signals the cells are receiving may help to better understand how to control similar cells in a laboratory setting. Umulis said his model is a sort of template to allow researchers to test a number of hypotheses before conducting actual experiments. The information garnered from realistic 3-D models can guide the process and facilitate rapid discovery. Umulis' next step is to count the number of molecules needed to initiate specific cell responses during embryonic development. The National Institutes of Health and Purdue University funded his work. Writer: Brian Wallheimer, Purdue University |
March 09, 2010
Leaf veins inspire a new model for distribution networks![]() Veins’ looped network allows water and nutrients to flow around an injury (green dot) on the main vein of a lemon leaf. Credit: E. Katifori et al/PRL 2010 Posted: February 9, 2010
A straight line may be the shortest path from A to B, but it’s not always the most reliable or efficient way to go. In fact, depending on what’s traveling where, the best route may run in circles, according to a new model that bucks decades of theorizing on the subject. A team of biophysicists at Rockefeller University developed a mathematical model showing that complex sets of interconnecting loops — like the netted veins that transport water in a leaf — provide the best distribution network for supplying fluctuating loads to varying parts of the system. It also shows that such a network can best handle damage. The findings could change the way engineers think about designing networks to handle a variety of challenges like the distribution of water or electricity in a city. |
March 09, 2010
The mutual inspiration of art and mathematicswww.sciencenews.org By Julie Rehmeyer Web edition : Saturday, March 6th, 2010
Mathematics is art, and art is mathematics. So claim the father-son pair of Erik and Martin Demaine of the Massachusetts Institute of Technology in Cambridge. “Our math and our art have blended together so much we can’t tell them apart anymore,” Martin Demaine says. |
March 09, 2010
Mathematician, longtime Vanderbilt professor Charles K. Megibben dies![]() Charles K. Megibben 3/5/2010 10:12 am
Charles K. Megibben, who played a major role in developing the mathematics department of Vanderbilt University into a major research center, has died. He was 73.
Survivors include wife Dottie Megibben, four sons, one daughter, one brother, nieces, nephews, grandchildren and great-grandchildren. Mathematician, longtime Vanderbilt professor Charles K. Megibben dies |
March 09, 2010
BWW REVIEWS: PARTITION - Play By The NumbersIn playwright Ira Hauptman's work, "Partition," British mathematician Harold Hardy explains "partition theory" as the number of ways one may express a whole number through the addition of other whole numbers. By way of example, the partition of 3 is 3: there's 3+0, 2+1, and 1+1+1. Three ways to get to three. Partition theory might seem to give credence to the notion that the whole cannot be more than the sum of its parts...for no matter how you break down "three," it is never more or less than three. Of course, this works fine with integers, but people...that's another matter. There is much "numerical" about Hauptman's play which is based on real-life figures G. Harold Hardy who, in 1914, took it upon himself to mentor a young Indian named Srinivasa Iyengar Ramanujan. Ramanujan was working as a clerk (as it seems the fate of such geniuses...Einstein anyone?) when he caught Hardy's attention, sending the Cambridge University scholar samples of his theorems. As Wikipedia relates, Ramanujan "became a Fellow of the Royal Society and a Fellow Trinitiy College, Cambridge" before "dying of illness, malnutrition and possibly liver infection in 1920 at the age of 32." That's the historical framework of the play. Ivan Zizek plays Hardy and Maboud "E" Ebrahimzadeh portrays Ramanujan; there is also intermittent appearances by Pierre de Fermat, a 17th century lawyer and amateur mathematician who is considered one of the progenitors of modern calculus. His famed "Last Theorem" left the wreckage of more than three centuries' worth of frustrated mathematicians in its wake, all trying in vain to prove it (it finally would be proven in 1995). Actor Thom Eric Sinn plays Fermat as a comic, pompous, mischievous, Rene DesCartes-hating soul who purposely destroyed his copy of the theorem's proof as a white-glove-cross-the-face to the generations to follow. Proving Fermat's Theory becomes a tragic quest for Ramanujan, who accepts the challenge at his mentor's request and pursues it obsessively, perhaps due to mental illness, due to cultural and religious beliefs, a sense of personal honor or simply because he could not stop. Hardy claims that while Ramanujan's ability to delve new theorems is "Hopp's class" (named for a top cricketer of the time), his protégé is only "half a mathematician" for he is not adept at developing proofs. "What good are theorems you cannot prove?" Hardy asks, a mindset shaped by proper English pragmatism. It is ironic, as Hardy speaks before an assembly of Royal Society of mathematicians, claiming that "applied mathematics is not real mathematics at all," that the true beauty of mathematics lies in its "utter uselessness." He quotes Oscar Wilde, "Art is for art's sake," then claims that math should be "for art's sake" as well. One senses that this is how Ramanujan looks at math. Theorems are the stuff of dreams, quite literally, as the Hindu goddess, Namagiri Lakshmi (Devika Bhise) visits Ramanujan while he sleeps, leaving him the poetry of mathematics on his tongue so it is "the first thing he tastes" when he awakens the next day. Ebrahimzadeh portrays Ramanujan as a man pulled by forces beyond his own control. He cannot care properly for himself, and is visited by Namagiri who is more mother hen than goddess, clucking about Ramanujan's missing blanket and shoes like a soccer Mom dealing with an eternally distracted, messy teenager. Ramanujan's ability with numbers is simply a gift, something that flows from him, but in which he seems to have no personal interest. There are no passages where Ramanujan explains his affinity with numbers or if they mean anything at all to him. One senses that if Namagiri had left him recipes on his tongue, he'd have been sending instructions on how to make the perfect flourless chocolate torte to Julia Child. As the title of the play suggests, there are many "partitions" in this play; partitions not only between the characters who are separated by class, culture and ethnicity, but partitions within the characters themselves. Zizek does an exceptionally good job in this regard, as his Hardy seems at odds with everything, clashing with his friend, Alfred (Fred Nelson), the police (Andrew Keating as Police Officer) and Ramanujan. Zizek plays Hardy as perpetually stiff, moving and speaking in a halting manner as if his mouth can't keep up with his brain. Hardy definitely comes across as a mathematician, that is, a man much more comfortable in the company of algebraic formulas than human beings. Nelson's Alfred is the humanist in this particular theatrical equation; unlike Hardy and Ramanajan, the character of AlFred Billington is a creation of the playwright, though is based "on members of the Cambridge University Apostles Society, especially the classics scholars John T. Sheppard and Henry Jackson," according to director John Sadowsky's "Director's Notes." While Zizek's Hardy moves about like a man wearing starched underwear too sizes too small, Nelson's Alfred lumbers like a likeable bear; his speech, like his attitude, friendly, smooth, and warm. Alfred is not afraid to show his emotions, and does so, particularly when he senses what might be Ramanujan's ultimate fate. As is typical of a Spotlighers production, less is more, as director Sadowsky manages to transform the theater's intimate stage into a university assembly hall, a train station, Ramanujan's sparse room, and more. "Partition" continues its run at The Spotlighters, 817 St. Paul Street in downtown Baltimore, now through March 28th. For more information, call 410-752-1225 or visit www.spotlighters.org. |
March 09, 2010
All is set for event to boost interest in mathBy Beniel Seka
When you mention ‘Pi-Day’, many people may ask: What is it about? Who discovered it?
Mr Beniel Seka is a freelance writer. |
March 02, 2010
The Mathematics Of Cancer![]() Larry Norton 02.25.10, 08:40 AM EST Forbes Magazine dated March 15, 2010
Larry Norton sees some of the toughest cases as deputy physician-in-chief for breast cancer at Memorial Sloan-Kettering Cancer Center. He has access to the most advanced imaging machines, the best surgeons and numerous new tumor-fighting drugs. But often the fancy technology helps only temporarily. Sometimes a big tumor will shrink dramatically during chemotherapy. Then all of a sudden it comes back in seven or eight locations simultaneously. |
March 02, 2010
Fill in the Blanks: Using Math to Turn Lo-Res Datasets Into Hi-Res Samples![]() Using a mathematical concept called sparsity, the compressed-sensing algorithm takes lo-res files and transforms them into sharp images. Illustration: Gabriel Peyre By Jordan Ellenberg February 22, 2010 | 12:00 pm | Wired March 2010
In the early spring of 2009, a team of doctors at the Lucile Packard Children’s Hospital at Stanford University lifted a 2-year-old into an MRI scanner. The boy, whom I’ll call Bryce, looked tiny and forlorn inside the cavernous metal device. The stuffed monkey dangling from the entrance to the scanner did little to cheer up the scene. Bryce couldn’t see it, in any case; he was under general anesthesia, with a tube snaking from his throat to a ventilator beside the scanner. Ten months earlier, Bryce had received a portion of a donor’s liver to replace his own failing organ. For a while, he did well. But his latest lab tests were alarming. Jordan Ellenberg (ellenber@math.wisc.edu), an associate professor of mathematics at the University of Wisconsin, wrote about the Netflix Prize in issue 16.03. Fill in the Blanks: Using Math to Turn Lo-Res Datasets Into Hi-Res Samples |
March 02, 2010
OKIE IN EXILE: My life as a scientistBy BOBBY WINTERS The Morning Sun Posted Mar 01, 2010 @ 11:26 PM PITTSBURG —
When I was a little boy, I wanted to be a scientist. More specifically, I wanted to be the Professor on Gilligan’s Island. (There was just something about Ginger...) I took all of the science that we had at dear old McLish High School, which wasn’t all that much. There was biology and chemistry, and that was it. The chemistry I had as a senior was the last chemistry course I ever had. Bobby Winters is Assistant Dean of the College of Arts and Sciences, Professor of Mathematics, and Acting Chair of the Department of Chemistry at Pittsburg State University. Copyright 2010 Morning Sun. Some rights reserved. |
March 02, 2010
Descartes Letter Found, Therefore It IsBy PATRICIA COHEN Published: February 24, 2010
It was the Great Train Robbery of French intellectual life: thousands of treasured documents that vanished from the Institut de France in the mid-1800s, stolen by an Italian mathematician. Among them were 72 letters by René Descartes, the founding genius of modern philosophy and analytic geometry. |
March 02, 2010
Mathematician Wins NSF CAREER to Study Geometric Group TheoryA relatively new branch of mathematics called geometric group theory that considers a broad range of spatial relationships is the research focus of Daniel Groves, University of Illinois at Chicago assistant professor of mathematics, statistics and computer science. Groves just won a five-year, $400,000 National Science Foundation Faculty Early Career Development award for the application of geometric group theory to surface bundles and logic. "Generally speaking, a group is the set of symmetries of some mathematical space, and geometric group theory studies groups and spaces via the interaction of these groups and spaces," said Groves. His NSF-funded project has three main components. First, Groves hopes to develop a general structure theory to understand spaces called surface bundles. "Surface bundles arise in many parts of pure mathematics, so I hope my structure theory for them has broad applications throughout topology, geometry, group theory and other fields," he said. Second, he will work with Henry Wilton, senior research fellow at the California Institute of Technology, to analyze the geometry of negative curvature from an algorithmic viewpoint. They will try to develop algorithms for general decision processes as applied to first-order logic and groups. First-order logic is used in mathematics, but also in such fields as linguistics and philosophy. This, they hope, will yield a method to determine the truth of a logical sentence, as applied to negatively curved groups. a Finally, Groves will run four annual summer workshops and conferences for graduate students. The workshops, Groves said, "will each be in a different subject at the interface of geometric group theory and another field, or fields, within pure mathematics." NSF's Faculty Early Career Development award is its most prestigious honor given to junior faculty members in the sciences and engineering who have shown a demonstrated commitment to research and education. a For more information about UIC, visit www.uic.edu Mathematician Wins NSF CAREER to Study Geometric Group Theory |
March 02, 2010
15 Questions with John Banville![]() Courtesy Douglas Banville By Michelle B. Timmerman, CRIMSON STAFF WRITER Published: Friday, February 26, 2010
With his new book "The Infinities," John Banville, explores the life of a dying mathematician across two parallel universes, as seen from the perspective of the Greek gods. FM sat down with the author to talk about simpler things: "the gray north," brandy, and a love for words which has translated into an award-winning career. |
March 02, 2010
Mathematical model for empirically optimizing |