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  • September 9, 2013
  • 03:15 AM

What can theoretical computer science offer biology?

by Artem Kaznatcheev in Evolutionary Games Group

If there is anything definitive that can be said about biology then it is that biology is messy and complicated. The stereotypical image of a biology major is in the library memorizing volumes of loosely (at best) related facts only to have them overturned in the next semester. Concepts are related only vaguely, to the […]... Read more »

  • September 7, 2013
  • 07:57 AM

The biggest microscope

by Perikis Livas in Tracing Knowledge

Fermions and bosons. Mesons and baryons. Electrons and protons. Researchers of the subatomic world must know the identity and understand the behavior of dozens of different kinds of particles. However, not all particles are equal. While all are interesting in their own ways, certain ones have a more widespread utility. One such particle is the muon.... Read more »

Don Lincoln. (2013) The biggest microscope. Fermilab Today. DOI: arXiv:1306.6905v1  

  • September 6, 2013
  • 02:44 PM

Can DNA Template Lead to Future Technologies?

by Jason Carr in Wired Cosmos

DNA is the blueprint for life. Could it also become the template for making a new generation of computer chips based not on silicon, but on an experimental material known as graphene? That’s the theory behind a process that Stanford chemical engineering professor Zhenan Bao reveals in Nature Communications (citation below). Bao and her co-authors, former post-doctoral fellows Anatoliy Sokolov … Read More →... Read more »

A.N. Sokolov, F. L. Yap, N. Liu, K. Kim, L. Ci, O. B. Johnson, H. Wang, M. Vosgueritchian, A. L. Koh, J Chen, J. Park.... (2013) Direct growth of aligned graphitic nanoribbons from a DNA template by chemical vapour deposition. Nature Communications. DOI: 10.1038/ncomms3402  

  • September 5, 2013
  • 02:35 PM

Where is the model?

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

Wouldn’t it be a great idea to put all these homology modeled structures that were published (of course, in a peer-reviewed journal) in one place? For some researchers, homology models are usually considered with a pinch (sorry a bucket!) of salt. Still, why should I spend time on modeling the protein, if a model exists already?... Read more »

  • September 4, 2013
  • 12:54 PM

Layered Semiconductors May Greatly Improve Photoelectrochemical Cells

by dailyfusion in The Daily Fusion

Theoretical simulations reveal that layered semiconductors with magnetic interfaces can be used to increase the efficiency of photoelectrochemical cells. According to a new study by researchers at the A*STAR Institute of High Performance Computing, model interfaces made from gallium nitride (GaN) and zinc oxide (ZnO) semiconductors have tunable magnetic and light-harvesting capabilities—factors that can greatly improve the photocatalytic transformation of water into hydrogen fuel.... Read more »

  • August 31, 2013
  • 03:30 AM

Computational complexity of evolutionary equilibria

by Artem Kaznatcheev in Evolutionary Games Group

The first half of the 20th century is famous for revolutionary changes — paradigm shifts as Kuhn would say — across the sciences and other systems of thought. Disheartened by the scars of the First World War, European thinkers sought refuge by shifting their worldviews away from those of their fathers. In fields like biology, […]... Read more »

  • August 29, 2013
  • 11:14 AM

Understanding the Basis of Human Intelligence

by Sedeer El-Showk in United Academics

From Siri answering our questions and Watson advising nurses to smart apps that aggregate information to help us out (or spy on us), artificial intelligence is transforming our world. Despite incredible advances, somehow these amazingly “intelligent” systems sometimes seem profoundly stupid. Hector Levesque, a professor of computer science at the University of Toronto, likens them to savants. He was recently awarded the Research Excellence Award at the International Joint Conference on Artificial Intelligence in Beijing; he used his acceptance speech to highlight important questions about our approach to artificial intelligence and what it can tell us about ourselves.... Read more »

Rahman, Altaf and Ng, Vincent. (2013) Resolving Complex Cases of Definite Pronouns: The Winograd Schema Challenge. Proceedings of the 2012 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning. info:/

  • August 29, 2013
  • 10:06 AM

Open-Source Energy Model for Policy Makers Will Increase Transparency

by dailyfusion in The Daily Fusion

Computer models are used to inform policy decisions about energy, but existing models are generally “black boxes” that don’t show how they work, making it impossible for anyone to replicate their findings. Researchers from North Carolina State University have developed a new open-source model and are sharing the data they put into it, to allow anyone to check their work—an important advance given the environmental and economic impact of energy policy decisions.... Read more »

  • August 26, 2013
  • 08:52 AM

Chemists Combine Natural Materials With Synthetic Ones to ‘Upgrade’ Photosynthesis

by dailyfusion in The Daily Fusion

A ring of protein and pigments, half synthetic and half natural, can be used to quickly prototype light-harvesting antennas that absorb more sunlight than fully natural ones.... Read more »

Kunche Aravindu, Olga Mass, Pothiappan Vairaprakash, Joseph W. Springer, Eunkyung Yang, Dariusz M. Niedzwiedzki, Christine Kirmaier,b David F. Bocian, Dewey Holten, Jonathan S. Lindsey. (2013) Amphiphilic chlorins and bacteriochlorins in micellar environments. Molecular design, de novo synthesis, and photophysical properties. Chemical Science, 4(9), 3459-3477. DOI: 10.1039/c3sc51335a  

  • August 25, 2013
  • 11:30 PM

NK and block models of fitness landscapes

by Artem Kaznatcheev in Evolutionary Games Group

On February 12, 2001, the human genome project released its first formal report. It was a great day for biology, and a wonderful birthday present for Darwin. However, it was also a humbling confrontation with complexity and prompted Steven Jay Gould to write in the New York Times: [The Human Genome project revealed that] Home […]... Read more »

Kauffman S, & Levin S. (1987) Towards a general theory of adaptive walks on rugged landscapes. Journal of Theoretical Biology, 128(1), 11-45. PMID: 3431131  

  • August 22, 2013
  • 12:47 PM

All digital images are just large arrays of numbers

by Olga Vovk in Milchstraße

If we look at image processing from the mathematical perspective, all digital images are just arrays of numbers. Across different fields of study, image processing applications (although initially developed for very specific needs) often use similar image processing routines based on common algorithms. Why I am writing all this?... Read more »

Jennifer L. West, & Ian D. Cameron. (2006) Using the medical image processing package, ImageJ, for astronomy. J.Roy.Astron.Soc.Canada100:242-248,2006. arXiv: astro-ph/0611686v1

Michelle Borkin (Initiative in Innovative Computing, Harvard University), Alyssa Goodman (Initiative in Innovative Computing/Harvard-Smithsonian Center for Astrophysics), Michael Halle (Initiative in Innovative Computing/Harvard Medical School), Douglas A. (2006) Application of Medical Imaging Software to 3D Visualization of Astronomical Data. info:/

Covington K, McCreedy ES, Chen M, Carass A, Aucoin N, & Landman BA. (2010) Interfaces and Integration of Medical Image Analysis Frameworks: Challenges and Opportunities. Annual ORNL Biomedical Science and Engineering Center Conference ORNL Biomedical Science and Engineering Center Conference, 1-4. PMID: 21151892  

  • August 21, 2013
  • 05:47 PM

Fungus and Bacteria Create Isobutanol from Waste Plant Material

by dailyfusion in The Daily Fusion

A fungus and E. coli bacteria have joined forces to turn tough, waste plant material into isobutanol, a biofuel that matches gasoline’s properties better than ethanol. University of Michigan research team members said the principle also could be used to produce other valuable chemicals such as plastics.... Read more »

Jeremy J. Mintya, Marc E. Singera, Scott A. Scholzb, Chang-Hoon Baea, Jung-Ho Ahna, Clifton E. Fosterc, James C. Liaod, Xiaoxia Nina Lin. (2013) Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. DOI: 10.1073/pnas.1218447110  

  • August 17, 2013
  • 09:37 AM

Smart Window Coating Can Regulate Heat and Light Coming Through

by dailyfusion in The Daily Fusion

Large glass windows provide better natural lighting conditions, but also let in more heat, therefore bringing higher air-conditioning bills. The Harvard researchers recently proposed to solve the problem by fitting the windows with a bioinspired microfluidic circulatory system. Now, researchers at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have designed a new material—a thin coating of nanocrystals embedded in glass—that can dynamically modify sunlight as it passes through a window.... Read more »

  • August 16, 2013
  • 11:00 PM

Fitness landscapes as mental and mathematical models of evolution

by Artem Kaznatcheev in Evolutionary Games Group

As Jacob Scott pointed out, everybody — theorist or experimentalist — “has a logical construct (a model) in his or her head” when studying anything. This model might be mathematically explicit or implicit in the mind, but it is there and if the world is mechanistic (or if we only want to consider mechanistic theories […]... Read more »

Wright, S. (1932) The roles of mutation, inbreeding, crossbreeding, and selection in evolution. Proceedings of the Sixth International Congress of Genetics, 356-366. info:/

  • August 16, 2013
  • 11:33 AM

New Polymer Semiconductors Increase Plastic Solar Cells’ Efficiency

by dailyfusion in The Daily Fusion

A research team led by Professor Tobin J. Marks of Northwestern University reports the design and synthesis of new polymer semiconductors and the realization of polymer solar cells with fill factors of 80 percent a first. This number is close to that of silicon solar cells.... Read more »

Xugang Guo, Nanjia Zhou, Sylvia J. Lou, Jeremy Smith, Daniel B. Tice, Jonathan W. Hennek, Rocío Ponce Ortiz, Juan T. López Navarrete, Shuyou Li, Joseph Strzalka, Lin X. Chen, Robert P. H. Chang, Antonio Facchetti, Tobin J. Marks. (2013) Polymer solar cells with enhanced fill factors. Nature Photonics. DOI: 10.1038/nphoton.2013.207  

  • August 15, 2013
  • 05:46 PM

Wireless Devices That Harvest Energy out of Thin Air Developed

by dailyfusion in The Daily Fusion

Scientists at the University of Washington have developed a new wireless communication system that allows devices to interact with each other without relying on batteries or wires for power. The devices are using existing radio signals scattered around both as a power source and as a signal carrier.... Read more »

Liu V., Parks A., Talla V., Gollakota S., Wetherall D., Smith J. (2013) Ambient Backscatter: Wireless Communication Out of Thin Air. Proceedings of the ACM SIGCOMM 2013 conference, 39-50. DOI: 10.1145/2486001.2486015  

  • August 15, 2013
  • 11:54 AM

Low-Temperature Combustion Will Make Diesel Engines Cleaner, More Efficient

by dailyfusion in The Daily Fusion

As demand rises for more fuel-efficient vehicles, knowledge compiled over several years about diesel engines and a new strategy known as “low-temperature combustion” (LTC) might soon lead auto manufacturers and consumers to broader use of cleaner diesel engines in the United States.... Read more »

Mark P.B. Musculus, Paul C. Miles, Lyle M. Pickett. (2013) Conceptual models for partially premixed low-temperature diesel combustion. Progress in Energy and Combustion Science, 39(2-3), 246-283. DOI: 10.1016/j.pecs.2012.09.001  

  • August 14, 2013
  • 07:30 AM

Silicon replacement parts for the brain

by Sean Fannon in Brave Neuro World

Pioneering research in neuroengineering is bringing us closer to creating neural prostheses that replicate the function damaged brain tissue.... Read more »

Berger TW, Hampson RE, Song D, Goonawardena A, Marmarelis VZ, & Deadwyler SA. (2011) A cortical neural prosthesis for restoring and enhancing memory. Journal of neural engineering, 8(4), 46017. PMID: 21677369  

Hampson RE, Song D, Chan RH, Sweatt AJ, Riley MR, Gerhardt GA, Shin DC, Marmarelis VZ, Berger TW, & Deadwyler SA. (2012) A nonlinear model for hippocampal cognitive prosthesis: memory facilitation by hippocampal ensemble stimulation. IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society, 20(2), 184-97. PMID: 22438334  

  • August 13, 2013
  • 05:56 PM

Brain Reading Reads “Brains” From A Reading Brain

by Neuroskeptic in Neuroskeptic_Discover

A neat paper from Schoenmakers et al of the Dutch Donders Institute reports on Linear reconstruction of perceived images from human brain activity It introduces a new mathematical approach for decoding (or ‘brain reading’) the image that someone is looking at, pixel-by-pixel, based on the pattern of neural activity in their visual cortex. The results [...]The post Brain Reading Reads “Brains” From A Reading Brain appeared first on Neuroskeptic.... Read more »

  • August 13, 2013
  • 05:16 PM

Roberts Prize for best paper published in 2012 - PMB

by Know Your Images in Know Your Images

Physics in Medicine and Biology is one of my favorite journals and recently they have awarded the best paper published in 2012: Defrise M, Rezaei A, & Nuyts J (2012). Time-of-flight PET data determine the attenuation sinogram up to a constant. Physics in medicine and biology, 57 (4), 885-99 PMID: 22290428 I have scan through this paper before, since it is actually a topic close to my work. Time-Of-Flight Positron Emission Tomography is one of the great trends of PET imaging and attenuation correction can be a struggle, specially for the new PET-MRI scanners, so the use of new information for attenuation correction will be important.I have met the authors in conferences, two seniors Prof. Nuyts (researcher best known for Maximum a Posteriori reconstruction) and Prof. Defrise (researcher best known for Fourier Rebinning) and A. Rezaei is a young researcher with a promising career. Congratulations!Image from here... Read more »

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