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Browsing MIT Open Access Articles by Title

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  • Winston, Patrick Henry; Finlayson, Mark A.; Richards, Whitman A. (Association for the Advancement of Artificial Intelligence, 2010-04)
    On October 8-10, 2009 an interdisciplinary group met at the Wylie Center in Beverley, Massachusetts to evaluate the state of the art in the computational modeling of narrative. Three important findings emerged: (1) current ...
  • Shabalina, Svetlana A.; Ogurtsov, Aleksey Y.; Spiridonov, Alexey Nikolaevich (BioMed Central Ltd, 2006-02)
    Background: Small interfering RNAs (siRNAs) have become an important tool in cell and molecular biology. Reliable design of siRNA molecules is essential for the needs of large functional genomics projects. Results: To ...
  • Dauvermann, Maria R.; Whalley, Heather C.; Schmidt, Andre; Lee, Graham; Romaniuk, Liana; Roberts, Neil; Johnstone, Eve C.; Lawrie, Stephen M.; Moorhead, Thomas W. J. (Frontiers Research Foundation, 2014-03)
    Computational modeling of functional brain networks in fMRI data has advanced the understanding of higher cognitive function. It is hypothesized that functional networks mediating higher cognitive processes are disrupted ...
  • Ferguson, Andrew L.; Falkowska, Emilia; Walker, Laura M.; Seaman, Michael S.; Burton, Dennis R.; Chakraborty, Arup K. (Public Library of Science, 2013-12)
    Broadly neutralizing monoclonal antibodies effective against the majority of circulating isolates of HIV-1 have been isolated from a small number of infected individuals. Definition of the conformational epitopes on the ...
  • Srikanth, Manohar; Bala, Kavita; Durand, Fredo (Elsevier, 2015-03)
    Lighting plays a major role in photography. Professional photographers use elaborate installations to light their subjects and achieve sophisticated styles. However, lighting moving subjects performing dynamic tasks presents ...
  • Berger, Bonnie; Peng, Jian; Singh, Mona (Nature Publishing Group, 2013-04)
    High-throughput experimental technologies are generating increasingly massive and complex genomic data sets. The sheer enormity and heterogeneity of these data threaten to make the arising problems computationally infeasible. ...
  • Haslinger, Robert Heinz; Klinkner, Kristina Lisa; Cosma, Rohilla Shalizi (MIT Press, 2010-01)
    Neurons perform computations, and convey the results of those computations through the statistical structure of their output spike trains. Here we present a practical method, grounded in the information-theoretic ...
  • Duda, Timothy F.; Lin, Ying-Tsong; Zhang, Weifeng Gordon; Cornuelle, Bruce D.; Lermusiaux, Pierre F. J. (2011-04)
    Time-evolving three-dimensional (four-dimensional) numerical modeling of sound is performed for ocean environmental conditions calculated using regional ocean flow models. The flow models solve the appropriate nonlinear ...
  • Zhao, Wei; Dauwels, Justin H. G.; Niles, Jacquin; Cao, Jianshu (BioMed Central Ltd, 2012-06)
    Background Microarrays are widely used to investigate the blood stage of Plasmodium falciparum infection. Starting with synchronized cells, gene expression levels are continually measured over the 48-hour intra-erythrocytic ...
  • Rajapakse, Jagath (Institute of Electrical and Electronics Engineers, 2009-07)
    Bioinformatics data come in various forms such as biological sequences, molecular structures, gene and protein expressions, molecular networks, cellular images, and literature. A major aspect of discovering biological ...
  • Hafner, Michael R.; Del Vecchio, Domitilla (Society for Industrial and Applied Mathematics, 2011-12)
    This paper addresses the two-agent safety control problem for piecewise continuous systems with disturbances and imperfect state information. In particular, we focus on a class of systems that evolve on a partial order and ...
  • Agrawal, Neeraj J.; Helk, Bernhard; Trout, Bernhardt L. (Elsevier, 2013-11)
    Identifying hot-spot residues – residues that are critical to protein–protein binding – can help to elucidate a protein's function and assist in designing therapeutic molecules to target those residues. We present a novel ...
  • Hasanhodzic, Jasmina; Lo, Andrew W.; Viola, Emanuele (Taylor & Francis, 2011-06)
    We study market efficiency from a computational viewpoint. Borrowing from theoretical computer science, we define a market to be efficient with respect to resources S (e.g., time, memory) if no strategy using resources S ...
  • Rutishauser, Ueli; Douglas, Rodney J.; Slotine, Jean-Jacques E. (Public Library of Science, 2015-01)
    Previous explanations of computations performed by recurrent networks have focused on symmetrically connected saturating neurons and their convergence toward attractors. Here we analyze the behavior of asymmetrical connected ...
  • Reid, M. T. Homer; White, Jacob K.; Johnson, Steven G. (American Physical Society, 2011-07)
    We extend a recently introduced method for computing Casimir forces between arbitrarily shaped metallic objects [ M. T. H. Reid et al. Phys. Rev. Lett. 103 040401 (2009)] to allow treatment of objects with arbitrary material ...
  • Rausch, Sebastian; Rutherford, Thomas Fox (Springer Netherlands, 2010-06)
    This paper develops a decomposition algorithm by which a market economy with many households may be solved through the computation of equilibria for a sequence of representative agent economies. The paper examines local ...
  • Green, William H.; Sharma, Sandeep (American Chemical Society, 2009-07)
    Using quantum chemical methods, we have explored the region of the C[subscript 6]H[subscript 8] potential energy surface that is relevant in predicting the rate coefficients of various wells and major product channels ...
  • Amarasinghe, Saman P.; Amin, Nada; Thies, William (Institute of Electrical and Electronics Engineers, 2009-01)
    Microfluidic chips are emerging as a powerful platform for automating biology experiments. As it becomes possible to integrate tens of thousands of components on a single chip, researchers will require design automation ...
  • Curran, Timothy G.; Bryson, Bryan D.; Reigelhaupt, Michael; Johnson, Hannah; White, Forest M. (Elsevier, 2013-03)
    Advances in mass spectrometry-based proteomic technologies have increased the speed of analysis and the depth provided by a single analysis. Computational tools to evaluate the accuracy of peptide identifications from these ...
  • Neugebauer, Timothy C.; Perreault, David J. (Institute of Electrical and Electronics Engineers (IEEE), 2003-05)
    This paper investigates computer-aided optimization of DC/DC converters, with a focus on converters for dual-voltage automotive electrical systems. A new CAD optimization approach based on Monte Carlo search methods is ...
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