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Browsing MIT Open Access Articles by Title

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  • Shim, Eun Bo; Heldt, Thomas; Amano, Akira; Rhee, Kyehan (Hindawi Publishing Corporation, 2012)
    The human body requires a complex circulatory system to supply nutrients to, and to remove metabolic waste products from, its tissues. Given this primary purpose, circulatory function is closely related to the hemodynamic ...
  • Ohler, Uwe; Liao, Guo-chun; Niemann, Heinrich; Rubin, Gerald M (BioMed Central Ltd, 2002-12)
    Background: The core promoter, a region of about 100 base-pairs flanking the transcription start site (TSS), serves as the recognition site for the basal transcription apparatus. Drosophila TSSs have generally been mapped ...
  • Washietl, Stefan; Will, Sebastian; Hendrix, David A.; Goff, Loyal; Rinn, John L.; Berger, Bonnie; Kellis, Manolis (John Wiley & Sons, Inc, 2012-11)
    Noncoding RNAs have emerged as important key players in the cell. Understanding their surprisingly diverse range of functions is challenging for experimental and computational biology. Here, we review computational methods ...
  • Lee, Hyungsuk; Hwang, Wonmuk; Kamm, Roger Dale; Kim, Taeyoon (Springer Boston, 2009-02)
    Mechanical force plays an important role in the physiology of eukaryotic cells whose dominant structural constituent is the actin cytoskeleton composed mainly of actin and actin crosslinking proteins (ACPs). Thus, knowledge ...
  • Hwang, Wonmuk; Lee, Hyungsuk; Kim, Taeyoon; Kamm, Roger Dale (Public Library of Science, 2009-07)
    Mechanical force plays an important role in the physiology of eukaryotic cells whose dominant structural constituent is the actin cytoskeleton composed mainly of actin and actin crosslinking proteins (ACPs). Thus, knowledge ...
  • Liu, Bing; Zhang, Jing; Tan, Pei Yi; Hsu, David; Blom, Anna M.; Leong, Benjamin; Sethi, Sunil; Ho, Bow; Ding, Jeak Ling; Thiagarajan, P. S. (Public Library of Science, 2011-01)
    The complement system is key to innate immunity and its activation is necessary for the clearance of bacteria and apoptotic cells. However, insufficient or excessive complement activation will lead to immune-related diseases. ...
  • Stitziel, Nathan O.; Kiezun, Adam; Sunyaev, Shamil R. (BioMed Central Ltd., 2011-09)
    New sequencing technology has enabled the identification of thousands of single nucleotide polymorphisms in the exome, and many computational and statistical approaches to identify disease-association signals have emerged.
  • Stitziel, Nathan O.; Kiezun, Adam; Sunyaev, Shamil R. (BioMed Central Ltd., 2011-09)
    New sequencing technology has enabled the identification of thousands of single nucleotide polymorphisms in the exome, and many computational and statistical approaches to identify disease-association signals have emerged.
  • Gong, Sherry; Ren, Qingchun; Schedler, Travis; Etingof, Pavel I.; Pacchiano Camacho, Aldo (Taylor & Francis, 2012-05)
    We reduce the computation of Poisson traces on quotients of symplectic vector spaces by finite subgroups of symplectic automorphisms to a finite one by proving several results that bound the degrees of such traces as well ...
  • Xue, Tianfan; Rubinstein, Michael; Liu, Ce; Freeman, William T. (Association for Computing Machinery (ACM), 2015-08)
    We present a unified computational approach for taking photos through reflecting or occluding elements such as windows and fences. Rather than capturing a single image, we instruct the user to take a short image sequence ...
  • Demaine, Erik D.; Okamoto, Yoshio; Uehara, Ryuhei; Uno, Yushi (Institute of Electronics, Information and Communications Engineers, 2014-06)
    Shakashaka is a pencil-and-paper puzzle proposed by Guten and popularized by the Japanese publisher Nikoli (like Sudoku). We determine the computational complexity by proving that Shakashaka is NP-complete, and furthermore ...
  • Aaronson, Scott; Arkhipov, Aleksandr (Association for Computing Machinery, 2011)
    We give new evidence that quantum computers---moreover, rudimentary quantum computers built entirely out of linear-optical elements---cannot be efficiently simulated by classical computers. In particular, we define a model ...
  • Drennan, Catherine L.; Baker, David; Ting, Alice Y.; Liu, Daniel S.; Nivon, Lucas G.; Richter, Florian; Goldman, Peter J.; Yao, Jennifer Z.; Phipps, William S.; Ye, Anne Z.; Deerinck, Thomas J.; Richardson, Douglas; Ellisman, Mark H. (National Academy of Sciences (U.S.), 2014-10)
    Chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a ...
  • Bharaj, Gaurav; Levin, David I. W.; Tompkin, James; Fei, Yun; Pfister, Hanspeter; Matusik, Wojciech; Zheng, Changxi (Association for Computing Machinery (ACM), 2015-11)
    Metallophones such as glockenspiels produce sounds in response to contact. Building these instruments is a complicated process, limiting their shapes to well-understood designs such as bars. We automatically optimize the ...
  • Vattre, Aurelien; Abdolrahim, Niaz; Kolluri, Kedarnath; Demkowicz, Michael J. (Nature Publishing Group, 2014-08)
    Patterning is a familiar approach for imparting novel functionalities to free surfaces. We extend the patterning paradigm to interfaces between crystalline solids. Many interfaces have non-uniform internal structures ...
  • Wang, Xiangfeng; Laurie, John D.; Liu, Tao; Wentz, Jacqueline; Liu, X. Shirley (Elsevier, 2011-02)
    The profiling of small RNAs by high-throughput sequencing (smRNA-Seq) has revealed the complexity of the RNA world. Here, we describe a computational scheme for dissecting the plant smRNAome by integrating smRNA-Seq datasets ...
  • Dash, Sanjeeb; Vielma, Juan Pablo; Gunluk, Oktay (Institute for Operations Research and the Management Sciences (INFORMS), 2014-06)
    In this paper, we study whether cuts obtained from two simplex tableau rows at a time can strengthen the bounds obtained by Gomory mixed-integer (GMI) cuts based on single tableau rows. We also study whether cross and ...
  • Buchwald, Stephen Leffler; Jones, Gavin O.; Houk, K. N.; Liu, Peng (American Chemical Society (ACS), 2010-04)
    Computational investigations of ligand-directed selectivities in Ullmann-type coupling reactions of methanol and methylamine with iodobenzene by β-diketone- and 1,10-phenanthroline-ligated CuI complexes are reported. Density ...
  • Hauert, Sabine; Berman, Spring; Nagpal, Radhika; Bhatia, Sangeeta N. (Elsevier, 2013-12)
    Targeted nanoparticles are increasingly being engineered for the treatment of cancer. By design, they can passively accumulate in tumors, selectively bind to targets in their environment, and deliver localized treatments. ...
  • Shapiro, Jeffrey H. (Institute of Electrical and Electronics Engineers, 2009-08)
    A computational ghost-imaging arrangement that uses only a single-pixel detector is described. It affords a new 3D sectioning capability and matches the resolution of pseudothermal ghost imaging.
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