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New architectures for a new biology

D.E. Shaw
2006 The Twelfth International Symposium on High-Performance Computer Architecture, 2006.  
Chem.26, Oct. 2005 Desirable Properties Ideally, a parallel algorithm for the range-limited n-body problem would:Exploit the range limitation to reduce computational load Scale such that data transfer  ...  parallel algorithms New Algorithms Range-Limited Pairwise Particle Interactions Efficient methods known for distant interactions R Pairwise, non-bonded interactions dominate Range-limited  ...  Only slightly more inter-process communication than NT for problems and machines of practical size  ... 
doi:10.1109/hpca.2006.1598107 dblp:conf/hpca/Shaw06 fatcat:mamem4osfncczgyegwlqeeqqoq

CRISPR/Cas9 offers a new tool for studying the role of chromatin architecture in disease pathogenesis

Xiang Guo, Ann Dean
2018 Genome Biology  
A recent study used CRISPR/Cas9 to reveal long-range looping between disease-related genes and their regulatory elements that is mediated by the CCCTC-binding factor (CTCF) in prostate cancer.  ...  In this issue of Genome Biology, Guo et al.  ...  Structural studies after the deletions could provide support for this idea and might also reveal what new CTCF-CTCF associations occur that could help to explain why the deletion of one loop anchor participant  ... 
doi:10.1186/s13059-018-1569-z pmid:30400943 pmcid:PMC6219166 fatcat:yybcjmzlq5dnjkxo5oyf7frz4y

A new plug-in software architecture applied for a portable molecular structure browser

Y Ueno, K Asai
1997 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
A new software configuration method using plug-in style components was established for the tool with the incremental development of software used in protein structural study.  ...  This plug-in software architecture is generally useful for large-scale software development and for prototyping parts of the system.  ...  Availability Source code of prototype is available upon e-mail request for developers and our molecular structure browser will be released at ftp://ftp.etl.go.jp/pub/bioinfo.  ... 
pmid:9322057 fatcat:32keg2kxlnevpalbkhrbwe7egu

Cryoelectron microscopy of vitrified sections: a new challenge for the analysis of functional nuclear architecture

C. Bouchet-Marquis, J. Dubochet, S. Fakan
2005 Histochemistry and Cell Biology  
Cryoelectron microscopy of vitrified sections has become a powerful tool for investigating the fine structural features of cellular compartments.  ...  Voinesco for the careful preparation of cell cultures. We thank Prof. M. Trendelenburg (Heidelberg) for kindly providing PtK2 cells.  ...  Introduction The functional architecture of the cell nucleus has been extensively studied for several decades using various methods of ultrastructural research.  ... 
doi:10.1007/s00418-005-0093-x pmid:16328430 fatcat:j76mxdgq6bf7loaysmzoee6iam

A new application of the phase-field method for understanding the mechanisms of nuclear architecture reorganization

S. Seirin Lee, S. Tashiro, A. Awazu, R. Kobayashi
2016 Journal of Mathematical Biology  
Here, we propose a new mathematical approach to the understanding of nuclear architecture dynamics using the phase-field method.  ...  Specific features of nuclear architecture are important for the functional organization of the nucleus, and chromatin consists of two forms, heterochromatin and euchromatin.  ...  Irina Solovei for valuable comments and discussion.  ... 
doi:10.1007/s00285-016-1031-3 pmid:27241726 pmcid:PMC5206286 fatcat:n4paermadnhqjedonwfdxuj6wu

A New Protein Architecture for Processing Alkylation Damaged DNA: The Crystal Structure of DNA Glycosylase AlkD

Emily H. Rubinson, Audrey H. Metz, Jami O'Quin, Brandt F. Eichman
2008 Journal of Molecular Biology  
Together, these data provide important insight into the requirements for alkylation repair within DNA and suggest that AlkD utilizes a novel strategy to manipulate DNA in its search for alkylpurine bases  ...  Structural analysis of the variant HEAT repeats in AlkD provides a rationale for how this protein scaffolding motif has been modified to bind DNA.  ...  Acknowledgments The authors wish to thank Zdzislaw Wawrzak for help with data collection, and the staff at the Life Sciences (LS-CAT) and Southeast Regional Collaborative Access Teams (SER-CAT) at the  ... 
doi:10.1016/j.jmb.2008.05.078 pmid:18585735 pmcid:PMC3763988 fatcat:6yj7vgwkjnas5lxuvgsnq7f2uy

A new role for the architecture of microvillar actin bundles in apical retention of membrane proteins

Céline Revenu, Florent Ubelmann, Ilse Hurbain, Fatima El-Marjou, Florent Dingli, Damarys Loew, Delphine Delacour, Jules Gilet, Edith Brot-Laroche, Francisco Rivero, Daniel Louvard, Sylvie Robine (+1 others)
2012 Molecular Biology of the Cell  
These findings illustrate, in vivo, a precise role for local actin filament architecture in the stabilization of apical cargoes into microvilli.  ...  for normal intestinal physiology.  ...  ACKNOWLEDGMENTS We are grateful to A. Quaroni (Cornell University), R. Jacob  ... 
doi:10.1091/mbc.e11-09-0765 pmid:22114352 pmcid:PMC3258176 fatcat:ekh6xyjd4jftzhgn2ywomyn5xm

BIOMIMICRY ARCHITECTURE, FROM THE INSPIRATION BY NATURE TO THE INNOVATION OF THE SAHARAN ARCHITECTURE

Yassine Benyoucef, Peoples' Friendship University of Russia, Andrey Razin, Peoples' Friendship University of Russia
2018 Architecture and Engineering  
The aim of the article is to present a synthesis of biomimicry approach and propose the biomimicry as a solution for the development of Saharan architecture which can use this approach as a sustainable  ...  Moreover, the Sahara can be a favorable soil for great changes, the use of this approach is the key for the most optimal strategies and sustainable development of the Saharan architecture. .  ...  According to Frei Otto, the biology has become indispensable for architecture but architecture has also become indispensable for biology.  ... 
doi:10.23968/2500-0055-2018-3-4-3-12 fatcat:762ijrcpdfccdirrkmsqwcq2km

New Curriculum Design Model for Bioinformatics Postgraduate program using Systems Biology Approach

Ragunath PK
2009 Journal of computer science and systems biology  
Hence, the need arises for developing a new method for curriculum development for a course in Bioinformatics (which is a truly interdisciplinary in nature).  ...  We have evolved a new curriculum design using the System Biology Approach (SRU Model) for the M.Sc. bioinformatics course in the Department of Bioinformatics in Sri Ramachandra University, India.  ...  Hence, the need arises for developing a new method for curriculum development for a course in Bioinformatics (which is a truly interdisciplinary in nature).  ... 
doi:10.4172/jcsb.1000046 fatcat:gsvz2zggnrgytogpndgf5lhibe

The Evolution of Architectural Morphogenesis at the Beginning of XXI Century in the Context of Scientific Advances

Nickolay V. Kasyanov
2016 Procedia Engineering  
Computer simulation reveals a new range of geometric shapes as well as various types of partitioning and filling of two-dimensional surface and threedimensional space.  ...  This is necessary for the further development of the creative potential of architecture and engineering.  ...  Patterns of connections and contact surfaces are the same for our three-dimensional world -in biology, crystallography and architecture.  ... 
doi:10.1016/j.proeng.2016.08.113 fatcat:lh4ld3ypsnfwziyzxybpxt6y34

New Advances in Chromosome Architecture [chapter]

Mark C. Leake
2016 Msphere  
Our knowledge of the 'architecture' of chromosomes has grown enormously in the past decade.  ...  Here, I discuss these advances, and take stock on the current state of our knowledge of chromosome architecture and speculate where future advances may lead.  ...  Acknowledgments MCL was assisted by a Royal Society URF and research funds from the Biological Physical Sciences Institute (BPSI) of the University of York, UK.  ... 
doi:10.1007/978-1-4939-3631-1_1 pmid:27283297 fatcat:h73gvdwkdfernheiy756emkv3q

Synthetic biology: Living quarters

Rachel Armstrong, Neil Spiller
2010 Nature  
BOOKS & ARTS COMMENT 9 1 6 | N A t U r e | V o L 4 6 7 | 2 1 o c t o b e r 2 0 1 0  ...  Synthetic biology could offer truly sustainable approaches to the built environment, predict Rachel Armstrong and Neil Spiller.  ...  Terreform One, an interdisciplinary architectural design practice in New York, has envisaged growing a leathery skin for covering buildings, dubbed 'Meat House' .  ... 
doi:10.1038/467916a fatcat:xljhg3uddnhu5o75icgcayew2y

Frontiers of Adaptive Design, Synthetic Biology and Growing Skins for Ephemeral Hybrid Structures [chapter]

Sandra Giulia Linnea Persiani, Alessandra Battisti
2018 Energy-Efficient Approaches in Industrial Applications [Working Title]  
a high potential for innovation.  ...  The introduction of new engineered materials and techniques, combined with a growing interest for Nature-inspired technologies are progressively merging man-made artifacts and biological processes with  ...  A. Battisti, Operational coordination Ph.D. Sandra G. L. Persiani.  ... 
doi:10.5772/intechopen.80867 fatcat:3y4iih7b25frhfgswfhguamqyq

Design scrying: an alternative aesthetics for synthetic biology

Rachel Armstrong
2016 arq: Architectural Research Quarterly  
In 1911, Stéphane Leduc originally proposed that synthetic biology is a branch of synthetic chemistry that can offer a portfolio of design tools that broaden the possibilities of an aesthetics of life.  ...  considered through the possibility of using lifelike materials in the choreography of space where lifelike materials, trembling interfaces, and living technologies give rise to the emergence 'soft living architectures  ...  She is a Rising Waters II Fellow with the Robert Rauschenberg Foundation (April-May 2016), TWOTY futurist 2015, Fellow of the British Interplanetary Society and a 2010 Senior TED Fellow.  ... 
doi:10.1017/s1359135516000178 fatcat:csujt5z72fcsfixkaiyeprc4ja

COUPLING INTERACTING PARTICLE SYSTEMS

CHRISTIAN MAES
1993 Reviews in Mathematical Physics  
Since about a decade some new trends in the study of interacting particle systems can be identified.  ...  I give them here a short introduction. 1  ...  A new trend in biology-related IPS is to recognize that and to go to meet the true questions of the biology community.  ... 
doi:10.1142/s0129055x93000139 fatcat:lc644ypombfcrknfjlnzf37wvq
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