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A formal approach to determining parallel resource bindings

J.A. Keane, W. Hussak
Proceedings of 16th International Conference on Software Engineering  
Acknowledgements Thanks to the Flagship and EDS groups, particularly Steve Leunig, Ken Mayes and Brian Warboys, who have contributed to our understanding of the design of parallel operating systems.  ...  Thanks also to the anonymous referees whose comments have improved the presentation of the work.  ...  formal methods experience.  ... 
doi:10.1109/icse.1994.296762 fatcat:zqfvtcjjxjfjvjqtovz44su7ou

Fleeting Perceptual Experience and the Possibility of Recalling Without Seeing

William Jones, Hannah Pincham, Ellis Luise Gootjes-Dreesbach, Howard Bowman
2020 Scientific Reports  
Our results show evidence for a dissociation between experience and reportability, whereby participants appear able to encode stimuli into working memory with little, if any, conscious experience of them  ...  This raises the possibility of a phenomenon that might be called sight-blind recall, which we discuss in the context of the current experience/reportability debate.  ...  Finally, we thank two anonymous referees, who gave extensive and insightful suggestions on this paper, which have enabled us to greatly improve it.  ... 
doi:10.1038/s41598-020-64843-2 pmid:32444667 fatcat:l4wyz5blkbgn3elzibqbtyboji

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments

Daniele Granata, Fahimeh Baftizadeh, Johnny Habchi, Celine Galvagnion, Alfonso De Simone, Carlo Camilloni, Alessandro Laio, Michele Vendruscolo
2015 Scientific Reports  
We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease.  ...  To characterize the structure and thermodynamics of this peptide, we extend to intrinsically disordered proteins a recently introduced approach that enables the characterisation of the free energy landscape  ...  Acknowledgments We acknowledge Cineca Supercomputer Center for technical support and computational resources (D.G., F.B. and A.L.).  ... 
doi:10.1038/srep15449 pmid:26498066 pmcid:PMC4620491 fatcat:e4lmstvh6rhbhcymssdbslyvsa

Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments

Wujie Wang, Laura M. Nocka, Brianne Z. Wiemann, Daniel M. Hinckley, Ishita Mukerji, Francis W. Starr
2016 Scientific Reports  
We combine simulations and experiments to evaluate the ability of the 3SPN.2 model, a coarse-grained representation designed to mimic B-DNA, to predict the properties of DNA Holliday junctions.  ...  Thus, in this study we combine simulations and experiments to investigate the ability of a coarse-grained model to predict junction thermodynamics and conformational populations.  ...  binding of ions to individual junctions also play a role.  ... 
doi:10.1038/srep22863 pmid:26971574 pmcid:PMC4789735 fatcat:ro4zgfgmqfhprhrik5v52yub2i

Growth of epitaxial graphene: Theory and experiment

H. Tetlow, J. Posthuma de Boer, I.J. Ford, D.D. Vvedensky, J. Coraux, L. Kantorovich
2014 Physics reports  
To make this text useful for a wider audience, a range of important experimental techniques that have been used over the last decade to grow (e.g.  ...  A detailed review of the literature for the last 5-10 years on epitaxial growth of graphene is presented.  ...  The choice of potential is determined by factors such as the bond type, the desired accuracy, transferability, and the available computational resources.  ... 
doi:10.1016/j.physrep.2014.03.003 fatcat:rvasbaovgvg35fkioglx5at5py

Deep Underground Neutrino Experiment (DUNE) Near Detector Conceptual Design Report [article]

A. Abed Abud, B. Abi, R. Acciarri, M. A. Acero, G. Adamov, D. Adams, M. Adinolfi, A. Aduszkiewicz, Z. Ahmad, J. Ahmed, T. Alion, S. Alonso Monsalve (+1054 others)
2021 arXiv   pre-print
This report describes the conceptual design of the DUNE near detector  ...  standard three-neutrino formalism.  ...  Incorporating Lessons from Current Experiments The approach followed in the design of the DUNE ND concept is to provide sufficient redundancy to address areas of known weaknesses in previous/current experiments  ... 
arXiv:2103.13910v1 fatcat:7nnk337au5bahov4g7g42vumfi

The Long Baseline Neutrino Experiment (LBNE) Water Cherenkov Detector (WCD) Conceptual Design Report (CDR) [article]

The LBNE Collaboration
2012 arXiv   pre-print
Conceptual Design Report developed for the Water Cherenkov Detector (WCD) option for the far detector of the Long Baseline Neutrino Experiment.  ...  Allocation of equipment and human resources The plan will determine and specify equipment and human resources needed for optimal production capacity.  ...  (The binding energy of oxygen is ignored in this expression.)  ... 
arXiv:1204.2295v1 fatcat:yuki457rivef5li4h2d3n3dyey

Binding Interactions of Peptide Aptamers

Roger R. C. New, Tam T. T. Bui, Michal Bogus
2020 Molecules  
However, no formal studies have been conducted to confirm the hypothesis that linear peptides will engage in stronger binding interactions with cyclic peptides than with other linear peptides.  ...  Peptide aptamers are short amino acid chains that are capable of binding specifically to ligands in the same way as their much larger counterparts, antibodies.  ...  , resources, formal analysis, software and visualisation, and M.B. for investigation, methodology and project administration.  ... 
doi:10.3390/molecules25246055 pmid:33371475 pmcid:PMC7767479 fatcat:4wpnvplldjcmbooxgvrahozfnq

Kinetics of Drug Binding and Residence Time

Mattia Bernetti, Matteo Masetti, Walter Rocchia, Andrea Cavalli
2019 Annual review of physical chemistry (Print)  
Here, we review and discuss the methodological approaches to estimating drug binding kinetics and residence time.  ...  The kinetics of drug binding and unbinding is assuming an increasingly crucial role in the long, costly process of bringing a new medicine to patients.  ...  ACKNOWLEDGMENTS The authors are very grateful to the Italian Institute of Technology and to the University of Bologna for the financial support. LITERATURE CITED  ... 
doi:10.1146/annurev-physchem-042018-052340 pmid:30786217 fatcat:sw3zpytw6nfu3fmrngxcjfnp4u

Summary Report of PQRI Workshop on Nanomaterial in Drug Products: Current Experience and Management of Potential Risks

Jeremy A. Bartlett, Marcus Brewster, Paul Brown, Donna Cabral-Lilly, Celia N. Cruz, Raymond David, W. Mark Eickhoff, Sabine Haubenreisser, Abigail Jacobs, Frank Malinoski, Elaine Morefield, Ritu Nalubola (+10 others)
2014 AAPS Journal  
This is a summary of the workshop presentations and discussions, including considerations for future regulatory guidance on drug products containing nanomaterials.  ...  workshop discussions identified areas where additional understanding of material attributes, absorption, biodistribution, cellular and tissue uptake, and disposition of nanosized particles would continue to  ...  Falk Ehmann, both from the EMA, Scientific Support, for their remote participation in the Q&A session on the "EMA Perspective on the Development of Nanomedicines."  ... 
doi:10.1208/s12248-014-9701-9 pmid:25421459 pmcid:PMC4287304 fatcat:inogpqtwenf5vbznuvr3cw6s24

Representing composed meanings through temporal binding

Hugh Rabagliati, Leonidas A.A. Doumas, Douglas K. Bemis
2017 Cognition  
A key feature of human thought and language is compositionality, the ability to bind pre-existing concepts and word meanings together in order to express new ideas.  ...  Here we ask how newly composed complex concepts are mentally represented and matched to the outside world, by testing whether it is harder to verify if a picture matches the meaning of a phrase, like big  ...  RPG-2014-253) to HR. Note that all data and analysis scripts can be found at https://github.com/hughrabagliati/CompositionalityPaper1.  ... 
doi:10.1016/j.cognition.2017.01.013 pmid:28212897 fatcat:tpgzvv47ojbrdapsaen5inijmu

Deep Underground Neutrino Experiment (DUNE), Far Detector Technical Design Report, Volume I: Introduction to DUNE [article]

B. Abi, R. Acciarri, Mario A. Acero, G. Adamov, D. Adams, M. Adinolfi, Z. Ahmad, J. Ahmed, T. Alion, S. Alonso Monsalve, C. Alt, J. Anderson (+954 others)
2020 arXiv   pre-print
to capture supernova neutrino bursts, and seeks to observe nucleon decay as a signature of a grand unified theory underlying the standard model.  ...  The Deep Underground Neutrino Experiment (DUNE) is an international world-class experiment dedicated to addressing these questions as it searches for leptonic charge-parity symmetry violation, stands ready  ...  formal computing technical design report (TDR).  ... 
arXiv:2002.02967v3 fatcat:x3zwdmkxrngrxoydxstbeaydy4

New perspectives on binding in visual working memory

Sebastian Schneegans, Paul M. Bays
2018 British Journal of Psychology  
How does visual working memory store the binding between different features of a visual object (like colour, orientation, and location), and does memorizing these bindings require additional resources  ...  A significant new perspective is that noise in neural representation limits the precision of recall, and several recent models incorporate this view to account for failures of binding in working memory  ...  The study of Shin and Ma (2017) likewise supports an object benefit based on formal model comparisons, attributing it to "leaking" of memory resources for each feature dimension to the stimuli for which  ... 
doi:10.1111/bjop.12345 fatcat:cauukdwcureoxlelgcv3nfn5oe

Rewriting procedures for batched bindings

Ravindra Guravannavar, S. Sudarshan
2008 Proceedings of the VLDB Endowment  
(b) Rewrite a stored procedure/function to accept a batch of bindings, instead of a single binding.  ...  (a) Automatically rewrite programs to replace multiple calls to a query by a batched call to a correspondingly rewritten query.  ...  Acknowledgments We would like to thank Yogesh Murarka for the many discussions on techniques used in parallelizing compilers.  ... 
doi:10.14778/1453856.1453975 fatcat:a56tvf2db5gjthhrxv5duro3ju

Grid-based steered thermodynamic integration accelerates the calculation of binding free energies

Philip W. Fowler, Shantenu Jha, Peter V. Coveney
2005 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
Initial results for the Src SH2 system are presented and compared to a reported experimental value. Finally, we discuss the significance of our approach.  ...  Although formally exact computational methods have the potential to complement, add to, and even compete with experimental approaches, they are difficult to use and extremely time consuming.  ...  We are grateful to ESPRC for funding much of this research through RealityGrid grant GR/R67699 and for providing a Ph.D. studentship for PWF.  ... 
doi:10.1098/rsta.2005.1625 pmid:16099763 fatcat:o5rrwkqjofafvh7ovk3jx7rn6e
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