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1
المؤلفون: Dustin J. Covell, Philip S. Lukeman, Tom P. Carberry
المصدر: Journal of Chemical Education. 96:1767-1772
مصطلحات موضوعية: Multimedia, business.industry, Computer science, Workload, General Chemistry, computer.software_genre, Partial credit, Automation, Education, Software, Scalability, ComputingMilieux_COMPUTERSANDEDUCATION, Statistical analysis, Grading (education), business, computer, Response system
الوصف: We present here an extension of Morrison’s and Ruder’s “Sequence-Response Questions” (SRQs) that allows for more nuance in the assessment of student responses to these questions. We have implemented grading software (which we call ANGST, “Automated Nuanced Grading & Statistics Tool”) in a Microsoft Excel sheet that can take SRQ answer data from any source and flexibly and automatically grade these responses with partial credit. This allows for instructors to assess a range of understanding of material from student-generated answers as in a traditional written exam, while still reducing grading workload for large classes. It also allows instructors to do automated statistical analysis on the most popular answers, and subanswers, either from sources like exams or classroom response systems (CRSs), to determine common misunderstandings and facilitate adjustments to instruction.
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2
المؤلفون: Michael Alexander Jong, Yoel P. Ohayon, Hatem O. Abdallah, Arun Richard Chandrasekaran, Michael G. Mohsen, Stephen L. Ginell, Ruojie Sha, Chengde Mao, Jens J. Birktoft, Nadrian C. Seeman, Philip S. Lukeman, Paul Chaikin, Carina Hernandez, Xinyu Wang
المصدر: ACS Nano. 13:7957-7965
مصطلحات موضوعية: Materials science, Surface Properties, Dimer, General Physics and Astronomy, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Article, law.invention, Crystal, chemistry.chemical_compound, X-Ray Diffraction, Sticky and blunt ends, law, General Materials Science, Particle Size, Crystallization, Resolution (electron density), General Engineering, DNA, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Crystallography, Monomer, chemistry, Pairing, Nucleic Acid Conformation, Thermodynamics, Self-assembly, 0210 nano-technology
الوصف: DNA tensegrity triangles self-assemble into rhombohedral three-dimensional crystals via sticky ended cohesion. Crystals containing two-nucleotide (nt) sticky ends (GA:TC) have been reported previously, and those crystals diffracted to 4.9 Å at beam line NSLS-I-X25. Here, we analyze the effect of varying sticky end lengths and sequences, as well as the impact of 5’- and 3’-phosphates on crystal formation and resolution. Tensegrity triangle motifs having 1-, 2- and 3-nt sticky ends all form crystals. X-ray diffraction data from the same beam line reveal that the crystal resolution for a 1-nt sticky end (G:C) and a 3-nt sticky end (GAT:ATC) were 3.4 Å and 4.2 Å respectively. Resolutions were determined from complete data sets in each case. We also conducted trials that examined every possible combination of 1-nucleotide and 2-nucleotide sticky-ended phosphorylated strands and successfully crystallized all 16 possible combinations of strands. We observed the position of the 5’-phosphate on either the crossover (1), helical (2), or central strand (3) affected the resolution of the self-assembled crystals for the 2-turn monomer (3.0 Å for 1–2P-3P) and 2-turn dimer sticky ended (4.1 Å for 1–2-3P) systems. We have also examined the impact of the identity of the base flanking the sticky ends, as well as the use of 3’-sticky ends. We conclude that crystal resolution is not a simple consequence of the thermodynamics of the direct nucleotide pairing interactions involved in molecular cohesion in this system.
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المؤلفون: Muaz Sadeia, Philip S. Lukeman, Chao-Min Huang, Roberto C. Andresen Eguiluz, Netzahualcóyotl Arroyo-Currás, Hai-Jun Su, Carlos E. Castro, Kevin W. Plaxco, Tammy Afif, Alexander K. Ng, Yekaterina Fyodorova, Nathan E. Ogden, Natalie Williams
المصدر: Nanoscale, vol 12, iss 26
مصطلحات موضوعية: Analyte, Technology, Materials science, Aptamer, Nanotechnology, Electrons, Bioengineering, DNA, Biosensing Techniques, Electrochemical Techniques, Electron transfer, Electrode, Physical Sciences, Chemical Sciences, Electrochemical biosensor, DNA origami, General Materials Science, Nanometre, Gold, Nanoscience & Nanotechnology, Nanoscopic scale, Electrodes, Biotechnology
الوصف: The specific detection in clinical samples of analytes with dimensions in the tens to hundreds of nanometers, such as viruses and large proteins, would improve disease diagnosis. Detection of these "mesoscale" analytes (as opposed to their nanoscale components), however, is challenging as it requires the simultaneous binding of multiple recognition sites often spaced over tens of nanometers. In response, we have adapted DNA origami, with its unparalleled customizability to precisely display multiple target-binding sites over the relevant length scale, to an electrochemical biosensor platform. Our proof-of-concept employs triangular origami covalently attached to a gold electrode and functionalized with redox reporters. Electrochemical interrogation of this platform successfully monitors mesoscale, target-binding-induced changes in electron transfer in a manner consistent with coarse-grained molecular dynamics simulations. Our approach enables the specific detection of analytes displaying recognition sites that are separated by ∼40 nm, a spacing significantly greater than that achieved in similar sensor architectures employing either antibodies or aptamers.
وصف الملف: application/pdf
URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d0bb452126b87a151fc3ec9f3fd5fe4f
https://escholarship.org/uc/item/342809hx -
4
المؤلفون: Stefan Howorka, Philip S. Lukeman
المصدر: Nature nanotechnology. 10(11)
مصطلحات موضوعية: ComputingMilieux_GENERAL, Medical education, ComputingMilieux_COMPUTERSANDEDUCATION, Biomedical Engineering, MEDLINE, General Materials Science, Bioengineering, Electrical and Electronic Engineering, Condensed Matter Physics, Psychology, Training programme, Engineering physics, Atomic and Molecular Physics, and Optics
الوصف: Philip S. Lukeman and Stefan Howorka provide a training programme to improve the interdisciplinary breadth and depth of a nanoscience research group.
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المؤلفون: Philip S. Lukeman
المصدر: Nature Nanotechnology. 8:784-786
مصطلحات موضوعية: Medical education, Engineering, Universities, ComputingMilieux_THECOMPUTINGPROFESSION, business.industry, Research, Mentors, Biomedical Engineering, ComputerApplications_COMPUTERSINOTHERSYSTEMS, Bioengineering, Condensed Matter Physics, Engineering physics, Biological Science Disciplines, Atomic and Molecular Physics, and Optics, ComputingMilieux_COMPUTERSANDEDUCATION, General Materials Science, Electrical and Electronic Engineering, Set (psychology), business
الوصف: Mentoring undergraduates in a research laboratory requires a different set of skills and approaches than for other lab members. However, if a mentor — be it a faculty member, postdoc or graduate student — can adopt these methods, it can lead to a significantly improved lab experience for everyone involved.
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المؤلفون: Philip S, Lukeman, Mary L, Stevenson, Nadrian C, Seeman
المصدر: Crystal growthdesign. 8(4)
مصطلحات موضوعية: Article
الوصف: Two-dimensional DNA lattices are grown under conditions that also are suitable for the magnesium-free growth of three-dimensional calcium carbonate crystals. These lattices are used to template morphology changes in calcium carbonate. The effects of DNA lattices, sub-assemblies, duplexes, single strands, dinucleotides, and mononucleotides on calcium carbonate morphology are studied. A ”rotated” morphology of calcite is found to predominate when a critical concentration of any polynucleotide is reached in the templating solution.
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المؤلفون: Philip S. Lukeman, Jeremy K. M. Sanders
المصدر: Tetrahedron Letters. 41:10171-10174
مصطلحات موضوعية: Bearing (mechanical), Organic Chemistry, Dimethylaniline, Biochemistry, Combinatorial chemistry, law.invention, chemistry.chemical_compound, Monomer, Molecular recognition, chemistry, law, Drug Discovery, Pyridine, Proton NMR, Organic chemistry
الوصف: Dynamic combinatorial libraries were generated incorporating new pyridine and dimethylaniline containing monomers. These libraries were analyzed using 1 H NMR and HPLC–UV–MS.
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المؤلفون: Mary L. Stevenson, Nadrian C. Seeman, Philip S. Lukeman
المصدر: Crystal Growth & Design. 8:1200-1202
مصطلحات موضوعية: Calcite, Morphology (linguistics), Mineralogy, chemistry.chemical_element, General Chemistry, Calcium, Condensed Matter Physics, Template reaction, chemistry.chemical_compound, Calcium carbonate, chemistry, Chemical engineering, Polynucleotide, General Materials Science, Crystallite, DNA
الوصف: Two-dimensional DNA lattices are grown under conditions that also are suitable for the magnesium-free growth of three-dimensional calcium carbonate crystals. These lattices are used to template morphology changes in calcium carbonate. The effects of DNA lattices, subassemblies, duplexes, single strands, dinucleotides, and mononucleotides on calcium carbonate morphology are studied. A polycrystalline morphology of calcite is found to predominate when a critical concentration of any polynucleotide is reached in the templating solution.
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9Engineering diversity into dynamic combinatorial libraries by use of a small flexible building block
المصدر: New Journal of Chemistry. 22:1015-1018
مصطلحات موضوعية: Xanthene, chemistry.chemical_compound, Chemistry, Block (telecommunications), Materials Chemistry, General Chemistry, Parallel computing, Combinatorial chemistry, Catalysis
الوصف: Oligomerization of preorganized cinchona and xanthene building blocks to produce dynamic combinatorial libraries results in libraries with only a few components. Diversity is generated by the addition of semi-flexible ephedrine and cholate building blocks.
URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::85909d29fd6e94aa3929c071b5165bce
https://doi.org/10.1039/a803935f -
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المؤلفون: Philip S. Lukeman
المصدر: DNA and RNA Nanobiotechnologies in Medicine: Diagnosis and Treatment of Diseases ISBN: 9783642368523
مصطلحات موضوعية: chemistry.chemical_classification, chemistry.chemical_compound, Materials science, Template, chemistry, Polynucleotide, Ribose, Phosphodiester bond, DNA nanotechnology, Nucleic acid, Nanotechnology, Polymer, DNA
الوصف: DNA-based nanotechnology has revolutionized the construction of nanoscale objects and devices—primarily by using Watson–Crick base-pairing to program the self-assembly (and reaction pathways) of DNA oligomers into branched structures. However, Watson–Crick-controlled self-assembly is not limited to the use of the “natural” d-(deoxy)ribose phosphodiester backbone.
URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::48574ceb7e432f18b9040e2803a478a6
https://doi.org/10.1007/978-3-642-36853-0_9
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