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220 lines
12 KiB
220 lines
12 KiB
@article{Ashkin:86,
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author = {A. Ashkin and J. M. Dziedzic and J. E. Bjorkholm and Steven Chu},
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journal = {Opt. Lett.},
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keywords = {Laser beams; Optical trapping; Optical tweezers; Particle scattering; Radiation pressure; Scattering},
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number = {5},
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pages = {288--290},
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publisher = {OSA},
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title = {Observation of a single-beam gradient force optical trap for dielectric particles},
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volume = {11},
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month = {5},
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year = {1986},
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_url = {http://ol.osa.org/abstract.cfm?URI=ol-11-5-288},
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doi = {10.1364/OL.11.000288},
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abstract = {Optical trapping of dielectric particles by a single-beam gradient force trap was demonstrated for the first reported time. This confirms the concept of negative light pressure due to the gradient force. Trapping was observed over the entire range of particle size from 10 $\mu$m to ~25 nm in water. Use of the new trap extends the size range of macroscopic particles accessible to optical trapping and manipulation well into the Rayleigh size regime. Application of this trapping principle to atom trapping is considered.},
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}
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@article{HARADA1996529,
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title = "Radiation forces on a dielectric sphere in the Rayleigh scattering regime",
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journal = "Optics Communications",
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volume = "124",
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number = "5",
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pages = "529 - 541",
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year = "1996",
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issn = "0030-4018",
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doi = "10.1016/0030-4018(95)00753-9",
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_doi = "https://doi.org/10.1016/0030-4018(95)00753-9",
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_url = "http://www.sciencedirect.com/science/article/pii/0030401895007539",
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author = "Yasuhiro Harada and Toshimitsu Asakura",
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abstract = "Theoretical expressions of the radiation pressure force for a dielectric sphere in the Rayleigh regime of light scattering under illumination of a Gaussian laser beam with the fundamental mode are derived in explicit form as a function of measurable quantities of the beam parameter in MKS units. Correctness of the derived expressions and validity of the size range of the Rayleigh approximation for the radiation forces as a sum of the scattering force and the gradient force are investigated by a graphical comparison of the calculated forces in longitudinal and transverse components with those obtained from the generalized Lorenz-Mie theory. Fairly good agreement in both components is found within ordinary particle-size ranges of the Rayleigh scattering theory. Furthermore, the good agreement in the transverse component, where the gradient force is dominant, is found to be satisfactory beyond the existing criterion in particle size of the Rayleigh scattering theory until the particle size becomes comparable with the spot size of the illuminating laser beam."
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}
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@article{10.1093/nar/28.1.27,
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author = {Kanehisa, Minoru and Goto, Susumu},
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title = "{KEGG: Kyoto Encyclopedia of Genes and Genomes}",
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journal = {Nucleic Acids Research},
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volume = {28},
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number = {1},
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pages = {27-30},
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year = {2000},
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month = {01},
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abstract = "{KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www.genome.ad.jp/kegg/ ).}",
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issn = {0305-1048},
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doi = {10.1093/nar/28.1.27},
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_url = {https://doi.org/10.1093/nar/28.1.27},
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_eprint = {https://academic.oup.com/nar/article-pdf/28/1/27/9895154/280027.pdf},
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}
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@article{10.1093/nar/gky962,
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author = {Kanehisa, Minoru and Sato, Yoko and Furumichi, Miho and Morishima, Kanae and Tanabe, Mao},
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title = "{New approach for understanding genome variations in KEGG}",
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journal = {Nucleic Acids Research},
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volume = {47},
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number = {D1},
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pages = {D590-D595},
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year = {2018},
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month = {10},
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abstract = "{KEGG (Kyoto Encyclopedia of Genes and Genomes; https://www.kegg.jp/ or https://www.genome.jp/kegg/) is a reference knowledge base for biological interpretation of genome sequences and other high-throughput data. It is an integrated database consisting of three generic categories of systems information, genomic information and chemical information, and an additional human-specific category of health information. KEGG pathway maps, BRITE hierarchies and KEGG modules have been developed as generic molecular networks with KEGG Orthology nodes of functional orthologs so that KEGG pathway mapping and other procedures can be applied to any cellular organism. Unfortunately, however, this generic approach was inadequate for knowledge representation in the health information category, where variations of human genomes, especially disease-related variations, had to be considered. Thus, we have introduced a new approach where human gene variants are explicitly incorporated into what we call ‘network variants’ in the recently released KEGG NETWORK database. This allows accumulation of knowledge about disease-related perturbed molecular networks caused not only by gene variants, but also by viruses and other pathogens, environmental factors and drugs. We expect that KEGG NETWORK will become another reference knowledge base for the basic understanding of disease mechanisms and practical use in clinical sequencing and drug development.}",
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issn = {0305-1048},
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doi = {10.1093/nar/gky962},
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_url = {https://doi.org/10.1093/nar/gky962},
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_eprint = {https://academic.oup.com/nar/article-pdf/47/D1/D590/27436321/gky962.pdf},
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}
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@article{doi:10.1002/pro.3715,
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author = {Kanehisa, Minoru},
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title = {Toward understanding the origin and evolution of cellular organisms},
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journal = {Protein Science},
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volume = {28},
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number = {11},
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pages = {1947-1951},
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keywords = {KEGG, KEGG MEDICUS, KEGG module, pathway mapping, reaction module},
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doi = {10.1002/pro.3715},
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_url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.3715},
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_eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/pro.3715},
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abstract = {Abstract In this era of high-throughput biology, bioinformatics has become a major discipline for making sense out of large-scale datasets. Bioinformatics is usually considered as a practical field developing databases and software tools for supporting other fields, rather than a fundamental scientific discipline for uncovering principles of biology. The KEGG resource that we have been developing is a reference knowledge base for biological interpretation of genome sequences and other high-throughput data. It is now one of the most utilized biological databases because of its practical values. For me personally, KEGG is a step toward understanding the origin and evolution of cellular organisms.},
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year = {2019}
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}
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@article{Capitanio2012,
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doi = {10.1038/nmeth.2152},
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_url = {https://doi.org/10.1038/nmeth.2152},
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year = {2012},
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month = sep,
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publisher = {Springer Science and Business Media {LLC}},
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volume = {9},
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number = {10},
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pages = {1013--1019},
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author = {Marco Capitanio and Monica Canepari and Manuela Maffei and Diego Beneventi and Carina Monico and Francesco Vanzi and Roberto Bottinelli and Francesco Saverio Pavone},
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title = {Ultrafast force-clamp spectroscopy of single molecules reveals load dependence of myosin working stroke},
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journal = {Nature Methods}
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}
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@manual{gclib,
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url = {http://www.galil.com/sw/pub/all/doc/gclib/html/index.html},
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title = {Communications API for Galil controllers and PLCs},
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author = {GalilMC}
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}
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@article{Muhamed2017,
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doi = {10.3390/bioengineering4010012},
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_url = {https://doi.org/10.3390/bioengineering4010012},
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year = {2017},
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month = feb,
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publisher = {{MDPI} {AG}},
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volume = {4},
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number = {4},
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pages = {12},
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author = {Ismaeel Muhamed and Farhan Chowdhury and Venkat Maruthamuthu},
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title = {Biophysical Tools to Study Cellular Mechanotransduction},
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journal = {Bioengineering}
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}
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@article{Arbore2019,
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doi = {10.1007/s12551-019-00599-y},
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_url = {https://doi.org/10.1007/s12551-019-00599-y},
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year = {2019},
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month = oct,
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publisher = {Springer Science and Business Media {LLC}},
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volume = {11},
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number = {5},
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pages = {765--782},
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author = {Claudia Arbore and Laura Perego and Marios Sergides and Marco Capitanio},
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title = {Probing force in living cells with optical tweezers: from single-molecule mechanics to cell mechanotransduction},
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journal = {Biophysical Reviews}
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}
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@article{Goldmann2016,
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doi = {10.1002/cbin.10563},
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_url = {https://doi.org/10.1002/cbin.10563},
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year = {2016},
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month = jan,
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publisher = {Wiley},
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volume = {40},
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number = {3},
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pages = {241--256},
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author = {Wolfgang H. Goldmann},
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title = {Role of vinculin in cellular mechanotransduction},
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journal = {Cell Biology International}
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}
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@article{Dumbauld2014,
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doi = {10.4161/cam.29139},
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_url = {https://doi.org/10.4161/cam.29139},
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year = {2014},
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month = oct,
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publisher = {Informa {UK} Limited},
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volume = {8},
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number = {6},
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pages = {550--557},
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author = {David W Dumbauld and Andr{\'{e}}s J Garc{\'{\i}}a},
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title = {A helping hand: How vinculin contributes to cell-matrix and cell-cell force transfer},
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journal = {Cell Adhesion {\&} Migration}
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}
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@article{Vasileva2020,
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doi = {10.1101/2020.05.14.095364},
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_url = {https://doi.org/10.1101/2020.05.14.095364},
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year = {2020},
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month = 5,
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publisher = {Cold Spring Harbor Laboratory},
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author = {Ekaterina Vasileva and Florian Rouaud and Domenica Spadaro and Wenmao Huang and Adai Colom and Arielle Flinois and Jimit Shah and Vera Dugina and Christine Chaponnier and Sophie Sluysmans and Isabelle M{\'{e}}an and Lionel Jond and Aur{\'{e}}lien Roux and Jie Yan and Sandra Citi},
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title = {Cingulin unfolds {ZO}-1 and organizes myosin-2B and $\Gamma$-actin to mechanoregulate apical and tight junction membranes}
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}
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@article{Monico2014,
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doi = {10.3791/51446},
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_url = {https://doi.org/10.3791/51446},
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year = {2014},
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month = aug,
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publisher = {{MyJove} Corporation},
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number = {90},
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author = {Carina Monico and Gionata Belcastro and Francesco Vanzi and Francesco S. Pavone and Marco Capitanio},
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title = {Combining Single-molecule Manipulation and Imaging for the Study of Protein-{DNA} Interactions},
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journal = {Journal of Visualized Experiments}
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}
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@article{Gittes1998,
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doi = {10.1007/s002490050113},
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_url = {https://doi.org/10.1007/s002490050113},
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year = {1998},
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month = jan,
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publisher = {Springer Science and Business Media {LLC}},
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volume = {27},
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number = {1},
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pages = {75--81},
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author = {Frederick Gittes and C. F. Schmidt},
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title = {Thermal noise limitations on micromechanical experiments},
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journal = {European Biophysics Journal}
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}
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@article{Welch1967,
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doi = {10.1109/tau.1967.1161901},
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_url = {https://doi.org/10.1109/tau.1967.1161901},
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year = {1967},
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month = jun,
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publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
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volume = {15},
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number = {2},
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pages = {70--73},
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author = {P. Welch},
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title = {The use of fast Fourier transform for the estimation of power spectra: A method based on time averaging over short, modified periodograms},
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journal = {{IEEE} Transactions on Audio and Electroacoustics}
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}
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@article{Oheim2019,
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doi = {10.1016/j.bpj.2019.07.048},
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_url = {https://doi.org/10.1016/j.bpj.2019.07.048},
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year = {2019},
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month = sep,
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publisher = {Elsevier {BV}},
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volume = {117},
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number = {5},
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pages = {795--809},
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author = {Martin Oheim and Adi Salomon and Adam Weissman and Maia Brunstein and Ute Becherer},
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title = {Calibrating Evanescent-Wave Penetration Depths for Biological {TIRF} Microscopy},
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journal = {Biophysical Journal}
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}
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