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Статті в журналах з теми "Single-molecule biophysic"

Автор: Grafiati

Опубліковано: 10 березня 2023

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1

Noji, Hroyuki. "SINGLE MOLECULE BIOPHYSICS OF F_1-ATPase motor protein." Proceedings of the Asian Pacific Conference on Biomechanics : emerging science and technology in biomechanics 2007.3 (2007): S1. http://dx.doi.org/10.1299/jsmeapbio.2007.3.s1.

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2

Weng, Zhuangfeng, Yuan Shang, Zeyang Ji, Fei Ye, Lin Lin, Rongguang Zhang, and Jinwei Zhu. "Structural Basis of Highly Specific Interaction between Nephrin and MAGI1 in Slit Diaphragm Assembly and Signaling." Journal of the American Society of Nephrology 29, no. 9 (July 13, 2018): 2362–71. http://dx.doi.org/10.1681/asn.2017121275.

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BackgroundThe slit diaphragm is a specialized adhesion junction between opposing podocytes, establishing the final filtration barrier that prevents passage of proteins from the capillary lumen into the urinary space. Nephrin, the key structural and signaling adhesion molecule expressed in the slit diaphragm, contains an evolutionally conserved, atypical PDZ-binding motif (PBM) reported to bind to a variety of proteins in the slit diaphragm. Several mutations in NPHS1 (the gene encoding nephrin) that result in nephrin lacking an intact PBM are associated with glomerular diseases. However, the molecular basis of nephrin-PBM–mediated protein complexes is still unclear.MethodsUsing a combination of biochemic, biophysic, and cell biologic approaches, we systematically investigated the interactions between nephrin-PBM and PDZ domain–containing proteins in the slit diaphragm.ResultsWe found that nephrin-PBM specifically binds to one member of the membrane-associated guanylate kinase family of scaffolding proteins, MAGI1, but not to another, MAGI2. The complex structure of MAGI1-PDZ3/nephrin-PBM reveals that the Gly at the −3 position of nephrin-PBM is the determining feature for MAGI1-PDZ3 recognition, which sharply contrasts with the typical PDZ/PBM binding mode. A single gain-of-function mutation within MAGI2 enabled nephrin-PBM binding. In addition, using our structural analysis, we developed a highly efficient inhibitory peptide capable of specifically blocking the nephrin/MAGI1 interaction.ConclusionsMAGI1 interacts with nephrin-PBM with exquisite specificity. A newly developed, potent inhibitory peptide that blocks this interaction may be useful for future functional investigations in vivo. Our findings also provide possible explanations for the diseases caused by NPHS1 mutations.

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3

LI, Chun-Biu, and Tamiki KOMATSUZAKI. "Handling Noisy Data from Single Molecule Experiments." Seibutsu Butsuri 54, no. 5 (2014): 257–58. http://dx.doi.org/10.2142/biophys.54.257.

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4

Joshi, Prakash, and Partha Pratim Mondal. "Single-Molecule Clustering for Super-Resolution Optical Fluorescence Microscopy." Photonics 9, no. 1 (December 24, 2021): 7. http://dx.doi.org/10.3390/photonics9010007.

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Molecular assembly in a complex cellular environment is vital for understanding underlying biological mechanisms. Biophysical parameters (such as single-molecule cluster density, cluster-area, pairwise distance, and number of molecules per cluster) related to molecular clusters directly associate with the physiological state (healthy/diseased) of a cell. Using super-resolution imaging along with powerful clustering methods (K-means, Gaussian mixture, and point clustering), we estimated these critical biophysical parameters associated with dense and sparse molecular clusters. We investigated Hemaglutinin (HA) molecules in an Influenza type A disease model. Subsequently, clustering parameters were estimated for transfected NIH3T3 cells. Investigations on test sample (randomly generated clusters) and NIH3T3 cells (expressing Dendra2-Hemaglutinin (Dendra2-HA) photoactivable molecules) show a significant disparity among the existing clustering techniques. It is observed that a single method is inadequate for estimating all relevant biophysical parameters accurately. Thus, a multimodel approach is necessary in order to characterize molecular clusters and determine critical parameters. The proposed study involving optical system development, photoactivable sample synthesis, and advanced clustering methods may facilitate a better understanding of single molecular clusters. Potential applications are in the emerging field of cell biology, biophysics, and fluorescence imaging.

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5

Kinz-Thompson, Colin D., Korak Kumar Ray, and Ruben L. Gonzalez. "Bayesian Inference: The Comprehensive Approach to Analyzing Single-Molecule Experiments." Annual Review of Biophysics 50, no. 1 (May 6, 2021): 191–208. http://dx.doi.org/10.1146/annurev-biophys-082120-103921.

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Biophysics experiments performed at single-molecule resolution provide exceptional insight into the structural details and dynamic behavior of biological systems. However, extracting this information from the corresponding experimental data unequivocally requires applying a biophysical model. In this review, we discuss how to use probability theory to apply these models to single-molecule data. Many current single-molecule data analysis methods apply parts of probability theory, sometimes unknowingly, and thus miss out on the full set of benefits provided by this self-consistent framework. The full application of probability theory involves a process called Bayesian inference that fully accounts for the uncertainties inherent to single-molecule experiments. Additionally, using Bayesian inference provides a scientifically rigorous method of incorporating information from multiple experiments into a single analysis and finding the best biophysical model for an experiment without the risk of overfitting the data. These benefits make the Bayesian approach ideal for analyzing any type of single-molecule experiment.

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6

Gopich, Irina V. "2SD0925 Theory of single-molecule photon trajectories and FRET efficiency distributions(2SD Bridging Single Molecule Biophysics and System Biology:New Experimental and Theoretical Challenges,The 48th Annual Meeting of the Biophysical Society of Japan)." Seibutsu Butsuri 50, supplement2 (2010): S12. http://dx.doi.org/10.2142/biophys.50.s12_2.

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7

Ritchie, Ken. "S01H3 Single molecule imaging of diffusion in E. Coll membranes(Systems Biology of Intracellular Signaling as Studied by Single-Molecule Imaging)." Seibutsu Butsuri 47, supplement (2007): S1. http://dx.doi.org/10.2142/biophys.47.s1_3.

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8

Cao, Jianshu. "1S5-5 Generic models for single molecule biological processes : Generic models for single molecule biological processes(1S5 Linking single molecule spectroscopy and energy landscape perspectives,The 46th Annual Meeting of the Biophysical Society of Japan)." Seibutsu Butsuri 48, supplement (2008): S5. http://dx.doi.org/10.2142/biophys.48.s5_1.

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9

Sei, Kazuto, Akinori Baba, Chun Biu Li, and Tamiki Komatsuzaki. "1P537 Randomness and Memory in Single Molecule Time Series(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S281. http://dx.doi.org/10.2142/biophys.46.s281_1.

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10

Fernandez, Julio M. "S3B1 Protein mechanics studied with single molecule AFM techniques.(Single Molecure Dynamics and Reactions)." Seibutsu Butsuri 42, supplement2 (2002): S13. http://dx.doi.org/10.2142/biophys.42.s13_4.

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11

Fujisawa, Ryo, Daichi Okuno, and Hiroyuki Noji. "1P526 Single-molecule analysis of F_1-motor loaded with nonhydrolyzable substrate(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S278. http://dx.doi.org/10.2142/biophys.46.s278_2.

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12

Ueno, Taro, Takashi Tanii, Naonobu Shimamoto, Takeo Miyake, Hironori Sonobe, Iwao Odomari, and Takashi Funatsu. "1P542 Single molecule imaging of chaperonin functions using zero-mode waveguides(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S282. http://dx.doi.org/10.2142/biophys.46.s282_2.

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13

Otsuka, Shotaro, Hirohide Takahashi, and Shige H. Yoshimura. "1P543 Single-molecule structural and functional analyses of nuclear pore complex(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S282. http://dx.doi.org/10.2142/biophys.46.s282_3.

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14

Morimatsu, Miki, Hiroaki Takagi, Kosuke Ohta, Toshio Yanagida, and Yasushi Sako. "1P547 Kinetic analysis of EGFR/Grb2 interactions using single-molecule imaging(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S283. http://dx.doi.org/10.2142/biophys.46.s283_3.

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15

Gopich, Irina V. "1S5-4 Decoding the pattern of photon colors in single-molecule FRET : Decoding the pattern of photon colors in single-molecule FRET(1S5 Linking single molecule spectroscopy and energy landscape perspectives,The 46th Annual Meeting of the Biophysical Society of Japan)." Seibutsu Butsuri 48, supplement (2008): S4—S5. http://dx.doi.org/10.2142/biophys.48.s4_6.

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16

Nguyen, Anh Thi Van, Y. Kamio, and H. Higuchi. "1H1430 Single-Molecule Visualization of Hemolysin Assembly on Erythrocyte Membranes." Seibutsu Butsuri 42, supplement2 (2002): S44. http://dx.doi.org/10.2142/biophys.42.s44_3.

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17

Ueno, Hiroshi, Kazuhito Tabata, Toshiharu Suzuki, Toru Ide, Masasuke Yoshida, and Hiroyuki Noji. "1P528 Development of the Single Molecule Imaging System of the F_0 Motor(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S278. http://dx.doi.org/10.2142/biophys.46.s278_4.

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18

Thumkeo, Dean, Takuji Yoshihara, Toshio Yanagida, and Masahiro Ueda. "1P538 Single-molecule imaging of Ras-PI3K signaling in chemotaxing Dictyostelium cells(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S281. http://dx.doi.org/10.2142/biophys.46.s281_2.

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19

Baba, Akinori, and Tamiki Komatsuzaki. "1P539 Applicability of local ergodic state analysis of single molecule time series(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S281. http://dx.doi.org/10.2142/biophys.46.s281_3.

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20

Yokota, Hiroaki, Yong-Woon Han, Jean-Francois Allemand, Xugang Xi, Vincent Croquette, David Bensimon, and Yoshie Harada. "1P556 Novel microscopy for simultaneous single molecule measurement of DNA/protein interaction(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S285. http://dx.doi.org/10.2142/biophys.46.s285_4.

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21

Taniguchi, Masateru. "1SBP-04 Single Molecule Electrical Sequencing of DNA and microRNA(1SBP Advanced Single Molecule Sequencing System,Symposium,The 51th Annual Meeting of the Biophysical Society of Japan)." Seibutsu Butsuri 53, supplement1-2 (2013): S87. http://dx.doi.org/10.2142/biophys.53.s87_5.

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22

Nakamura, Mariko, Hiroshi Ueno, Hiromi Imamura, and Hiroyuki Noji. "1P525 Designing a mutant F_1-ATPase for easy and rapid single molecule analysis(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S278. http://dx.doi.org/10.2142/biophys.46.s278_1.

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23

Kobayashi, T., M. Murakami, T. Kawasaki, A. Yoshimura, and A. Kusumi. "S2L1 Single molecule analysis of intracellular signal transduction in living cells." Seibutsu Butsuri 42, supplement2 (2002): S11. http://dx.doi.org/10.2142/biophys.42.s11_1.

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24

Tao, Nongjian. "Nanoelectronics, sensors and single molecule biophysics." Journal of Physics: Condensed Matter 24, no. 16 (March 30, 2012): 160301. http://dx.doi.org/10.1088/0953-8984/24/16/160301.

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25

Ma, Long, and Scott L. Cockroft. "Biological Nanopores for Single-Molecule Biophysics." ChemBioChem 11, no. 1 (November 24, 2009): 25–34. http://dx.doi.org/10.1002/cbic.200900526.

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26

Leake, Mark C. "The physics of life: one molecule at a time." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1611 (February 5, 2013): 20120248. http://dx.doi.org/10.1098/rstb.2012.0248.

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The esteemed physicist Erwin Schrödinger, whose name is associated with the most notorious equation of quantum mechanics, also wrote a brief essay entitled ‘What is Life?’, asking: ‘How can the events in space and time which take place within the spatial boundary of a living organism be accounted for by physics and chemistry?’ The 60+ years following this seminal work have seen enormous developments in our understanding of biology on the molecular scale, with physics playing a key role in solving many central problems through the development and application of new physical science techniques, biophysical analysis and rigorous intellectual insight. The early days of single-molecule biophysics research was centred around molecular motors and biopolymers, largely divorced from a real physiological context. The new generation of single-molecule bioscience investigations has much greater scope, involving robust methods for understanding molecular-level details of the most fundamental biological processes in far more realistic, and technically challenging, physiological contexts, emerging into a new field of ‘single-molecule cellular biophysics’. Here, I outline how this new field has evolved, discuss the key active areas of current research and speculate on where this may all lead in the near future.

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27

Tani, Tomomi, Shalin Mehta, Rudolf Oldenbourg, and Amy Gladfelter. "2P298 Fluorescent Single Molecule Orinetation Imaging in Living Cells(27. Bioimaging,Poster)." Seibutsu Butsuri 53, supplement1-2 (2013): S208. http://dx.doi.org/10.2142/biophys.53.s208_3.

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28

Nguyen, Anh Thi Van, Y. Kamio, and H. Higuchi. "2N1630 Single-Molecule Imaging of Cooperative Assembly of Hemolysin on Erythrocyte Membranes." Seibutsu Butsuri 42, supplement2 (2002): S143. http://dx.doi.org/10.2142/biophys.42.s143_3.

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29

Nakada, C., Kenneth Ritchie, T. Fujiwara, M. Nakamura, Y. Oba, Y. Hotta, R. Iino, K. Yamaguchi, and A. Kusumi. "LS3A1 Diffusion barrier in the neuronal cell membrane : a single molecule study." Seibutsu Butsuri 42, supplement2 (2002): S223. http://dx.doi.org/10.2142/biophys.42.s223_4.

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30

Sakamoto, Kuniko, Takahiro Fujiwara, and Akihiro Kusumi. "1P550 Detection of transient arrest of lateral diffusion of membrane molecules in single-molecule tracking trajectories(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S284. http://dx.doi.org/10.2142/biophys.46.s284_2.

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31

Ritchie, Kenneth, and A. Kusumi. "S3B3 Single molecule scanning in-plane force imaging of the membrane of live cells(Single Molecure Dynamics and Reactions)." Seibutsu Butsuri 42, supplement2 (2002): S14. http://dx.doi.org/10.2142/biophys.42.s14_2.

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32

Li, Chun Biu, and Tamiki Komatsuzaki. "1P535 Extracting Dynamics from Time Series Data of Single Molecule Experiments on a Photo-by-Photo Basis(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S280. http://dx.doi.org/10.2142/biophys.46.s280_3.

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33

Jarzynski, Christopher. "Work Fluctuation Theorems and Single-Molecule Biophysics." Progress of Theoretical Physics Supplement 165 (2006): 1–17. http://dx.doi.org/10.1143/ptps.165.1.

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34

Krapf, Diego. "Dynamic fluctuations in single-molecule biophysics experiments." Physics of Life Reviews 13 (June 2015): 148–49. http://dx.doi.org/10.1016/j.plrev.2015.04.019.

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35

Makarov, Dmitrii E., and Benjamin Schuler. "Preface: Special Topic on Single-Molecule Biophysics." Journal of Chemical Physics 148, no. 12 (March 28, 2018): 123001. http://dx.doi.org/10.1063/1.5028275.

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36

Yanagida, Toshio. "S2h1-2 Single molecule study for elucidating the mechanism involved in utilizing fluctuations by biosystems(S2-h1: "Single Molecule Analysis of Molecular Motor",Symposia,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S127. http://dx.doi.org/10.2142/biophys.46.s127_1.

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37

Su, Qian Peter, and Lining Arnold Ju. "Biophysical nanotools for single-molecule dynamics." Biophysical Reviews 10, no. 5 (August 18, 2018): 1349–57. http://dx.doi.org/10.1007/s12551-018-0447-y.

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38

Stratmann, S. A., and A. M. van Oijen. "DNA replication at the single-molecule level." Chem. Soc. Rev. 43, no. 4 (2014): 1201–20. http://dx.doi.org/10.1039/c3cs60391a.

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39

Tsukasaki, Yoshikazu, Kazuo Kitamura, Kazuya Shimizu, Atsuko_H Iwane, Yoshimi Takai, and Toshio Yanagida. "1P541 Multiple domain interactions between the single cell adhesion molecule, nectin and cadherin, revealed by high sensitive force measurements(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S282. http://dx.doi.org/10.2142/biophys.46.s282_1.

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40

Fujiwara, Takahiro, Kokoro Iwasawa, Ken Ritchie, Kotono Murase, Yasuhiro Umemura, Hidetoshi Yamashita, Kenichi Suzuki, and Akihiro Kusumi. "1P548 Corralling of phospholipids and transmembrane proteins by "fences" and "pickets" in the cell membrane : single-molecule tracking study(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S283. http://dx.doi.org/10.2142/biophys.46.s283_4.

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41

Umemura, Yasuhiro, Takahiro Fujiwara, Kenichi Suzuki, Marija Vrljic, Stefanie Y. Nishimura, W. E. Moerner, Harden M. McConnell, and Akihiro Kusumi. "1P549 Both MHC class II and its GPI-anchored form undergo hop diffusion as observed by single-molecule tracking(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S284. http://dx.doi.org/10.2142/biophys.46.s284_1.

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42

Hayashi, Masahito, and Yoshie Harada. "1P553 Direct observation of the twisting motion of a single DNA molecule caused by the intercalation of ethidium bromide(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S285. http://dx.doi.org/10.2142/biophys.46.s285_1.

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43

Li, Chun Biu, and Tamiki Komatsuzaki. "2SD1105 When one plus one is more than two : Theoretical challenges in learning from the next generation single- and multiple- molecule experiments(2SD Bridging Single Molecule Biophysics and System Biology:New Experimental and Theoretical Challenges,The 48th Annual Meeting of the Biophysical Society of Japan)." Seibutsu Butsuri 50, supplement2 (2010): S13. http://dx.doi.org/10.2142/biophys.50.s13_2.

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44

Tani, Tomomi, Kenta Saito, and Takeharu Nagai. "1P536 Single molecule imaging of nerve growth factor receptor trkA expressed in the growth cones of dorsal root ganglion explants(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S280. http://dx.doi.org/10.2142/biophys.46.s280_4.

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45

Komatsuzaki, Tamiki. "1S5-1 Multiscale Complex Network and Effective Free Energy Landscape Extracted from Single-Molecule Time Series(1S5 Linking single molecule spectroscopy and energy landscape perspectives,The 46th Annual Meeting of the Biophysical Society of Japan)." Seibutsu Butsuri 48, supplement (2008): S4. http://dx.doi.org/10.2142/biophys.48.s4_4.

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46

Shashkova, Sviatlana, and Mark C. Leake. "Systems biophysics: Single-molecule optical proteomics in single living cells." Current Opinion in Systems Biology 7 (February 2018): 26–35. http://dx.doi.org/10.1016/j.coisb.2017.11.006.

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47

Qian, Hong, and S. C. Kou. "Statistics and Related Topics in Single-Molecule Biophysics." Annual Review of Statistics and Its Application 1, no. 1 (January 3, 2014): 465–92. http://dx.doi.org/10.1146/annurev-statistics-022513-115535.

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48

Grohmann, Dina, Finn Werner, and Philip Tinnefeld. "Making connections—strategies for single molecule fluorescence biophysics." Current Opinion in Chemical Biology 17, no. 4 (August 2013): 691–98. http://dx.doi.org/10.1016/j.cbpa.2013.05.020.

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49

Wichner, Sara M., Mark A. DeWitt, Bruce E. Cohen, and Ahmet Yildiz. "Novel Quantum Dot Probes for Single-Molecule Biophysics." Biophysical Journal 106, no. 2 (January 2014): 633a. http://dx.doi.org/10.1016/j.bpj.2013.11.3500.

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Anselmetti, Dario, Jürgen Fritz, Benjamin Smith, and Xavier Fernandez-Busquets. "Single Molecule DNA Biophysics with Atomic Force Microscopy." Single Molecules 1, no. 1 (April 2000): 53–58. http://dx.doi.org/10.1002/(sici)1438-5171(200004)1:1<53::aid-simo53>3.0.co;2-u.

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