Momoko KUMEMURA, Dr.

kumemura_photo__2.JPG Host Laboratory FUJITA LAB.
Position in LIMMS CNRS Post-Doc, Research Engineer

Main Research Topic in LIMMS

Bio-MEMS - Detection of circular DNA pathogens using rolling circle amplification by MEMS devices

Keywords

RCA, DNA amplification, Silicon nanotweezers
Contact

LIMMS/CNRS-IIS (UMI 2820)
Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
Phone:+81 (0)3 5452 6036 / Fax:+81 (0)3 5452 6088

E-mail momo at iis.u-tokyo.ac.jp
Download icon_pdf.gifAbstract2015_MKumemura.pdf ,

Resume

Short resume :
2012-now Actual position
2008-2012 Here
2004-2008 Here
2001-2003 Here

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Research Projects in Limms

1- Detection of circular DNA pathogens using rolling circle amplification by MEMS devices

Context :
Rolling Circle amplification (RCA) is important and powerful analytical method for the detection of circular DNA sequences. Isothermal capacity of RCA offers important advantage over existing DNA amplification strategies which eliminates the need for a thermal cycler and permits operation at near room temperatures reaching amplification rates of up to 10,000-fold in a few hours [1].
Objectives & Methods :
This project aims to develop a simple diagnostic microchip for infectious disease. With integration of electrodes, employing specific anchoring of primers, multiple bacterial and viral pathogens will be detected. To achieve this final gold, we are investigating RCA using silicon nanotweezers (SNT). Condition of DNA amplification and detection was optimized by an established SNT.
Results :
We prepared simple glass slit for DNA amplification. Introducing SNT tips into reaction solution in the glass slit, RCA was proceeded. After 2 hours incubation, SNT was completely retrieved and DNA bridge formed between the tips was visually confirmed (Fig. 1 and 2). The current of bridged DNA between tips was measured. According to our measurements, the current increased nearly 1,000,000 times after DNA amplification. This large increase could be partially due to a deposition of salts on the arms of the SNT during the incubation steps resulting in the increase of overall SNT conductivity. After this experiment, we found we can prevent this effect by coating hydrophobic surface between tips end and SNT main body. Further optimization is underway.

Fig1.png

Fig. 1 ssDNA bridge between the tips of the SNT (in air).

Fig2.png

Fig. 2 Schematic RCA and ssDNA bridging of SNT tips via dielectrophoresis.

References :
[1]  F. B. Dean, J. R. Nelson, T. L. Giesler, R. S. Lasken, Genome Res., 11, pp. 1095-1099, 2001.
[2] M. Kumemura, S.L. Karsten, D. Collard, H. Fujita, Proceedings of The Asia-Pacific Interdisciplinary Research Conference 2011 (AP-IRC 2011), p.190, Toyohashi, Japan, 2011.
[3] M. Kumemura, S. L. Karsten, N. Lafitte, H. Guillou, L. Jalabert, H. Fujita, D. Collard, Proceedings of The 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS 2013), pp.1992-1994, Oct. 31. 2013. Freiburg, Germany.

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Main publication List (papers, conferences and patent)

2014

Journals
  1. R. Renaudot, Y. Fouillet, L. Jalabert, M. Kumemura, D. Collard, H. Fujita, et al., "Performances of a broad range of dielectric stacks for Liquid Dielectrophoresis transduction," Microfluidics Nanofluidics, vol. 16, pp. 620-626, 2014.
  2. R. Renaudot, Y. Fouillet, L. Jalabert, M. Kumemura, D. Collard, H. Fujita, et al., "Programmable LDEP technology to fabricate versatile master molds for PDMS continuous-flow microfluidic applications," Microfluid Nanofluid, vol. 16, pp. 701-710, 2014.
  3. N. Lafitte, Y. Haddab, Y. Le Gorrec, M. Kumemura, L. Jalabert, C. Yamahata, et al., "DNA manipulation based on nanotweezers " in Enclyclopedia of nanotechnology, B. Bhusban, Ed., ed: Springer, 2014, p. (in press).
  4. D. Collard, N. Lafitte, H. Guillou, M. Kumemura, L. Jalabert, and H. Fujita, "Silicon Nano Tweezers for molecules and cells manipulation and characterization," in Emerging Tools for Micro and Nano Manipulation, X. Liu and Y. Sun, Eds., ed: Wiley-VCH, 2014, p. (in press).
Conferences
  1. G. Perret, T. Lacornerie, M. Kumemura, H. Guillou, L. Jalabert, E. Lartigau, T. Fujii, F. Cleri, H. Fujita, D. Collard, "Silicon nanotweezers inside liquid for the real time characterization of DNA degradation under radiotherapy treatment", E-MRS Spring meeting 2014, Symposium N, May 26-29, Lille (France).
  2. M. Kumemura, S. L. Karsten, N. Lafitte, H. Guillou, L. Jalabert, H. Fujita, D. Collard, ELECTRICAL DETECTION OF AMPLIFIED DNA USING SILICON NANOTWEEZERS, 7th Asia-Pacific Conference on Transducers and Micro/Nano Technologies (APCOT2014), 11-3 (2pages), June 29 - July 2, 2014 / EXCO, Daegu, Korea.
  3. H. Guillou, N. Iwanaka, N. Lafitte, M. Kumemura, K. Shimizu, L. Jalabert, S. Kaneda, T. Fujii, H. Fujita, K. Sakata, S. Konishi, D. Collard, SILICON NANO TWEEZERS WITH FORCE/STIFFNESS/LOSSES MEASUREMENTS OF LOCAL CONTRACTILITY OF MYOCYTES, 7th Asia-Pacific Conference on Transducers and Micro/Nano Technologies (APCOT2014), 11-6 (2pages), June 29 - July 2, 2014 / EXCO, Daegu, Korea.
  4. P-T. Chiang, M. Kumemura , H.Fujita, G. Perret, N. Lafitte, L.Jalabert, D. Collard, A. Enomoto, K. Miyagawa, Real-time Measurement of DNA Degradation under Radiation by Silicon Nanotweezers Coupled with Microfluidic Cavity, Technical Meeting on Sensors and Micromachines 2014.

 

2013

Journals
  1. M. Kumemura, et al, Proc. MicroTAS 2013, pp.1992-1994, 2013.
  2. R. Renaudot, V. Agache, Y. Fouillet, G. Laffite, L. Jalabert, E. Bisceglia, M. Kumemura, D. Collard and H. Fujita, "A programmable and reconfigurable microfluidic chip", Lab Chip,Lab Chip, 2013,13, 4517-4524, DOI: 10.1039/C3LC50850A
  3. R. Renaudot, Y. Fouillet, L. Jalabert, M. Kumemura, D. Collard, H. Fujita, V. Agache “Programmable LDEP technology to fabricate versatile master molds for PDMS continuous-flow microfluidic applications”, Microfluidics and Nanofluidics, Sept. 2013, DOI 10.1007/s10404-013-1256-z
  4. D. Collard, S. H. Kim, T. Osaki, M. Kumemura, B. Kim, D. Fourmy, T. Fujii, S. Takeuchi, S. L. Karsten, and H. Fujita, "Nano bioresearch approach by microtechnology," Drug Discov Today, vol. 18, pp. 552-559, 2013.
  5. R. Renaudot, T. Nguyen, Y. Fouillet, D. Jary, M. Kumemura, L. Jalabert, D. Collard, H. Fujita, V. Agache, "Alternative method for local surface functionalization using Liquid Dielectrophoresis: an application with PolyEthyleneImine polymer for bacteria trapping onto a surface", RSC Adv., 2013, DOI: 10.1039/C3RA40700D
  6. R. Renaudot, V. Agache, Y. Fouillet, M. Kumemura, L. Jalabert, D. Collard, H. Fujita, Performances of a broad range of dielectric stacks for liquid dielectrophoresis transduction, Microfluidics Nanofluidics, 2013, DOI 10.1007/s10404-013-1156-2.
  7. M. Usami, T. Ishida, M. Kumemura, L. Jalabert, D. Collard, H. Fujita, Four-terminal electrical measurement of a DNA molecular bundle captured by silicon nanotweezers, IEEJ Transaction on Sensors and Micromachines, vol 133, n3, pp98-99.
  8. B. Daunay, R. Renaudot, M. Kumemura, V. Agache, L. Jalabert, D. Collard and H. Fujita, Optimized micro devices for liquid-dielectrophoresis (LDEP) actuation of conductive solutions,Sensors and Actuators B: Chemical, Volume 177, February 2013, Pages 620–626,  http://dx.doi.org/10.1016/j.snb.2012.11.049.
Conferences
  1. G. Perret, T. Lacornerie, M. Kumemura, N. Lafitte, H. Guillou, L. Jalabert, E. Lartigau, T. Fuji, F. Cleri, H. Fujita, D. Collard, Real Time Biomechanical Characterization of DNA Damage under Therapeutic Radiation Beams, MRS Boston, Dec. 3rd 2013 (Oral).
  2. M. Kumemura, S. L. Karsten, N. Lafitte, H. Guillou, L. Jalabert, H. Fujita, D. Collard, Isothermal amplification of DNA on tips of silicon nanotweezers and its electrical and mechanical characterizations,  MicroTAS 2013, October 27-31, 2013, Freiburg, Germany.(oral).
  3. R. Renaudot, T. Nguyen, Y. Fouillet, L. Jalabert, M. Kumemura, D. Collard, H. Fujita, V. Agache, Local surface modification at the microscale enabled by liquid dielectrophoresis, MicroTAS 2013, October 27-31, 2013, Freiburg, Germany.(poster)
  4. G.Perret, T.Lacornerie, M.Kumemura, N.Lafitte, H.Guillou, L.Jalabert, E.Lartigau, T.Fujii, F.Cleri, H. Fujita, D.Collard , Real time bio mechanical characterization of DNA damage under therapeutic radiation beams,  MicroTAS 2013, October 27-31, 2013, Freiburg, Germany. (poster)
  5. N. Lafitte, Y. Haddab, Y. Le Gorrec, H. Guillou, M. Kumemura, L. Jalabert, H. Fujita, D. Collard, Closed-loop control of silicon nanotweezers for improvement of sensitivity to mechanical stiffness measurement and bio-sensing on DNA molecules, 2013 IEEE/RSJ International Conference on Intelligent Robots and Systems (Oral).
  6. H. Guillou, N. Lafitte, L. Jalabert, M. Kumemura, T. Fujii, H. Fujita, D. Collard, SILICON NANO TWEEZERS FOR EASY CELL BIOMECHANICAL MEASUREMENTS, NMC 2013 Workshop, May 1-3, 2013, Stanford, CA, USA. (poster)
  7. J. Lee, K. Yagi, M. Kumemura, T. Sato, L. Jalabert, D. Collard, H. Houjou, and H. Fujita, CHARACTERIZATION OF Π-CONJUGATED METALLOPOLYMER’S MECHANICAL STIFFNESS BY USING SILICON NANOTWEEZERS, IEEE Transducers 2013, June, Barcelona (Spain).(Oral)
  8. R. RenaudotY. Fouillet, VAgache, MKumemura, LJalabert, D. Collard and H. Fujita, FAST CONTINUOUS PARAFFIN WAX CHANNEL-BASED MICROFLUIDIC CHIPS FABRICATION USING LIQUID DIELECTROPHORESIS AND ELECTROWETTING, IEEE Transducers 2013, June, Barcelona (Spain).(poster)
  9. N. Lafitte, Y. Haddab, Y. Le Gorrec, H. Guillou, M. Kumemura, L. Jalabert, D. Collard and H. Fujita, ACTIVE CONTROL OF SILICON NANOTWEEZERS DETECTS ENZYMATIC REACTION AT THE MOLECULAR LEVEL, IEEE Transducers 2013, June, Barcelona (Spain). (poster).

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2012

Journals
  1. M. Kumemura, D. Collard, S. Yoshizawa, B. Wee, S. Takeuchi, and H. Fujita, “Enzymatic Reaction in Droplets Manipulated with Liquid Dielectrophoresis,” ChemPhysChem, vol. 13, no. 14, pp. 3308–3312, Jul. 2012.
  2. B. Daunay, P. Lambert, L. Jalabert, M. Kumemura, R. Renaudot, V. Agache and H. Fujita, Effect of Substrate Wettability in Liquid Dielectrophoresis (LDEP) Based Droplets Generation: Theoretical Analysis and Experimental Confirmation, Lab Chip, 2012, 12, 361, DOI 10.1039/C1LC20625G.
Conferences
  1. Dominique Collard, Thomas Lacornerie, Momoko Kumemura, Nicolas Lafitte, Herve Guillou, Laurent Jalabert, Eric Lartigau, Teruo Fujii, Fabrizio Cleri, Hiroyuki Fujita, "SILICON NANO TWEEZERS FOR REAL TIME BIOMECHANICAL ASSAY ON DNA DAMAGE BY THERAPEUTIC RADIATION BEAMS" (Oral), MicroTAS, Okinawa, JAPAN, Oct. 28 – Nov. 1, 2012. 
  2. M. C. Tarhan,1 D. Collard, L. Jalabert, M. Kumemura, N. Lafitte, Q. Delouvee, S. L. Karsten and H. Fujita, "CONTINUOUS REAL-TIME MONITORING OF MOLECULAR DETECTION BY SILICON NANOTWEEZERS-INTEGRATED MICROFLUIDIC DEVICE", MicroTAS, Okinawa, JAPAN, Oct. 28 – Nov. 1, 2012.
  3. Y. Tauran, M. Kumemura, N. Lafitte, R. Ueno, L. Jalabert, Y. Takayama, D. Collard, H. Fujita, A. W. Coleman and B-J. Kim, ‘Mechanical effect of calix[n]arene capped silver nanoparticles on DNA measured with silicon nano tweezers’, MicroTAS, Okinawa, JAPAN, Oct. 28 – Nov. 1, 2012.
  4. R. Renaudot, V. Agache, L. Jalabert, M. Kumemura, D. Collard, H. Fujita, Performances of High-K dielectric materials (Al2O3, HfO2, ZrO2) for Liquid Dielectropphoresis (LDEP) microfluidic devices, 16th International Conference on Miniaturized Systems for Chemistry and Life Sciences (µTAS 2012), 28 Oct-1 Nov, Okinawa, Japan.
  5. R. Renaudot, Y. Fouillet, V. Agache, L. Jalabert, M. Kumemura, D. Collard, H. Fujita, New approach for continuous based-channels microfluidic chips fabrication using EWOD and/or LDEP transductions, 8th International Meeting on Electrowetting, 21-23 June 2012, Athens, Greece. Best poster award.

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2011

Journals
  1. R. Renaudot, V. Agache, B. Daunay, P. Lambert, M. Kumemura, Y. Fouillet, D. Collard and H. Fujita, "Optimization of Liquid DiElectroPhoresis (LDEP) Digital Microfluidic Transduction for Biomedical Applications", Micromachines 2011, 2(2), 258-273; doi:10.3390/mi2020258
  2. M. Kumemura, D. Collard, N. Sakaki, C. Yamahata, M. Hosogi, G. Hashiguchi and H. Fujita, Single-DNA-molecule trapping with silicon nanotweezers using pulsed dielectrophoresis. Journal of Micromechanics and Microengineering 21, 054020 (2011).
  3. M. Kumemuraet al, Proc. of The Asia-Pacific Interdisciplinary Research Conference 2011 (AP-IRC 2011), p.190, Toyohashi, Japan, 2011
Conferences
  1. M. Kumemura, S.L. Karsten, D. Collard, and H. Fujita, "Rolling Circle Amplification (RCA) and Trapping of DNA on a Microchip", The Asia-Pacific Interdisciplinary, Toyohashi University of Technology, Aichi, Japan, Nov 18, 2011.
  2. M. Kumemura, D. Collard, R. Tourvielle, N. Lafitte, K. Montagne, S. Yoshizawa, D. Fourmy, L. Jalabert, Y. Sakai, S. Takeuchi, T. Fujii, and H. Fujita, INTEGRATED MEMS PLATFORM WITH SILICON NANOTWEEZERS AND OPEN MICROFLUIDIC DEVICE FOR MOLECULAR AND CELLULAR BIOMECHANICAL ASSAYS, Accepted as an oral presentation at IEEE Int. Conference on MEMS 2011, Cancun, Mexico.
  3. N. Lafitte, M. Kumemura, D. Collard, R. Tourvielle, K. Montagne, S. Yoshizawa, D. Fourmy, L. Jalabert, Y. Sakai, S. Takeuchi, T. Fujii and H. Fujita, “Silicon nanotweezers for molecular and cellular biomechanical assays,” The 6th International Conference on Microtechnologies in Medicine and Biology, Lucerne, Switzerland, MMB 2011.

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2010

Journals
  1. L. Jalabert, M. Kumemura, C.Bottier, H. Fujita, “Nanoscale surface engineering of PDMS by embedding vertical nanosheets of materials.”, Microelectronics Engineering, 87 (2010) 1431–1434.
Conferences
  1. N. Lafitte, M. Kumemura, D. Collard, S. Yoshizawa, D. Fourmy, L. Jalabert, S. Takeuchi, T. Fujii, H. Fujita, Direct bio-mechanical sensing analysis of enzymatic reactions on DNA by silicon nanotweezers, Technical Meeting on Micromachine and Sensor Systems, IEE Japan, 2010, June 17-18, Tokyo.
  2. Grenier K.,Dubuc D.,P.-E. Poleni.,Kumemura M.,Fujii T.,Toshiyoshi H. and Fujita H., Resonant based microwave biosensor for biological cells discrimination, IEEE Radio and Wireless Symposium 2010, New Orleans, USA, 2010.
  3. L. Jalabert, T. Sato, M.Kumemura, D. Bolsee, C. Hermans, A. BenMoussa, H.Fujita, EMBEDDING VERTICAL NANOSHEETS OF METALS INTO PDMS WITH A REUSABLE TEMPLATE ENGINEERING, IEEE Int. Conf. on MEMS 2010, Hong Kong.
  4. N. Lafitte, M. Kumemura, D. Collard, S. Yoshizawa, D. Fourmy, L. Jalabert, S. Takeuchi, T. Fujii and H. Fujita, “Direct bio-mechanical sensing of enzymatic reaction on DNA by silicon nanotweezers," IEJ Workshop management system, The papers of technical meeting on Micromachine and Sensor System, The Institute of Electrical Engineers of Japan, pp.127-131, Tokyo 2010.
  5. N. Lafitte, M. Kumemura, M. Nagai, L. Jalabert, D. Collard and H. Fujita, “An open microfluidic device with acrive valves for accurate trapping of DNA by silicon nanotweezers," Proc. of 14th International Conference on Miniaturized Systems for Chemistry and Life Sciences, pp. 1865-1867, Groningen, The Netherlands, μTAS 2010.

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2009 and prior

Journals

2009

  1. Jalabert L.,Bottier C.,Kumemura M. and Fujita H., Embedded SiO2 nanosheets in PDMS using an alternative nanopatterning process, Journal of Vacuum Science and Technology B, 27(6), 2009.
  2. Nagai M. and Kumemura M.,Asai H., and Fujita H., Binding of artificial object to vorticella for a microsystem powered by a microorganism, e-Journal of surface science and nanotechnology, 7: 673-676, 2009.

2008

  1. C.Yamahata, C.; Collard, D.; Legrand, B.; Takekawa, T.; Kumemura, M.; Hashiguchi, G.; Fujita.H., Silicon Nanotweezers With Subnanometer Resolution for the Micromanipulation of Biomolecules. Journal of Microelectromechanical Systems 2008, Vol.17, (No.3), pp.623-631.
  2. C.Yamahata, C.; Collard, D.; Takekawa, T.; Kumemura, M.; Hashiguchi, G.; Fujita, H., Humidity Dependence of Charge Transport through DNA Revealed by Silicon-based Nanotweezers Manipulation. Biophysical Journal 2008, 94, (1), 63-70.

2007

  1. M. Kumemura, D. Collard, C. Yamahata, N. Sakaki, G. Hashiguchi, H. Fujita,"Single DNA Molecule isolation and trapping in a microfluidic device" ,' Chemphyschem (2007) vol. 8 (12) pp. 1875-1880.

 

Conferences

2009

  1. Grenier K.,Dubuc D.,Kumemura M.,Toshiyoshi H. and Fujita H., Contact less radio-frequencies biosensor for biological parameters analysis, Int. Conf. on Biomedical Electronics and Devices, BIODEVICES, Portugal, 398-401, 2009.
  2. Grenier K.,Dubuc D.,Poleni P.E.,Kumemura M.,Fujii T.,Toshiyoshi H. and Fujita H., New broadband and contact less RF / microfluidic sensor dedicated to bioengineering, IEEE MTT-S International Microwave Symposium, USA, 1329-1332, 2009.
  3. Grenier K.,Dubuc D.,Poleni P.E.,Kumemura M.,Toshiyoshi H.,Fujii T and Fujita H., Integrated Broadband Microwave and Microfluidic Sensor Dedicated to Bioengineering, IEEE Transaction on Microwave Theory and Techniques, 2009.
  4. Jalabert L.,Kumemura M.,Bottier C. and Fujita H., Nanoscale surface engineering of PDMS by embedding vertical SiO2 nanosheets, 35th Int. Conf. on Micro and Nano Engineering, MNE 09, Belgium, 2009.
  5. Jalabert L.,Kumemura M.,Bottier C. and Fujita H., Toward nanoscale functional PDMS by embedding vertical Au/SiO2/Au nanosheets for wettability enhancement, 22nd Int. Conf. on Microprocesses and Nanotechnology, IMNC 09, Japan, 2009.
  6. Kumemura M.,Yoshizawa S.,Collard D. and Fujita H., Droplet formation and fusion for enzyme activity measurement by liquid dielectrophoresis, 15th Int. Conf. on Solid State Sensors, Actuators and Microsystems, Transducers 09, Denver, USA, 813-816, 2009.
  7. Yamahata C.,Sarajic E.,Collard D.,Jalabert L.,Kumemura M. and Fujita H., Mechanical characterization of biomolecules in liquid using silicon tweezers with subnanonewton resolution, IEEE 22th Int. Conf. on Micro Electro Mechanical Systems, MEMS 09, Sorrento, Italy, 607-610, 2009.

2008

  1. Wee, B.; Kumemura, M.; Collard, D.; Fujita, H. Isolation of Single DNA Molecule in Picolitre-sized Droplet Formed by Liquid Dielectrophoresis, 12th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS'08, San Diego, USA, Oct. 12-16, 2008.
  2. Wee, B.; Kumemura, M.; Collard, D.; Fujita, H. Integration of Closed Microfluidics and Open Droplet Actuation on a Single Lab-on-a-chip Device, Intelligence and Precision Equipment IIP 2008, Tokyo, Japan, 2008.
  3. Wee, B.; Kumemura, M.; Collard, D.; Fujita, H. Integration of Microfluidics and Droplet Manipulation of DNA Solution on a Single Lab-on-a-chip Device, 4th Asia-Pacific Conference on Transducers and Micro-Nano Technology, APCOT'08, Tainan, Taiwan, Jun. 22-25, 2008.
  4. Wee, B.; Kumemura, M.; Collard, D.; Fujita, H. Droplet Extraction from PDMS Surface using Liquid Dielectrophoresis, International Symposium on Surface Science and Nanotechnology, 2008.
  5. Yamahata, C.; Collard, D.; Domenget, A.; Hosogi, M.; Kumemura, M.; Hashiguchi, G.; Fujita, H. Silicon Nanotweezers: a New Biophysical Tool for Molecular Experimentation, 21st IEEE Int. Conf. on Microelectromechanical Systems, MEMS'08, Tucson, USA, Jan. 13-17, 2008.

2007

  1. M. Kumemura, D. Collard, C. Yamahata, N. Sakaki, G. Hashiguchi, H. Fujita, "Isolation of DNA molecule in microchannel and a single molecule trapping between microelectrodes", 11th Int Conf. on Miniaturized Systems for Chemistry and Life Sciences, MicroTas 07, 2007, Paris, France.
  2. C. Yamahata, T. Takekawa, M. Kumemura, G. Hashiguchi, D. Collard, H. Fujita, "Electrical and mechanical charactersitics of DNA bundles revealed by Silicon nanotweezers",14 Int. Conf. on Solid State Sensors, Actuators and Microsystems, Transducers'07, 2007, Vol. 1, Lyon, France, June 10-14

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eujo limms