Levy Group | Physics | Binghamton University

Research

We investigate the statistical mechanical properties of soft materials, like biomolecules, in confined topologies. We are interested in exploring the scaling laws predicting the conformation and dynamics of polymers, like individual DNA molecules, in nanofluidic structures. We typically fabricate nanofluidic channels in fused silica wafers using tools available at the Binghamton Nanofabrication Lab or at Cornell's Nanoscale Facility. We electrophoretically manipulate DNA inside these channels to study their biophysical and transport properties. DNA molecules are extremely interesting polymers due to their high linear charge, flexibility, aspect ratio, and genetic role in biological organisms.

Fused Silica Nanochannels — Top down scanning electron micrograph of an array of nanofluidic channels (bottom) etched in fused silica. The channels are approximately 150 nm in width and depth and tens of microns in length. At the top of the image the outline of a larger microfluidic loading channel can be seen. We used similar devices to study the entropic unfolding of DNA molecules within the channels. Photography: photo credit.

Images of a DNA molecule unfolding in time (from top to bottom) inside a nanofluidic channel. It is important to note that no external potentials are being applied. Over the time scale of approximately one minute, the T4 DNA molecule unfolds to increase its entropy within the channel. The final unfolded length of the molecule is approximately thirty microns. Photography: photo credit.

Silicon Master for Microfluidic Assay — Image of a silicon chip that has been deep etched to serve as a master for a PDMS mold. Photography: photo credit.

PDMS Chip — PDMS microfluidic chip on an inverted microscope. The chip has several pieces of tubing connected to external valves for flow control. Photography: photo credit.

Magentic Bead Assay — Images of magnetic beads trapped in the microfluidic device. The beads are functionalized with an antibody to an interleukin-8 protein. A secondary antibody with a fluorescent label is convected across the bead bed. By measuring the fluorescent intensity of the beads we can determine the concentration of the interleukin in the sample. The assay is sensitive to concentrations between 1 and 10,000 pg/mL of interleukin-8. Photography: photo credit.

Publications

L. Dai, J. Jones, A. Klotz, S. Levy, P. Doyle. "Nanoconfinement greatly speeds up the nucleation and the annealing in single-DNA collapse." Soft Matter, 2017, Advance Article.

DOI: 10.1039/C7SM01249G

A. Klepinger, M. Greenier, and S. Levy. "Stretching DNA Molecules in Strongly Confining Nanoslits." Published on web, Macromolecules, December, 2015. DOI:10.1021/acs.macromol.5b01712

A. Bevan et al. [BaBar and Belle Collaborations], "The Physics of the B Factories," Eur. Phys. J. 2014, C 74, 3026.

L. Wu and S. Levy. "Fluctuations of DNA mobility in nanofluidic entropic traps," Biomicrofluidics 2014, 8, 044103.
DOI:10.1063/1.4887395

J. Benitez, J. Topolancik, H. Tian, C. Wallin, D. Latulippe, K. Szeto, P. Murphy, B. Cipriany, S. Levy, P. Soloway, H. Craighead, "Microfluidic Extraction, Stretching and Analysis of Human Chromosomal DNA from Single Cells," Lab on a Chip 2012, 12, 4848–4854.
DOI:10.1039/c2lc40955k

B. Cipriany, P. Murphy, J. Hagarman, A. Cerf, D. Latulippe, S. Levy, J. Benítez, C. Tan, J. Topolancik, P. Soloway, H. Craighead, "Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel," Proceedings of the National Academy of Sciences 2012, 109, 8477–8482.
DOI:10.1073/pnas.1117549109

J. Tang, S. Levy, D. Trahan, J. Jones, H. Craighead, P. Doyle. "Revisiting the Conformation and Dynamics of DNA in Slitlike Confinement," Macromolecules 2010, 43, 7368-7377.
DOI: 10.1021/ma101157x

B.R. Cipriany, R. Zhao, P.J. Murphy, S.L. Levy, C.P. Tan, P.D. Soloway, H.G. Craighead. "Single Molecule Epigenetic Analysis in a Nanofluidic Channel," Analytical Chemistry 2010, 82, 2480-2487.
DOI: 10.1021/ac9028642

S. Levy, H. Craighead. "DNA Manipulation, Sorting and Mapping in Nanofluidic Systems," Chemical Society Reviews 2010, 39, 1133-1152.
DOI: 10.1039/B820266B

S. Levy§, J. Mannion§, J. Cheng, C. Reccius, H. Craighead. "Entropic Unfolding of DNA Molecules in Nanofluidic Channels," Nano Letters 2008, 8, 3839-3844.
§These authors contributed equally.
DOI: 10.1021/nl802256s

E. Strychalski§, S. Levy§, H. Craighead. "DNA Diffusion in Nanoslits," Macromolecules 2008, 41, 7716-7721.
§These authors contributed equally.
DOI: 10.1021/ma801313w
Selected High Energy Physics Publications
B. Aubert et al. "Measurement of the branching fraction and polarization for the decay B- --> D0* K-," Physical Review Letters 2004, 92, 141801.
DOI: 10.1103/PhysRevLett.92.141801
B. Aubert et al. "Measurement of the CP-violating asymmetry amplitude sin2beta with B0 mesons," Physical Review Letters 2002, 89, 201802.
DOI: 10.1103/PhysRevLett.89.201802

B. Aubert et al. "Observation of CP violation in the B0 meson system," Physical Review Letters 2001, 87, 091801.
DOI: 10.1103/PhysRevLett.87.091801

A. A. Affolder et al. "Test of CMS tracker silicon detector modules with the ARC system," Nuclear Instruments and Methods A 2004, 535, 374.
DOI: 10.1016/j.nima.2004.07.155

S. L. Levy, "Observation of CP violation in the neutral B meson system," SLAC-R-072
PhD Thesis

G. P. Gilfoyle, S. Levy, and M. Mestayer, "Spatial resolution of the nose cone prototype drift chamber", 1997, CLAS-Note-96-009.

All 134 CDF Publications (from inSPIRE)

All 196 Babar Publications (from inSPIRE)
News
August 2015
Alexander submits his paper on Stretching DNA in Nanoslits to Macromolecules
June 2015
Congratulations to Lingling for defending her thesis!

January 2015
Madeline and Katerina present their posters on the Free Energy of Confined DNA and Testing Students Misconceptions on the Photoelectric Effect respectively at the APS Conference for Undergraduate Women in Physics.

August 2014
Professor Levy wins a Faculty Early Career Development award from the NSF to study DNA molecules transported through carbon nanotubes.

July 2014
Lingling's paper on fluctuations of DNA mobility in nanofluidic entropic traps is published in Biomicrofluidics.

March 2014
Lingling presents her results on mobility fluctuations of DNA in entropic traps at the American Physical Society Meeting in Colorado.

July 2011
Undergraduates Amber Whelsky (Physics) and Nicholas Gonzalez (Biology) present a poster on the diffusion of individual p53 molecules to targets on stretched DNA as part of the Binghamton-HHMI interdisciplinary research program. Their work received an Honorable Mention for being in the top 10% of the 850 applications to the Council of Undergraduate Research 'Posters on the Hill'.
Links
Other Groups and Collaborators:
- Harold Craighead (Cornell)
- Paul McEuen (Cornell)
- Bob Austin (Princeton)
- Pat Doyle (MIT)
- Jongyoon Han (MIT)
- Walter Reisner (McGill)
- Robert Riehn (NC State)
- Derek Stein (Brown)
- David Hoagland (UMass Amherst)
- Susannah Gal (Binghamton)
- Paul Soloway (Cornell)

Group Members

Stefan McCarthy
Graduate Student
Office: S2-G53
Email: stefanjmccarty@gmail.com

Madeline Greenier
Undergraduate
Email: mgreeni1@binghamton.edu

Graduate Students

Lingling Wu (PhD)
Alexander Klepinger: Physics graduate student at The Ohio St. University
TaeKen Kim: Physics graduate student at Penn State
Gavin Osterhoudt: Physics graduate student at Boston College
Amber Whelsky: Graduate student at Dartmouth Thayer School of Engineering
Dimitrius Khaladj: PhD student in Nanoengineering and Sciences at the Albany College of Nano Science and Engineering
Melissa Stanke

Contact Info

Stephen L. Levy

Chair; Associate Professor

Physics, Applied Physics and Astronomy

slevy@binghamton.edu

607-777-3066

SN 2210