Drndić Lab



News from our lab

Come see our work at the Philly Science Festival Carnival on May 3, 2014.

The Carnival runs from 10am to 4pm, and our group will demonstrate our work at a booth between 21st and 22nd on Benjamin Franklin Parkway.

The Philadelphia science carnival features more than 175 exhibitors offering non-stop, family-friendly experiments, interactive activities, games, and a packed line-up of live entertainment. Enjoy making slime, meeting live zoo animals, checking out the inner-workings of robots, taking a tour of a helicopter, extracting DNA from a strawberry, testing a "crime scene" for forensic evidence, and so much more! For more information, please go to philasciencefestival.org

Marija Drndić Named 2014 APS Fellow

Professor Marija Drndić has been named an APS Fellow "For development of novel nanofabrication methods for graphene nanoelectronics and fast biomolecular analysis in solution."

Graphene nanoribbon-nanopore devices for DNA sequencing

Graphene-based nanopore devices are promising candidates for next-generation DNA sequencing. In this paper, we fabricated graphene nanoribbon-nanopore (GNR-NP) sensors for DNA detection. GNR conductance was monitored in situ during electron irradiation-induced nanopore formation inside a transmission electron microscope (TEM). We show that GNR resistance increases linearly with electron dose and that GNR conductance and mobility decrease by a factor of ten or more when GNRs are imaged at relatively high magnification with a broad beam prior to making a nanopore. By operating the TEM in scanning TEM (STEM) mode, in which the position of the converged electron beam can be controlled with high spatial precision via automated feedback, we were able to prevent electron beam-induced damage and make nanopores in highly conducting GNR sensors. This method minimizes the exposure of the GNRs to the beam before and during nanopore formation. The resulting GNRs with unchanged resistances after nanopore formation can sustain microampere currents at low voltages (around 50 mV) in buffered electrolyte solution and exhibit high sensitivity, with a large relative change of resistance upon changes of gate voltage, similar to pristine GNRs without nanopores.

Selected press:
      Penn News: Penn Produces Graphene Nanoribbons With Nanopores for Fast DNA Sequencing
      ScienceDaily: Graphene Nanoribbons With Nanopores Created for Fast DNA Sequencing




In a recent ACS Nano paper, "Differentiation of Short, Single-Stranded DNA Homopolymers in Solid-State Nanopores", we show that small solid-state nanopores similar in size to protein nanopores, combined with an optimized setup, can differentiate between single-stranded DNA homopolymers (with A, C, and T bases).
Selected press:
      Penn News: Penn Research Makes Advance in Nanotech Gene Sequencing Technique
      Genome Web: UPenn Team Shows Solid-state Nanopore Can Distinguish Different DNA Homopolymers

Graduate student Matt Hickman received a 2012 NSF Graduate Student Fellowship. Matt�s journey took him from high energy physics to his new passion for single molecule biophysics experiments using graphene nanopores (March 2012).

Results from our collaboration with Ken Shepard's group at Columbia University were just published in Nature Methods: "Integrated Nanopore Sensing Platform with Sub-Microsecond Temporal Resolution"
Selected press:
      Penn News: Penn Works with Columbia Engineers to Increase Speed of Single-Molecule Measurements

Graduate student Matt Puster received the NSF-IGERT Graduate Nanotechnology Fellowship (Feb 2012).

New NIH grant awarded to our lab to advance nanotechnology for DNA sequencing.
Selected press:
      NIH News: NHGRI funds development of revolutionary DNA sequencing technologies
      Penn News: Penn Researchers Awarded $1.5 Million to Advance Nanotechnology for Gene Sequencing

Former post-doc Meni Wanunu started an Assistant Professor position at Northeastern University (August 2011).

In a recent Nature Communications paper, "Collective fluorescence enhancement in nanoparticle clusters", we show that blinking nanorods (NRs) interact with each other in a cluster, and the interactions affect the blinking statistics.
Selected press:
      Penn News: Penn Physicists Observe Campfire Effect in Blinking Nanorod Semiconductors

Graduate student Jessamyn Fairfield received an NSF travel fellowship to attend the Pan-American Advanced Studies Institute (PASI) in Costa Rica on Scalable, Functional Nanomaterials (August 2011).

Post-doc Chris Merchant received the AAAS Science Policy Fellowship (July 2011).

Graduate student Lauren Willis used high resolution transmission electron microscopy (TEM) to image gold particles attached to peptides wrapped around individual single wall nantubes (SWNTs), which allowed quantitative analysis of particle spacing and configuration to confirm the computational model of the complex. This paper, Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces, was selected for the cover of Science.

We are seeking postdoc applications from outstanding candidates to join our effort on the advancement of fundamental science of ion/biomolecule/nanopore systems and the development of new sequencing technologies based on nanopores in graphene-based and silicon nitride-based platforms. Expertise in nanofabrication, electron beam lithography, transmission electron microscopy, electrical measurements with nanopores and microfluidics, biological sample preparation and handling, is a plus. Please send your interest to Prof. Drndić at drndic@physics.upenn.edu.

Graduate student Kim Venta received an NSF Graduate Student Fellowship. Kim works at an intersection of condensed matter physics, biophysics and chemistry on understanding and developing approaches for biomolecule manipulation and analysis, including DNA sequencing, using graphene.

The Economist published an article in its March 10th 2011 issue featuring our work on DNA translocation through graphene nanopores, entitled Nanopore sequencing: Towards the 15-minute genome.

Our group is preparing presentations for the upcoming Biophysical Society and American Physical Society meetings. At the annual BPS meeting, Chris Merchant will give a talk on DNA translocations through nanopores created in graphene membranes on March 9th at 8:15 AM, and Kimberly Venta will present a poster in the poster session on March 9th from 10:30-12:30. At the APS March Meeting, Jessamyn Fairfield will give a talk about Memory, Photoconductivity, and Traps in Semiconducting Nanocrystal Arrays on March 23rd at 4:54 PM, and Chris Merchant will give a talk about DNA translocation through graphene nanopores on March 23rd at 12:27 PM.

In our most recent paper, "Discrimination of methylcytosine from hydroxymethylcytosine in DNA molecules", we investigate the physical properties of DNA with modified cytosines. Molecular dynamics simulations reveal that polar cytosine modifications affect internal base pair dynamics, while experimental evidence suggests a correlation between the modified cytosine's polarity, DNA flexibility, and duplex stability. On the basis of these physical differences, solid-state nanopores can rapidly discriminate among DNA fragments with mC or hmC modification by sampling a few hundred molecules in the solution. This work has been reported in Epigenetics Headlines and Chemistry Views.



Our new paper, "Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors,", published in Nature Nanotechnology and featured on the journal cover page, develops a platform for electronic detection of probe-hybridized microRNAs. We find that reducing the thickness of the membrane containing the nanopore leads to increased signal amplitudes from biomolecules, and reducing the diameter of the nanopore allows the detection and discrimination of small nucleic acids based on differences in their physical dimensions. The work was done in collaboration with New England Biolabs.


Selected press:
      Penn News: University of Pennsylvania Scientists Develop Method for Detecting MicroRNA From Living Cells
      AZoNano: MicroRNA Detection Using Nanopores
      Nano: Detecting microRNA from living cells
      HealthCanal: University of Pennsylvania Scientists Develop Method for Detecting MicroRNA From Living Cells
      R&D Magazine: Scientists develop a new method for detecting microRNA from living cells

Research from our group was presented at the Workshop on Electronic Transport in Nanoengineered Materials, at the University of Chicago September 16-18, 2010. Marija Drndić gave a talk on "Nanogap quantum dot photoconductivity", Matt Puster presented the poster "Electronic Transport Imaged via Electrostatic Force Microscopy in PbSe Nanocrystal Arrays", and Lauren Willis and Jessamyn Fairfield presented the poster "Memory in Photoconductivity of Nanocrystal Arrays".

On August 24, 2010, Marija Drndić attended the Recovery Innovation Report White House event. Vice President Joe Biden detailed the role the Recovery Act has played in funding innovation.

Meni Wanunu and Lauren Willis each gave a talk to high school teachers as part of the Research Experience for Teachers program organized by the Nano-Bio Interface Center (NBIC) at Penn.

Highlights on our work are mentioned in the article The Road to the $1000 Genome - A Roundup of Sequencing Technology Developments by the National Human Genome Research Institute (NHGRI) on August 3, 2010.

On July 30th, 2010, Marija Drndić gave a talk to the Penn Summer Science Academy (PSSA) and the Quarknet High School Students. Read more about Penn's high school outreach and physics department outreach.

New research from our group on graphene nanopores was published in Nano Letters. Our paper, DNA translocation through graphene nanopores, demonstrates DNA translocation through synthetic nanopore materials with atomic thickness and electrical addressability, which may serve as a step toward nanopore-based DNA sequencing. We envision graphene-based nanopore devices that sense and control the electric potential locally at the nanopore and are capable of measuring transverse current across the pore aperture.

Selected press:
      Penn News: First Step Towards Electronic DNA Sequencing
      Institute of Nanotechnology: Nanoscale platform detects single DNA molecules
      Graphene Times: Penn Researchers Provide First Step Towards Electronic DNA Sequencing
      Nanotechnology Now: Translocation Through Graphene Nanopores
      EE Times: Researchers say carbon-based platform beats silicon for detection
      ScienceDaily: First Step Toward Electronic DNA Sequencing
      PhysOrg.com: Translocation through graphene nanopores
      IEEE Spectrum: The Race to Design a Nanopore Gene Sequencer Heats Up

Post-doc Meni Wanunu gave an invited talk at the Biosensing with Channels summer school in Berder Island, France in August 2010. Graduate Student Kimberly Venta presented a poster titled "Graphene Nanopores" at this conference as well.

Post-doc Meni Wanunu gave the UPenn Department of Physics and Astronomy Condensed Matter Seminar on April 28th, 2010.

Graduate student Jessamyn Fairfield was awarded the 'Best Poster Award' at the NaNaX 4:Nanoscience with Nanocrystals conference on April 14th, 2010 in Tutzing, Germany.
Jessamyn Fairfield at NaNaX 4


Research from our lab was featured on the History Channel show The Works on July 24th, 2008
  THE WORKS: POWER TOOLS (Thursday, July 24th at 10pm ET/PT) Since the Egyptians invented them three thousand years ago, power tools have transformed the face of the earth. As we trace their evolution, we find out their hidden commonalities: from power tools that slice mountains in half to new breakthroughs in nanotechnology that enable them to literally split hairs. Follow the life of a power tool as it goes from an idea to our garage shelf as we discover how they're being used in surprising ways in sports, medicine and art.
Invited lecture on TEBAL: Nanosculpting devices with electrons in a transmission electron microscope by Marija Drndić at the APS March Meeting 2008, Focus session Nanotechnology II, in New Orleans, March 10-14, 2008. (Abstract)

Graduate student Michael Fischbein was awarded the 2007 Graduate Student Research Excellence Award from the Nano/Bio Interface Center. The associated 15-minutes presentation will preceed this year's keynote lecture by Charles Lieber during the NanoDay@Penn on October 24, 2007.

Interdisciplinary Workshop Excited state processes in electronic and bio nanomaterials (ESP2007)
Los Alamos National Laboratory, October 1-4, 2007

Graduate student Michael Fischbein was awarded the Elias Burstein Prize in Condensed Matter Physics
for his creative and prolific work on nanolithography and its technological applications.

Graduate student Lauren Willis was awarded the NSF-IGERT graduate fellowship.

Selected press releases about TEBAL nanofabrication technique:
      IEEE Spectrum: Power tools for making nanoscale objects, July 2007.
      Nature Nanotechnology research highlight: Electron beam lithography: Body-sculpting, May 2007.
      PhysOrg.com: Scientists Hand-Make Devices Smaller than 10 Nanometers, April 2007.


Selected previous events:
Werner B. Teutsch Prize awarded to Lauren Willis (2006).
PECASE Award (Presidential Early Career Award for Scientists and Engineers) awarded to Marija Drndić (2005).
NSF-IGERT graduate fellowship awarded to Michael Fischbein (2004-2007).
Arnold M. Denenstein Prize awarded to Michael Fischbein (2004).


2013, Marija Drndić