News

  • August 2024

New paper from our lab in Nature Nanotechnology, fresh off the press:
“Coupled nanopores for single-molecule detection”, Yung-Chien Chou, Chih-Yuan Lin, Alice Castan, Joshua Chen, Rachael Keneipp, Parisa Yasini, Dimitri Monos & Marija Drndić
Nature Nanotechnology (2024). https://www.nature.com/articles/s41565-024-01746-7

We have developed a bilayer nanopore (GURU) platform for the ultrafast detection of unmodified molecules. The bottom layer slows and aligns molecules, while the top 2D nanopore (~2 nm) detects their position. Reducing the bottom layer to a single pore enhances sensing, enabling precise detection of molecule positions and fragment lengths. Thanks to advanced sensing resolution and nanofabrication, GURU platform offers improved molecular control and extended detection times.

  • June 2024
We have published our new work on analyzing RNA molecules with silicon nitride nanopores. In short, we have outlined the required nanopore parameters (diameter) and measurement conditions (salt concentration) to optimally differentiate different tRNA molecule conformations.  This study represents an  important step forward to explore changes in the conformational dynamics of RNA molecules in human diseases. Please see the abstract for more information. This work was performed in collaboration with our colleagues at Thomas Jefferson University.
“Unraveling RNA Conformation Dynamics in Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-like Episode Syndrome with Solid-State Nanopores”
Srilahari Namani, Kyril Kavetsky, Chih-Yuan Lin, Sunita Maharjan, Howard B. Gamper, Nan-Sheng Li, Joseph A. Piccirilli, Ya-Ming Hou*, and Marija Drndić*. ACS Nano, ASAP, 2024.
  • June 11 – 13, 2024. We have attended the NIH Grantee meeting in Connecticut. 
  • June 8 – 15, 2024. We have attended a conference in Cavtat, Croatia, featuring a Nanopore Symposium. 

Marija Drndic gave an invited talk entitled: “Coupled Nanopores for Single Molecule Detection”

Below are some photographs from the conference.

 

 

  • May 2024. Our work on nano sculpting of hBN was featured as cover art for the Journal of Physical Chemistry C.

 

  • March 2024. We helped Philadelphia high school students compete in the Regional Science Olympiad at Penn State Abington on March 8, 2024.

 

  • January  2024. Nanofluidics Conference, Switzerland, 2024.  January  2024. Nanofluidics Conference, Switzerland, 2024.
    Nanofluidics 2024 Swiss “2D materials sculpting for nanopore applications”

  • November 2023.

  • April 24, 2023.

On behalf of the Center for Undergraduate Research and Fellowships (CURF) and the Rose Award Faculty Selection Committee, Joshua Chen’s project under the direction of Prof. Marija Drndic, “Computer vision AC-STEM automated image analysis for 2D nanopore applications,” has been selected to receive a 2023 Rose Undergraduate Research Award. 

  • April 18-21, 2023.

Drndic lab helped with preparations for the  PA Science Olympiad and Prof. Drndic accompanied the students to the competition at Penn State Altoona on April 21, 20223. The Masterman High School team won several top 10 medals in Astronomy,  Environmental Chemistry and other subjects.  Three Philadelphia public schools qualified and participated at the state competition (Masterman, Central and Meredith middle school).

 

 

  • March 29, 2023.

Event at Penn Museum: “Are we just atoms and molecules… or something more?” This is also related the course Physics 80 “Physics and Consciousness” taught by Drndic. Next time she is teaching it in Fall 2023.

  • March 8 and 10, 2023. Outreach.  Marija visited the local Philly public high school on March 8 to help prepare the high school students in physics and astronomy for the Science Olympiad, and accompanied them to the competition on March 10, 2023.  The team has successfully passed to the next round of State Science Olympiad on April 22, 2023.   https://www.pascioly.org

  • February 25, 2023. Outreach. Graduate students Kyril Kavetskyand Jesse Elliot visited a local Philly public high school to help prepare the high school students for the Science Olympiad, specifically addressing Fermi-type questions including order of magnitude estimation.

  • February 2023. Our work and paper on   “Engineering adjustable two-pore devices for parallel ion transport and DNA translocations”, Yung-Chien Chou, Joshua Chen, Chih-Yuan Lin, Marija Drndić, Journal of Chemical Physics 154, 105012, 2021, was featured in the review article by Zuzanna Siwy, Merlin Bruening and Stefan Howorka in their paper

    “Nanopores: synergy from DNA sequencing to industrial filtration – small holes with big impact”, Chemical Society Reviews 2023, http://DOI https://doi.org/10.1039/D2CS00894G

(C) A sensing system composed of two nanopores with different thicknesses creates multiple blockage levels corresponding to different configurations of DNA molecules (unfolded and folded) passing through one or both nanopores. Each nanopore creates a distinct current signal enabling making correspondence of each current blockage to the number and configuration of the molecules. Adapted with permission from ref. 105. Copyright 2021 AIP Publishing.

  • February 2023. New Drndic lab patent cube 🙂

  • January 2023.

We attended the Nanofluidics Symposium in Singapore and presented our work entitled: “Sculpting of 2D materials: from pores to nanoporous membranes”. See more under travel and photos.

  • October 2022.

Latest Drndic lab paper in collaboration with Goeppert LLC, http://gppert.com
Here, collaborating with Goeppert we develop a low cost way to make SiN pores using pipetting.

“Silicon Nitride Nanopores Formed by Simple Chemical Etching: DNA Translocations and TEM Imaging”
Zehui Xia, Andre Scott, Rachael Keneipp, Joshua Chen, David J. Niedzwiecki, Brian DiPaolo, and Marija Drndić, ACS Nano 2022.

https://pubs.acs.org/doi/10.1021/acsnano.2c07240

  • September 2022.

Looking ahead to upcoming talks & conferences lined up: 

 

Princeton TEM stuff,

Delft nanopore/protein stuff,

Boston (MRS),

Cambridge UK 2D materials,

Germany (2D material defects)…

 

  • Marija is on sabbatical in academic year 2022/23 and traveling physically and mentally, giving talks and so on, so unless it is research related please allow tardy email responses during this period.

 

 

 

 

 

 

 

  • Upcoming activities

  • July 2022. The Simons Foundation, in partnership with the National Society for Black Physicists (NSBP), has put together a research program for undergraduate students that are also NSBP members. Our lab hosted a visiting day for the 15-20 students in the program on Tuesday, July 26th, 2022.

  • June 2022: From Biophysics to Solid State Physics, Dubrovnik.

  • June 2022: Astrobiology paper on use of solid-state pores for life exploration published online!

 

  • May 2022: Hawaii MRS Spring 2022 and Tahoe Nanofluidics 2022

  • :

 

  • March 2022:

Joshua Chen is one of the recipients of the 2022 Goldwater Scholarship to pursue his PhD.

https://www.physics.upenn.edu/news/congratulations-joshua-chen-receiving-goldwater-2022-scholarship

 

  • August 2021: 

In retrospect: Reflecting on 20 years of solid-state nanopores.

https://www.nature.com/articles/s42254-021-00363-w

  • July 2021: 

We gave a research presentation at the Experimental Penn Research Academy (EPRA) on July 10, 2021, to high school students from all over the world who participated in this Penn outreach summer program.

We published a paper in ACS Sensors reporting advanced multilayer nanopore devices including channels and scaffolds for biomolecule and DNA guiding and analysis.

Devices for Nanoscale Guiding of DNA through a 2D Nanopore,
David J. Niedzwiecki, Brian DiPaolo, Chih-Yuan Lin, Alice Castan, Rachael Keneipp, Marija Drndić, ACS Sensors, 2021.

https://pubs.acs.org/doi/10.1021/acssensors.1c00829

 

  • June 2021:

Our talk on June 29, 2021: “2D membranes: are they realistically useful?”

New institute opening in Karlsruhe ! Membranes and more membranes, small, large, thick and thin, all goes… from new funky physics to water cleaning. Registration is free, deadline June 27. Opening of the Institute for Advanced Membrane Technology (IAMT) 29 June 2021: Invitation to full day (online) workshop.

Very Important News : new lab stickers. Let us know if you would like some.

  • May 2021:

  • March 2021:

Priyanka Thiruraman defended her PhD Thesis entitled: “Low-Dimensional Material Devices for Atomic Defect Engineering, Ionic and Molecular Transport”.

 

Penn Today article about our two-pore devices for parallel DNA recording, entitled: “Developing a new platform for DNA sequencing”.

https://penntoday.upenn.edu/news/developing-new-platform-dna-sequencing

  • January 2021: Physics World article about 2D membranes with atom-size holes for gas transport:

  •  December 2020:

Gas flow achieved through atomic-scale apertures (in 2D membranes) 2020!

https://penntoday.upenn.edu/news/atomic-scale-apertures-represent-novel-regime-physics-and-materials-science

https://phys.org/news/2020-12-ultra-fast-gas-tiniest-holes-d.html

https://eurekalert.org/pub_releases/2020-12/uop-ugf121820.php

 

  • October 2020:

Talk @ Nanopore Electrochemistry Conference, Nanjing 2020

  • July 2020:

https://www.youtube.com/watch?v=fxL-B1pViCY&feature=youtu.be

Outreach Science Video (chip fabrication, 2D materials CVD growth, nanopores, measurements), Summer 2020.(for high school students, part of Penn Summer Science Academy (PSSA), thanks to Mary Marcopul & team for running this program). Jothi Priyanka Thiruraman, Paul Masih Das, PhD, Yung-Chien (Killian) Chou, Alice Castan

Penn Summer Science Academy (PSSA),  July 10th.Drndic gave a 90 minute lecture to high school students part of the PSSA.

Our works on advancement of  in situ TEM electrical measurements of 2D materials  as well as the characterization of silicon nitride pore lifetime and stability were published, among others (See publications).

  • May 2020:

Sharing raw data files and protocols on our lab website

We uploaded our data on our laboratory web site for unrestricted download. This is an easy way to share our raw data and get others to analyze it and perform additional work.  You can use this data for example to compare the signal-to-noise ratios from various pores, to test your analysis algorithms and so on. Please contact us for any discussions.

Below is the raw 10 MHz data from solid-state pores that can be downloaded from the link below. Please let us know if you have questions. You can find specific info on these pores in the paper below (pores are listed by name).

Download from here: https://upenn.app.box.com/s/trcq67eso0hea57r1anfc77uf10hbdqj

Find details here:Single-Stranded DNA Translocation Recordings Through Solid-State Nanopores on Glass Chips at 10-MHz Measurement Bandwidth, Chien Chen-Chi, Siddharth Shekar, David J. Niedzwiecki, Kenneth L. Shepard, Marija Drndić, ACS Nano, 13 (9), 10545, 2019. DOI:10.1021/acsnano.9b04626

PDF 

Supplementary Material

 

Dr.  Paul Masih Das 

 

  • April 2020:

Paul Masih Das defends his PhD theses “Nanostructure Engineering in 2D Materials Beyond Graphene”.

Group meetings on Zoom

 

  • March 2020:

Sarah Friedensen received the 2020-2021 SAS Dissertation Completion Fellowship. (Currently she is the NSF Graduate Fellow)

Our invited perspective on ion flow in nanometer pores was published in ACS Nano.

Portable nanopore setup used for detecting particles in Antarctic samples and   synthetic seawater. Review of Scientific Instruments 91, 031301 (2020); https://doi.org/10.1063/1.5138210 .  AIP highlight: https://aip.scitation.org/doi/10.1063/10.0001022

 

  • October 2019:

IRIS 2019 symposium, Berlin:  2D Based Heterostructures, Energy Conversion, Data Science and Emerging Fields. 

http://www.iris-adlershof.de/de/IRIS2019.html

Photo: Marija Drndic with Prof. Andrea Schäfer.

  • October 2019: Marija Drndic presented lab’s work at the Harvard CIQM Quantum Material and Devices Seminar.

  • September 2019:

Cover of ACS Nano September Issue: Single-stranded DNA recorded at 10 MHz bandwidth through nanopores in glass chips. This unique work of art, illustrating the rapid movement and entropy of DNA molecules through nanopores, was created by Milivoj Šegan, an internationally acclaimed sculptor. Illuminating the sculpture from the inside and using the so-called “Lumino Mobile” effect, his digital camera captured the diffracted light, creating an illusion.

https://pubs.acs.org/doi/10.1021/acsnano.9b04626

 

On September 19 & 20, 2019, we hosted the:

NSF-funded Workshop: Enabling Quantum Leap: Achieving Room-Temperature Quantum Logic through Improved Low-Dimensional Materials

http://web.sas.upenn.edu/quantumleap2019/

  • August 2019:

Our work with Ken Shepard’s lab on DNA detection at record speeds of 10MHz measurement bandwidth was published in ACS Nano.

Our work on making single-atom and few-atom vacancies in metal dichalcogenide (MoS2 and WS2) membranes using ion irradiation at various irradiation doses,  and related statistical and properties characterization or resulting nanoporous membranes was published in Advanced Functional Materials.

Marija presented a talk   “Once upon a time there was a 2D nanopore” at Carbonhagen 2019 in Copenhagen, Denmark, August 21-22, 2019.

  • July 2019:

Penn Summer Science Academy (Experimental Physics Research Academy @ Penn Summer): Graduate and Undergraduate students in our lab teaching high school students.

 

 

  • June 2019:  PhD student Paul Masih Das and Priyanka Thiruraman attend and present at the Graphene 2019 conference in Rome, Italy.

  • Marija Drndic presents our work on nanopores and 2D materials at AbSciCon 2019, Bellevue, WA.

  • June 2019:  Visit by Drndic lab alumni Gopi Danda (PhD, 2018)

 

 

  • June 2019: Students designed a new lab t-shirt (email us if you would like one at drndic@physics.upenn.edu)

 

  • May 2019:  Several undergraduates are working in the lab this summer on a range of topics from 2D materials growth to device physics and physical measurements:
  • Rachael Keneipp (joined the lab last year with the PURM 2018 program)
  • Hyong Min Kim (PURM 2019 program)
  • Luka Yancopoulos (VIPER 2019 program)
  • Luke Holtzman (REU 2019 program)
  • Joshua Chen (PURM 2019 program)
  • Srinivas Mandyam (VAGELOS 2019 program)
  • April 2019:  Paul Masih Das received the 2019-2020 SAS Dissertation Completion Fellowship (DCF) and the The Elias Burstein Prize – Provided from an endowment established by friends, colleagues, and students of Elias Burstein, upon his retirement as Mary Amanda Wood Professor of Physics on June 30, 1988. Awarded to the graduate student in Condensed Matter Physics judged by the Physics Department to have a made a significant contribution to our understanding of the subject.    Paul was awarded this prize “for his contributions to the field of two-dimensional materials including phosphorene and metal dichalcogenides, the illumination of the role of single-atom detects and dopants on materials properties, and his pioneering work on patterning nanopores, nanoribbons, antidot arrays, and nanoporous membranes”.

 

  • February 2019: Paul Masih Das is the winner of the Natural Sciences award of the Third Annual Penn Arts and Sciences Grad BEN Talks, for his presentation of “Quantum Materials: Making Smart Phones ‘Cool’ Again.”

https://omnia.sas.upenn.edu/story/2019-grad-ben-talks-video

 

  • Conferences and Lab Presentations  (February and March 2019)
GrapheneforUSA (Feb 14-15)
ENM Conference in STEM (Feb 21-23)
Biophysical Society Meetings (March 2-7)
American Physical Society (March 4-8)
IWEPNM 2019 (March 9-16)

 

  • American Physical Society Meeting, March 4-8, 2019, Boston, MA.

Zhaoli Gao will present our joint work with Charlie Johnson’s and other labs at Penn Physics.

APS.Session P12: 2D Materials: Probing and Tuning Electronic Structure2:30 PM–5:30 PM, Wednesday, March 6, 2019
BCEC Room: 153A
P12.00009 :Large-Area Epitaxial Growth of Curvature-Stabilized ABC Trilayer Graphene with Tunable Band Gap, 4:06 PM–4:18 PM

Abstract:

The physical properties of epitaxially-grown layered van der Waals (vdW) materials can be engineered to an extraordinary degree by manipulating the number of atomic layers, their compositions, and their relative stacking configurations and twist angles. vdW trilayer graphene (TLG) can stack in either a semi-metallic ABA configuration or a semi-conducting ABC configuration with a gate-tunable band gap but to this point has only been produced via exfoliation, which greatly limits its scientific and technological development. Here we present a scalable approach to epitaxial TLG growth via chemical vapor deposition that reliably enhances the fraction and size of ABC stacked TLG domains compared to other methods. The key insight is that nanoscale substrate curvature can locally stabilize ABC domains, typically leading to alternating regions of ABC and ABA on topographically corrugated growth substrates. Unambiguous electronic signatures of ABC-TLG were revealed by nano angle-resolved photoemission spectroscopy and infrared scanning near-field microscopy. The ABC fraction remains high after transfer onto a device substrate, as confirmed by transport measurements showing a sizable and tunable ABC-TLG band gap.
  • Biophysical Society Annual Meeting, March 2-6, 2019, Baltimore, MD.

Four posters presented (one featured below):

Silicon Nitride Nanopore Stability and Operational Lifetime for Biosensing Purposes

Yung-Chien Chou, Paul Masih Das, Marija Drndić,  University of Pennsylvania, Philadelphia, PA, USA

Abstract:

Nanopore sensors are promising for many applications including molecular filtration, detection and sequencing with long read length capabilities, high speed and high data throughput. Given their more robust mechanical nature, solid-state nanopores may be preferable candidates over their biological counterparts for some applications requiring durability and operation under a wider range of external parameters. Here we investigate the lifetime of 10-nm-thick, low-stress silicon nitride nanopores, fabricated in a transmission electron microscope, with diameters ranging from ~ 3 to 7 nm. We stored them in various solutions and measured the open pore conductance as a function of storage time, over periods of days. We report the rates of pore diameter increase as a function the electrolyte concentrations. In contrast, the pore wall etching process is negligible when nanopores are stored in ethanol/water solution, where the pore size is constant and the current-voltage characteristics are unchanged for more than 30 days.

 

IWEPNM 2019:    International Winterschool on Electronic Properties of Novel Materials.      https://www.iwepnm.org/2019/

ENM Conference in STEM (Feb 21-23), Washington, DC.

https://emerging-researchers.org

Undergraduate Students Rachael Keneipp and Mark D’Souza will be presenting their research posters.

February 14 -15, New York, NY.  Grapheneforus. http://www.grapheneforus.com/2019/

Paul Masih Das will present the poster below at the GrapheneForUs conference in NY city: “Nanotopography and Ion Transport in Centimeter-Scale MoS2 Membranes”. 

Past Events…

February 2019:

Priyanka Thiruraman presented the poster below at the Dead Sea Workshop entitled: “Ion transport in Angstrom-Size MoS2 Pores”

January 2019:

Penn Press: The Nanotopography of an Atomic Word

“You don’t need any special chemicals to make these membranes,” says Paul Masih Das, a graduate student who was the lead author of this study. “You could even make them in your basement.”

“We let it grow naturally,” Drndić says about the work done in her lab. “If we see another opportunity, we might jump on it. It’s nice to have that kind of freedom, where you’re not under pressure to always justify the cost or the application. It’s nice to be able to just explore and to bump onto new things.”

https://penntoday.upenn.edu/news/nanotopography-atomic-world

 

Wavelets in your “big” data analysis toolbox for filtering out all that noise while teasing out the signal. The principles are similar to those of Fourier analysis, which was first developed in the early part of the 19th century.

 

https://pubs.acs.org/doi/10.1021/acs.nanolett.8b04388

Wavelet denoising of high-bandwidth nanopore and ion channel signals Siddharth Shekar, Chen-Chi Chien, Andreas Hartel, Peijie Ong, Oliver B Clarke, Andrew Marks, Marija Drndic, and Kenneth L. Shepard Nano Lett., 2019 DOI: 10.1021/acs.nanolett.8b04388

 

December 2018:

New Nano Letters paper on centimeter-scale nanoporous MoS2  monolayers / few-layer membranes produced by simple wet etching (see list of publications).

November 2018:

Paul Masih Das presented a poster “Low-dimensional phosphorene nanostructures” at the Singh User Meeting: https://www.nano.upenn.edu/singh-annual-users-meeting/ , and at the Oak Ridge Workshop: https://www.mostlyphysics.net/visits-and-conferences/2018/11/1/ornl-workshop

Science Cafe Live

September 2018:  Conference in Shenyang, Liaoning Province, China.

July 2018:  

Graduate student Priyanka Jothi Thiruraman was selected to the 2018 class of Vagelos Institute for Energy Science and Technology (VIEST) Graduate Fellows.

https://penntoday.upenn.edu/news/penn-arts-and-sciences-launches-vagelos-institute-energy-science-and-technology

July 2018: Conference in Busan, South Korea.

June 2018:  Francis Chen-Chi Chien defended his PhD thesis

PhD defense of Francis Chen-Chi Chien, June 2018
Francis Defense June 2018

May/June 2018:   Five undergraduates join lab for summer research: Rachael Keneipp, Niels Rasmussen, Mark D’Souza, Chris Zhang, and Han Yan, recruited with the help of the Penn PURM program.

Summer Kickoff Lunch 2018 with the new undergraduate students:

Group lunch, June 2018

April/May 2018:  William Parkin and Gopinath Danda defended their PhD theses.

April 2018:  Trip to Delft, Netherlands, for a PhD Defense.

March 2018:   Penn Today Spotlight: Our group’s recent work on water filtration using nanopores was highlighted in the Penn Today!

Drndić Lab 2018:  Drndić Lab at a recent group lunch, March 2018.

Philly Materials Day participation by Drndic lab: At this year’s Philly Materials Day, the lab showcased a variety of demos to the general public.

 

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October 3, 2018:  Drndić Lab at Nano Day

Each year, the Nano/Bio Interface Center highlights nanotechnology across Penn.
High school classes, undergraduate and graduate students,
postdocs and faculty participate in exhibits, demonstrations, tours, posters and talks.
Find out more at NanoDay@Penn.

Graduate Student Sarah Friedensen ran a lab group for the Penn Summer Science Academy’s program in Experimental Physics Research in which explored a range of topics (standing waves on violin strings, Chaldni plates, and approximate spheres (water balloons) using a high-speed camera to film each experiment, as well as a strobe light for the water balloon).
Sarah and the high school students also used the high-speed camera to film collisions between two-by-fours, objects hitting both water and ooblek, and the bursting of the water balloon and a balloon filled with ooblek.
Sarah helped guide the group with respect to what was achievable in the time frame of one week, and the students worked together to develop the specific phenomena they wanted to investigate (the group theme was “film analysis”).
The students ranged from sophomore to senior in high school and were in a group of four.
By the end of the session, through their own research, students had connected the results of their experiments to models of the hydrogen atom.

Graduate student Priyanka Thiruraman ran GEMS, a summer school program at SEAS for middle school girls, helping out with nanotechnology sessions from July 24 to July 28, 2017.
Priyanka ran two sessions on:

  1. DNA extraction from strawberries, where she also touched upon the concept of DNA sequencing and nanopores (our lab’s research), and
  2. Nanotechnology in basic physics. Experiments included polymer synthesis, non-Newtonian liquids, lasers/ optics, polarizers, kinetic sand etc. Students were also given a tour of the Singh center to see the fabrication facilities, scanning microscopes and most importantly “the microscope that occupies an entire room” aka TEM.

See the program and a video.

Graduate student Paul Masih Das was in charge until May 2017 of a volunteer group called Moelis Access Science Physics.
A team of about 10-12 undergrads and Paul would take equipment from the physics department (with the help of Bill Berner) every week and go to various public schools in West Philly (Sayre HS, West Philly HS, Comegys MS), where they performed introductory physics experiments with the students.
Paul has also given 1-2 hour outreach talks on DNA sequencing and our lab’s research in various location including the Comegys MS, Huey MS, and the Franklin Institute.
For the past two summers, Paul helped with the Franklin Institute’s Summer Camp.
A few other physics grad students and Paul went to the Franklin Institute every other week and performed an educational science activity with middle school children (building hovercrafts, learning about constellations, making circuits, etc.).

July 6, 2017: Prof. Drndić gives lecture for high school students

Prof. Drndić gave a lecture to high school students participating at the Penn Summer Science Academy who joined Penn this summer from many different countries.

June 29, 2017: Drndić lab in the news

Our recent work on patterning superconductivity in a topological insulator has been featured in Penn News, Phys.org, and Science Daily.

June 1, 2017: Five undergraduate students have recently joined our lab

The Drndić lab welcomes new undergraduate students Nikhil Chari, Abby Kaplan, Seyoung Kim, Reginald Lamaute, and Lee Blackburn.

May 30, 2017: Plenary talk at EIPBN 2017

Prof. Drndić gave a plenary talk at the EIPBN 2017 entitled “2D Materials Nanosculpting in the Transmission Electron Microscope and Bioelectronics Applications” and an invited presentation at the Women in Nanofabrication (WIN) Luncheon Event at the same conference, sharing her own career path and lessons learned along the way.

 May 5, 2017: Graduate Student Sarah Friedensen awarded 2017 NSF Graduate Fellowship

Congratulations to Sarah Friedensen who received the 2017 NSF Graduate Fellowship. Sarah’s work includes electronics transport in topological and two-dimensional materials in the Drndic lab. At the 2017 APS March Meeting in New Orleans she gave a talk on “Electron-beam nanosculpting and materials analysis of exfoliated bismuth selenide”.

March 17, 2017: Drndić lab alum Jessamyn Fairfield on ‘Smarter Machines’

Penn Physics alum Jessamyn Fairfield has written a feature for the March 2017 issue of Physics World about neuromorphic electronics, novel devices whose function mimics synaptic function.
Neuromorphic features can be realized in a variety of materials, from nanomaterials to polymers, and may enable the development of electronic skin, novel computational paradigms, or smart neuroprosthetics.
Jessamyn is currently a professor at NUI Galway in Ireland, and did her PhD research in the Drndic lab on semiconducting nanocrystal optoelectronics.

Full text of the article is available here: http://jessamynfairfield.com/wp-content/uploads/2017/03/PWMar17Fairfield.pdf

March 16, 2017: Penn Researchers Study How New 2D Nanopores React to Light

Drndic and Johnson’s labs, together with researchers from Penn State, use light to control the size of two dimensional tungsten disulfide nanopores. Read more in the article in PennCurrent.

Drndić lab in the news : Our recent work on growth of monolayer WTe2 was featured in Penn News and Materials Today.

Feb 4, 2017: Drndic Lab at Philly Materials Day

At this year’s Philly Materials Day hosted by Drexel University, the lab showcased a variety of demos to the general public.
Students and parents alike were first shown the process of isolating thin 2D materials such as graphene via mechanical exfoliation.
They were then able to see the principles behind 2D-material-based water desalination using interactive large-scale models of filtration devices.

December 15, 2016: Early Access to Graduate Research Workshop

Graduate students Paul Masih Das, Francis Chien, Jothi Priyanka Thiruraman, and Gopinath Danda participated in the Early Access to Graduate Research workshop series at the nearby Franklin Institute.
They spent the afternoon teaching high school students from the Science Leadership Academy about the history, structure, and function of DNA.
The students also learned about various 2D materials and how they can be used in nanopore DNA sequencing.

 

December 14, 2016:  Physics at Masterman Middle and High School

Prof. Drndic gave a physics talk to about two hundred curious fifth graders in the Masterman Middle & High School. She talked about subfields of physics, how to become a physicists, and covered topics in kinematics (mass, velocity, force, energy, work) as well as example of motion in two dimensions, pendula, motion in two dimensions, momentum, collisions, motion on the inclined plane, as well as explained the origin behind gravitational acceleration. She also showed mechanics demos.

December 6, 2016: Outreach talk : Science and Comedy: Creativity in Public Engagement

Tue 12/6/2016 2-3 pm Singh 221

Jessamyn Fairfield, NUI Galway, Hosted by Prof. Marija Drndic

Jessamyn organized creative and effective education and public engagement initiatives for the AMBER materials research centre at Trinity College Dublin.
Her most successful project has been the development of Bright Club Dublin, a monthly research/comedy variety night featuring academics alongside comedians in a night of idea-driven entertainment.
Jessamyn is also a frequent contributor to Futureproof, the Newstalk science show.

December 5, 2016: Science Talk: Nanomaterials for Neuromorphic Devices

Mon, 12/5/2016,  12-1 pm, Singh  035

Jessamyn Fairfield, NUI Galway, Hosted by Marija Drndic

Imagine a world where materials can heal themselves and electronics are built to learn the way your brain does, all using wires tinier than a human hair.
My research lab at NUI Galway is focused on taking that world from science fiction to science fact!
We take materials that are very small, or nanoscale, in one dimension, spray them onto a variety of surfaces, and try to make circuitry from them.
Networks of nanowires are memristive, which means that their electronic behavior depends on their measurement history.

We use metal nanowires that can be sprayed onto a variety of surfaces to create random networks.
Light or electricity can change these networks of nanowires in useful ways.
Where two nanowires cross to form a junction, light or electricity can change the strength of the junction.
These individual changes change the overall behaviour of the network.
The changes are self-healing, so electrical currents can route around damaged sections of network.
The network also becomes ‘smarter’ controlled changes create new meaningful patterns of response to particular complex stimuli.
When they are built, traditional silicon architectures for computing have fixed structure and implicit fixed digital modes of computation.
Nanowire networks can create flexible computational modes that can adapt on the fly, which makes nanowire networks more like brains than like silicon chips.

from http://jessamynfairfield.com/research/

*light lunch will be provided

September 16, 2016: Prof. Drndic featured in the ACS Nano Podcast

July 15, 2016: Comegys Middle School Workshop

Graduate student Paul Masih Das gave a talk to 8th grade students at West Philadelphia’s Comegys Middle School about the ins and outs of DNA extraction and sequencing.
Afterwards, students performed a fun activity in which they extracted the DNA from strawberries using simple household products such as soap, salt, and ethanol…

Penn Summer Science Academy

This July, Prof. Drndic gave a research presentation to high school students from the Penn Summer Science Academy (PSSA).
Roughly 40 students went on a tour of our lab, in coordination with Bill Berner, where they learned about the process of fabricating and testing a solid-state nanopore.
They also learned about the wide variety of techniques and instrumentation that we use: chemical vapor deposition, photolithography, electron beam nanosculpting, and DNA translocation experiments.
More information about the Academy can be found here: http://www.physics.upenn.edu/~pssa/.

June 28, 2016: Phosphorene makes cover of ACS Nano

Our work on phosphorene
has been featured on the cover of ACS Nano, June 28, 2016 issue.

June 26, 2016: Sarah Friedensen awarded Arnold M. Denenstein Prize

This award is provided from an endowment established by the family, friends, and colleagues of Arnold M. Denenstein to honor his memory and his contributions to science. Awarded annually to a graduate student, judged by the Physics and Astronomy Department, who shows the most promise of becoming and outstanding experimental physicist.

June 20, 2016: Marija Drndić named Fay R. and Eugene L. Langberg Professor of Physics

Congratulations to professor Marija Drndić on being named the Fay R. and
Eugene L. Langberg Professor of Physics.

May 3, 2016: Shining a Light on Phosphorene’s Crystal Structure

Our joint research with collaborators from MIT, Tohoku University, Oak Ridge National Laboratory and Rensselaer Polytechnic Institute, published in Nano Letters, was featured in a IEEE Spectrum article.
Read the paper here and the article here.

May 2, 2016: NSF Graduate Research Fellowships

Graduate students Hannah Hughes received the NSF Graduate Research Fellowship and Paul Masih Das received the NSF Honorable Mention. Rebecca Engelke and Bart Machielse, who did their undergraduate research and authored several papers while in our lab, have also received the 2016 NSF Graduate Research Fellowship 2016. We wish them a great time during their PhD years at Harvard Physics, and we are looking forward to following their new scientific results!

April 30, 2016: Philly Science Festival

The Drndic group, Science Outreach Initiative of the School of Arts and Sciences, and Project BioEyes from University of Pennsylvania demonstrated how DNA affects physical features in living organisms, like zebrafish, and the importance of DNA sequencing in an educational exhibit at Philadelphia Science Festival on Saturday April 30 2016 as a part of National DNA Day initiative. Children from all age groups visited the booth, which was aptly titled “What Can Fish Tell Us About DNA?”, and learned about how a small
change in DNA sequence can create two different types of zebrafish – wildtype and albino – and how nanopore sequencing technology can help us find these differences easily.
Microscopes were installed in the booth to observe the physical differences between the two types of zebrafish larvae and adult, following which the visitor was handed an index card with a fish scale printed on one side and a colored DNA code on the other. These cards could then be inserted into punched envelopes revealing a specific color code, very similar to how nanopore DNA sequencing technology works. The color codes could be matched up to a map aiding in classification of the fish scale into the two types of fishes. A “DNA inside a nanopore” bracelet were also given to every visitor, which consisted of a colored strip of paper inside a rectangular movable sleeve with a hole in the middle.

The booth was managed by the volunteers from both the participating groups from 10 am to 4 pm at Penn’s Landing, Philadelphia. This exhibit was one of the two demonstrations which Drndic group participated in during the Philadelphia Science Festival, the other being “Nanopore Explorin’” on the previous Sunday, April 24 2016 in the Singh Nanotechnology Center, Philadelphia.

Continue reading“Philly Science Festival”

POSTED ONEDIT“FEATURE IN THE PENN CURRENT”

Feature in the Penn Current

Our work on in situ TEM fabrication and measurement of graphene nanoribbon transistors, In Situ Transmission Electron Microscopy Modulation of Transport in Graphene Nanoribbons by Julio A. Rodríguez-Manzo, Zhengqing John Qi, Alexander Crook, Jae-Hyuk Ahn, A. T. Charlie Johnson, and Marija Drndić, has been featured in the Penn Current.

See the news story here.

Continue reading“Feature in the Penn Current”

POSTED ONEDIT“PHILLY SCIENCE FESTIVAL”

Philly Science Festival

Drndić lab participate at two Philadelphia Science Festival events on April 24 and April 30, 2016.

The Drndic Lab has partnered with Dr. Slavko Milekic at Philadelphia’s University of the Arts to create two educational tools for this year’s Philadelphia Science Festival. The first “scanimation” uses an artistic technique known as persistence of vision to give the illusion of a fish swimming through an array of nanopores. The other is a cartoon-based game in which the user must guess the weight of characters in an elevator, effectively modeling nanopore DNA sequencing. Both tools are presented on portable tablet devices and suitable for a wide range of audiences.

Also, the Drndic Lab has developed a virtual nanopore app. Developed for Google Cardboard, the user can experience the actual translocation of a DNA strand through a nanopore in a stunning virtual reality environment.

Continue reading“Philly Science Festival”

POSTED ONEDIT“IN SITU TRANSMISSION ELECTRON MICROSCOPY MODULATION OF TRANSPORT IN GRAPHENE NANORIBBONS”

In Situ Transmission Electron Microscopy Modulation of Transport in Graphene Nanoribbons

Julio A. Rodríguez-Manzo, Zhengqing John Qi, Alexander Crook, Jae-Hyuk Ahn, A. T. Charlie Johnson, and Marija Drndić

ACS Nano, 2016, 10 (4), pp 4004–4010
2016

ACS Editors’ Choice Article

Marija Drndic discussed the in situ transmission electron microscopy modulation of transport in graphene nanoribbons. Hear this in Episode 105 of the ACS Nano Podcast.

Continue reading“In Situ Transmission Electron Microscopy Modulation of Transport in Graphene Nanoribbons”

POSTED ONEDIT“ANISOTROPIC ELECTRON-PHOTON AND ELECTRON-PHONON INTERACTIONS IN BLACK PHOSPHORUS”

Anisotropic Electron-Photon and Electron-Phonon Interactions in Black Phosphorus

Xi Ling, Shengxi Huang, Eddwi H. Hasdeo‡, Liangbo Liang, William M. Parkin, Yuki Tatsumi, Ahmad R. T. Nugraha, Alexander A. Puretzky, Paul Masih Das, Bobby G. Sumpter, David B. Geohegan, Jing Kong, Riichiro Saito, Marija Drndic, Vincent Meunier, and Mildred S. Dresselhaus

Nano Letters, 16 (4), pp 2260–2267
2016

Continue reading“Anisotropic Electron-Photon and Electron-Phonon Interactions in Black Phosphorus”

POSTED ONEDIT“DRNDIC LAB AT THE PHILADELPHIA SCIENCE CARNIVAL”

Drndic Lab at the Philadelphia Science Carnival

Graduate students Francis Chien Chen-Chi, Gopinath Danda, and Paul Masih Das are leading our group’s outreach effort at the Philadelphia Science Carnival, to be held on April 30th, 2016.
This is also part of the National DNA Day.

We are collaborating with the BioEYES, a partnership to advance K-12 science education.
We will present an integrated research exhibit spanning a range of topics related to DNA and genomics research.
We will discuss how the eye color in zebrafish is related to DNA and DNA sequencing.

We know that DNA is what genes are made up of, and that genes are responsible for the way we look and the traits we have.
Fish are an excellent animal model that allows us to visually study how the trait of dark pigmentation vs. albinism gets passed down from parents to offspring.
The title of this collaborative exhibit will be “What can a fish teach us about DNA?”

Continue reading“Drndic Lab at the Philadelphia Science Carnival”

POSTED ONEDIT“MAGNETORESISTANCE (MR) OF TWISTED BILAYER GRAPHENE ON ELECTRON TRANSPARENT SUBSTRATE”

Magnetoresistance (MR) of twisted bilayer graphene on electron transparent substrate

Sung Ju Hong, Julio A. Rodríguez-Manzo, Kyung Ho Kim, Min Park, Seung Jae Baek, Dmitry I. Kholin, Minwoo Lee, Eun Sang Choi, Dae Hong Jeong, Dawn A. Bonnell, Eugene J. Mele, Marija Drndic, A.T. Charlie Johnson, Yung Woo Park

Synthetic Metals, In Press, Corrected Proof, Available online 15 January 2016
2015

Continue reading“Magnetoresistance (MR) of twisted bilayer graphene on electron transparent substrate”

POSTED ONEDIT“SUSPENDED SOLID-STATE MEMBRANES ON GLASS CHIPS WITH SUB 1-PF CAPACITANCE FOR BIOMOLECULE SENSING APPLICATIONS”

Suspended Solid-state Membranes on Glass Chips with Sub 1-pF Capacitance for Biomolecule Sensing Applications

Adrian Balan, Chen-Chi Chien, Rebecca Engelke & Marija Drndić

Scientific Reports, 5, Article number: 17775
2015

Continue reading“Suspended Solid-state Membranes on Glass Chips with Sub 1-pF Capacitance for Biomolecule Sensing Applications”

POSTED ONEDIT“CROSS-TALK BETWEEN IONIC AND NANORIBBON CURRENT SIGNALS IN GRAPHENE NANORIBBON-NANOPORE SENSORS FOR SINGLE-MOLECULE DETECTION”

Cross-Talk Between Ionic and Nanoribbon Current Signals in Graphene Nanoribbon-Nanopore Sensors for Single-Molecule Detection

Matthew Puster, Adrian Balan, Julio A. Rodríguez-Manzo, Gopinath Danda, Jae-Hyuk Ahn, William Parkin, and Marija Drndić

Small, 2015, 11, No. 47, 6309–6316
2015

Continue reading“Cross-Talk Between Ionic and Nanoribbon Current Signals in Graphene Nanoribbon-Nanopore Sensors for Single-Molecule Detection”

POSTED ONEDIT“EFRI COLLABORATION KICKOFF”

EFRI Collaboration Kickoff

Led by Marija, a team with our collaborators from RPI, Rochester, Penn State and Northeastern won a 2M NSF EFRI grant. We held a kickoff meeting in August to get the ball rolling. More about the NSF grant here.

Included was a proposed portable museum exhibit to explain the concept of nanopore-based DNA sequencing, in partnership with the Franklin Museum in Philadelphia and Prof. Slavko Milekic (The University of the Arts).

Read more from PennNews.

Continue reading“EFRI Collaboration Kickoff”

POSTED ONEDIT“BART MACHIELSE SELECTED AS MIT SUMMER SCHOLAR”

Bart Machielse Selected As MIT Summer Scholar

Undergraduate student Bart Machielse was selected as one of twelve MIT summer scholars
from June 7 to August 8, 2015. Bart was chosen among 156 applicants.

University of Pennsylania junior physics major Bartholomeus Machielse says, “I’m looking forward to meeting scientists from around the country and to experiencing the unique research environment that MIT offers, while continuing to develop the skills I’ll need to one day run my own lab.” Machielse was lead co-author of “Improving Signal-to-Noise Performance for DNA Translocation in Solid-State Nanopores at MHz Bandwidths” (Nano Letters, Nov. 21, 2014) under Prof. Marija Drndić, Professor of Physics at Penn.

Continue reading“Bart Machielse Selected As MIT Summer Scholar”

POSTED ONEDIT“DRNDIĆ LAB PRESENTS AT APS MARCH MEETING 2015”

Drndić Lab presents at APS March Meeting 2015

Undergraduate Student, Rebecca Engelke, giving a talk at the APS march meeting 2015 in San Antonio.

The Drndić Lab traveled to APS March Meeting 2015 in San Antonio, Texas to give the following talks:

  • B1.00009 Effect of defects produced by electron irradiation on the electrical properties of graphene.
  • T15.00014 Reaching the Ionic Current Detection Limit in Silicon-Based Nanopores.
  • G43.00009 Improving signal-to-noise performance for DNA translocation in solid-state nanopores at MHz bandwidths.
  • G43.00010 DNA translocation measurements through low-capacitance solid-state nanopore chips at high bandwidths.
  • G43.00011 Up and down events in nanoparticle translocation through solid-state nanopores.
  • G48.00009 Obtaining structural information of small proteins using solid-state nanopores and high-bandwidth measurements.
  • T15.00003 Gold Nanorod translocations and charge measurement through solid-state nano pores.
  • W47.00010 Thinning silicon-based membranes with electron irradiation for solid-state nanopore sensors.

Continue reading“Drndić Lab presents at APS March Meeting 2015”

POSTED ONEDIT“DRNDIĆ LAB AT THE BIOPHYSICAL SOCIETY 59TH ANNUAL MEETING IN BALTIMORE”

Drndić Lab at the Biophysical Society 59th Annual Meeting in Baltimore

Undergraduate student Bart Machielse presented a poster entitled “Improving signal-to-noise performance for DNA translocation in solid-state nanopores at MHz bandwidths” at the Biophysical Society 59th Annual Meeting in Baltimore, MA from February 7-11, 2015.

Continue reading“Drndić Lab at the Biophysical Society 59th Annual Meeting in Baltimore”

POSTED ONEDIT“PAUL MASIH DAS RELEASES IPHONE SEQUENCING GAME MASTER SEQUENCER”

Paul Masih Das releases iPhone sequencing game Master Sequencer

Now available on the iTunes store!

In Master Sequencer, the player runs along a DNA strand, effectively threading it through a nanopore and allowing it to be sequenced. This model is based on nanopore DNA sequencing, in which characteristic current changes due to the presence of a DNA base-pair in a nanopore are converted into a DNA sequence. In both the game and reality, sequencing is terminated when the DNA strand crashes into the membrane. The iOS game is similar to the well-known Temple Run and appeals to a wide range of audiences.

Continue reading“Paul Masih Das releases iPhone sequencing game Master Sequencer”

POSTED ONEDIT“MARIJA DRNDIĆ SELECTED AS PENN FELLOW”

Marija Drndić selected as Penn Fellow

Prof. Marija Drndić has been chosen as a Penn Fellow for the next two years. The Penn Fellows program is designed to provide a select group of developing campus leaders with an opportunity to build University-wide networks, think strategically about higher education, and learn more about Penn and its programs by interacting informally with members of the University’s executive team.
Information about the current Fellows is listed at provost.upenn.edu/penn-fellows.

Continue reading“Marija Drndić selected as Penn Fellow”

POSTED ONEDIT“IMPROVING SIGNAL-TO-NOISE PERFORMANCE FOR DNA TRANSLOCATION IN SOLID-STATE NANOPORES AT MHZ BANDWIDTHS”

Improving signal-to-noise performance for DNA translocation in solid-state nanopores at MHz bandwidths

Adrian Balan, Bartholomeus Machielse, David Niedzwiecki, Jianxun Lin, Peijie Ong, Rebecca Engelke, Kenneth Shepard, and Marija Drndić

Nano Letters, 14 (12), 7215-7220
2014

Continue reading“Improving signal-to-noise performance for DNA translocation in solid-state nanopores at MHz bandwidths”

POSTED ONEDIT“SECOND ANNUAL AMC8 MATH DAY AT GREENFIELD ELEMENTARY SCHOOL”

Second Annual AMC8 Math Day at Greenfield Elementary School

For the second year in a row, Marija is organizing the Greenfield Math Day in Albert Greenfield Elementary School in Center City, Philadelphia, to be held on November 18, 2014. (Any interested parents or children from other local schools interested to participate are welcome to contact Marija).
Last year, the whole middle school consisting of about 200 students participated. The AMC8 is an international competition consisting of 25 multiple-choice questions and students have 40 minutes to work on it initiated by the Mathematical Association of America (MAA). MAA encourages all students in grades 6, 7 and 8 to participate in the AMC 8. All USA, USA embassy, Canadian and foreign school students in grade 8 or below are eligible to participate. Especially talented students as young as 8 years old have participated in the past.

Continue reading“Second Annual AMC8 Math Day at Greenfield Elementary School”

POSTED ONEDIT“VISIT US AT THE NANODAY@PENN ON OCTOBER 22, 2014”

Visit us at the NanoDay@Penn on October 22, 2014

Each year, the Nano/Bio Interface Center highlights nanotechnology across Penn.
High school classes, undergraduate and graduate students,
postdocs and faculty participate in exhibits, demonstrations, tours, posters and talks.
Find out more at NanoDay@Penn.

Kim Venta judging high school projects during last year’s NanoDay.

Continue reading“Visit us at the NanoDay@Penn on October 22, 2014”

POSTED ONEDIT“PENN TEAM STUDIES NANOCRYSTALS BY PASSING THEM THROUGH TINY PORES”

Penn Team Studies Nanocrystals By Passing Them Through Tiny Pores

Our MRSEC IRG-4 team (Drndić, Murray and Lukes labs) studies gold nanorods by passing them through nanopores (Nano Letters, 2014).

(MRSEC = Materials Research and Engineering Center; IRG = Interdisciplinary Research Group)

See the press release

Continue reading“Penn Team Studies Nanocrystals By Passing Them Through Tiny Pores”

POSTED ONEDIT“PHILLY SCIENCE FESTIVAL”

Philly Science Festival

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

Continue reading“Philly Science Festival”

POSTED ONEDIT“GRAPHENE NANORIBBON-NANOPORE DEVICES FOR DNA SEQUENCING”

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:

Continue reading“Graphene Nanoribbon-Nanopore Devices for DNA Sequencing”

POSTED ONEDIT“CONTINUOUS GROWTH OF HEXAGONAL GRAPHENE AND BORON NITRIDE IN-PLANE HETEROSTRUCTURES BY ATMOSPHERIC PRESSURE CHEMICAL VAPOR DEPOSITION”

Continuous Growth of Hexagonal Graphene and Boron Nitride In-Plane Heterostructures by Atmospheric Pressure Chemical Vapor Deposition

Gang Hee Han , Julio A. Rodriguez-Manzo , Chan-Woo Lee , Nicholas J. Kybert , Mitchell B. Lerner , Zhengqing John Qi , Eric N. Dattoli , Andrew M. Rappe , Marija Drndić, and A.T. Charlie Johnson

ACS Nano, 7 (11), 10129–10138
2013

POSTED ONEDIT“DRNDIĆ LAB WORKING ON OPEN-SOURCE TRANSLOCATION ANALYSIS SOFTWARE PYPORE”

Drndić Lab working on open-source translocation analysis software Pypore

The Drndić Lab has open-sourced the translocation analysis software Pypore.
This project is writting in a combination of Python and Cython for high-throughput nanopore data analysis. Please, fork the repo and send in your pull requests!

Continue reading“Drndić Lab working on open-source translocation analysis software Pypore”

POSTED ONEDIT“DIFFERENTIATION OF DNA HOMOPOLYMERS”

Differentiation of DNA Homopolymers

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:

Continue reading“Differentiation of DNA Homopolymers”

POSTED ONEDIT“COLLECTIVE FLUORESCENCE ENHANCEMENT IN NANOPARTICLE CLUSTERS”

Collective Fluorescence Enhancement In Nanoparticle Clusters

In a recent Nature Communications paper, “Collective fluorescence enhancement in nanoparticle clusters”, we show that blinking nanorods interact with each other in a cluster, and the interactions affect the blinking statistics.

Selected press:

Continue reading“Collective Fluorescence Enhancement In Nanoparticle Clusters”

POSTED ONEDIT“LAUREN WILLIS MAKES THE COVER OF SCIENCE”

Lauren Willis Makes The Cover Of Science

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.

Continue reading“Lauren Willis Makes The Cover Of Science”

POSTED ONEDIT“SEEKING POSTDOC APPLICATIONS”

Seeking Postdoc Applications

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.

Continue reading“Seeking Postdoc Applications”

POSTED ONEDIT“UPCOMING PRESENTATIONS”

Upcoming Presentations

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 Merchantwill give a talk about DNA translocation through graphene nanopores on March 23rd at 12:27 PM.

Continue reading“Upcoming Presentations”

POSTED ONEDIT“NANOPORES IDENTIFY MODIFIED DNA BASES”

Nanopores Identify Modified DNA Bases

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.

Selected press:

Continue reading“Nanopores Identify Modified DNA Bases”

POSTED ONEDIT“MICRORNA DETECTION PUBLISHED IN NATURE NANOTECHNOLOGY”

MicroRNA Detection Published in Nature Nanotechnology

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:

Continue reading“MicroRNA Detection Published in Nature Nanotechnology”

POSTED ONEDIT“RESEARCH PRESENTED AT UNIVERSITY OF CHICAGO”

Research Presented At University Of Chicago

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”.

Continue reading“Research Presented At University Of Chicago”

POSTED ONEDIT“DRNDIĆ LAB MEMBERS PRESENT AT BIOSENSING WITH CHANNELS SUMMER SCHOOL”

Drndić Lab Members Present at Biosensing With Channels Summer School

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.

Continue reading“Drndić Lab Members Present at Biosensing With Channels Summer School”

POSTED ONEDIT“DNA TRANSLOCATION THROUGH GRAPHENE NANOPORES PUBLISHED”

DNA Translocation Through Graphene Nanopores Published

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:

Continue reading“DNA Translocation Through Graphene Nanopores Published”

POSTED ONEDIT“FLUORESCENCE DYNAMICS OF SEMICONDUCTOR NANOROD CLUSTERS STUDIED BY CORRELATED ATOMIC FORCE, TRANSMISSION ELECTRON, AND FLUORESCENCE MICROSCOPY”

Fluorescence Dynamics of Semiconductor Nanorod Clusters Studied by Correlated Atomic Force, Transmission Electron, and Fluorescence Microscopy

Fluorescence Dynamics of Semiconductor Nanorod Clusters Studied by Correlated Atomic Force, Transmission Electron, and Fluorescence Microscopy

Claudia Querner, Siying Wang, Ken Healy, Jessamyn Fairfield, Michael D. Fischbein and Marija Drndić

Journal of Physical Chemistry C, 112 (50), 19945-19956
2008

POSTED ONEDIT“DRNDIĆ LAB RESEARCH FEATURED ON HISTORY CHANNEL SHOW THE WORKS”

Drndić Lab Research Featured On History Channel Show The Works

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.

Continue reading“Drndić Lab Research Featured On History Channel Show The Works”

POSTED ONEDIT“MICHAEL FISCHBEIN WINS 2007 GRADUATE STUDENT RESEARCH EXCELLENCE AWARD”

Michael Fischbein Wins 2007 Graduate Student Research Excellence Award

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

Continue reading“Michael Fischbein Wins 2007 Graduate Student Research Excellence Award”

POSTED ONEDIT“HIGHLIGHTING PAST AWARDS”

Highlighting Past Awards

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).