- 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
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.
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.
On September 19 & 20, 2019, we hosted the:
NSF-funded Workshop: Enabling Quantum Leap: Achieving Room-Temperature Quantum Logic through Improved Low-Dimensional Materials
- 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.
- Lecture @ Penn Summer Science Academy for high school students (Experimental Physics Research Academy) https://www.sas.upenn.edu/summer/programs/high-school/experimental-physics
- 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 email@example.com)
- 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.”
- 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
- Biophysical Society Annual Meeting, March 2-6, 2019, Baltimore, MD.
Silicon Nitride Nanopore Stability and Operational Lifetime for Biosensing Purposes
Yung-Chien Chou, Paul Masih Das, Marija Drndić, University of Pennsylvania, Philadelphia, PA, USA
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.
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”.
Priyanka Thiruraman presented the poster below at the Dead Sea Workshop entitled: “Ion transport in Angstrom-Size MoS2 Pores”
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.”
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.
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
New Nano Letters paper on centimeter-scale nanoporous MoS2 monolayers / few-layer membranes produced by simple wet etching (see list of publications).
Science Cafe Live
September 2018: Conference in Shenyang, Liaoning Province, China.
Graduate student Priyanka Jothi Thiruraman was selected to the 2018 class of Vagelos Institute for Energy Science and Technology (VIEST) Graduate Fellows.
July 2018: Conference in Busan, South Korea.
June 2018: Francis Chen-Chi Chien defended his PhD thesis
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:
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!
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.
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.
August 24, 2017: Academic and Summer 2017 outreach by graduate students: Physics Experiments for High-School Students during the Penn Summer Science Academy
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:
- DNA extraction from strawberries, where she also touched upon the concept of DNA sequencing and nanopores (our lab’s research), and
- 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.
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.).
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
The Drndić lab welcomes new undergraduate students Nikhil Chari, Abby Kaplan, Seyoung Kim, Reginald Lamaute, and Lee Blackburn.
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.
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”.
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
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.
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.
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.
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.
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.
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.
*light lunch will be provided
September 16, 2016: Prof. Drndic featured in the ACS Nano Podcast
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.
You can find the group’s paper, In Situ Transmission Electron Microscopy Modulation of Transport in Graphene Nanoribbons, in ACS Nano.
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…
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/.
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.
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
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!
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.
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.
Prof. Drndic gave a plenary talk and participated in a panel discussion at the international symposium on “Incredibly smart, efficient and compact devices by insect technology” in Nagoya, Japan on April 26-27, 2016.
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.
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
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.
Our paper “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 chosen as the ACS Nano Editors’ Choice Article.
William M. Parkin*, Adrian Balan*, Liangbo Liang*, Paul Masih Das, Michael Lamparski, Carl H. Naylor, Julio A. Rodríguez-Manzo, A. T. Charlie Johnson, Vincent Meunier, and Marija Drndić
ACS Nano, 2016, 10 (4), pp 4134–4142
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
Postdoc Jerome Mlack will be presenting at the APS U.S.-Brazil Young Physicists Forum for Early Career Physicists.
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?”
Graduate student Sarah Friedensen wins the Ella N. Pawling 2015-2016 Award.
Congratulations to Sarah Friedensen for being named the Ella N. Pawling 2015-2016 Fellow by the School of Arts and Sciences to support her academic pursuits.
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
Adrian Balan, Chen-Chi Chien, Rebecca Engelke & Marija Drndić
Scientific Reports, 5, Article number: 17775
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
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.
Mehdi B. Zanjani, Rebecca E. Engelke, Jennifer R. Lukes, Vincent Meunier, and Marija Drndić
Phys. Rev. E, 92, 022715
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.
Julio A. Rodríguez-Manzo, Matthew Puster, Adrien Nicolaï, Vincent Meunier, and Marija Drndic
ACS Nano, 2015, 9 (6), pp 6555–6564
The Drndić Lab attended the 2015 Philadelphia Science Festival, presenting nanopore demos.
Congratulations to Will Parkin on receiving the Arnold M. Denenstein Prize with the citation:
“For his exemplary work in combining in situ nanosculpting and aberration corrected electron microscopy of two dimensional materials.”
Matt Puster celebrating defending his PhD Thesis.
Continue reading“Congratulations to Matt Puster on defending his PhD Thesis!”
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.
Zhengqing John Qi , Colin Daniels , Sung Ju Hong , Yung Woo Park , Vincent Meunier , Marija Drndić , and A.T. Charlie Johnson
ACS Nano, 2015, 9 (4), pp 3510–3520
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.
Paul, Gopi, Priyanka and others from Drndic Lab participate in the Philly Materials Day 2015 on February 7, 2015 in the Bossone Research Enterprise Center at Drexel University, including lots of hands-on science and engineering fun for all ages!
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.
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.
Adrian Balan, Bartholomeus Machielse, David Niedzwiecki, Jianxun Lin, Peijie Ong, Rebecca Engelke, Kenneth Shepard, and Marija Drndić
Nano Letters, 14 (12), 7215-7220
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.
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.
(MRSEC = Materials Research and Engineering Center; IRG = Interdisciplinary Research Group)
See the press release
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
Professor Marija Drndić has been named an APS Fellow “For development of novel nanofabrication methods for graphene nanoelectronics and fast biomolecular analysis in solution.”
Nominated by: Division of Condensed Matter Physics
More info at the APS Fellow Archive.
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.
- Penn News: Penn Produces Graphene Nanoribbons With Nanopores for Fast DNA Sequencing
- ScienceDaily: Graphene Nanoribbons With Nanopores Created for Fast DNA Sequencing
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!
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).
- 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”.
Graduate student Matt Puster received the NSF-IGERT Graduate Nanotechnology Fellowship.
New NIH grant awarded to our lab to advance nanotechnology for DNA sequencing.
- 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.
Graduate student Jessamyn Fairfield received an NSF travel fellowship to attend the Pan-American Advanced Studies Institute in Costa Rica on Scalable, Functional Nanomaterials.
Post-doc Chris Merchant received the AAAS Science Policy Fellowship.
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.
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 firstname.lastname@example.org.
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.
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.
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.
- Chemistry Views: Nanopores Identify Modified DNA Bases
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.
- 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.
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.
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.
- 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 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.
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-minute 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).