Correlation dynamics and enhanced signals for the identification of serial biomolecules and DNA bases

Hot off the press! Recent publication by Dr. Haraldsen on correlation dynamics for the enhancement of electronic signals to identify serial biomolecules and DNA bases. Below is the abstract.

Nanopore-based sequencing has demonstrated a significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multilayered graphene-based nanopore device architecture for the recognition of single biomolecules. Molecular detection and analysis can be accomplished through the detection of transverse currents as the molecule or DNA base translocates through the nanopore. To increase the overall signal-to-noise ratio and the accuracy, we implement a new 'multi-point cross-correlation' technique for identification of DNA bases or other molecules on the single molecular level. We demonstrate that the cross-correlations between each nanopore will greatly enhance the transverse current signal for each molecule. We implement first-principles transport calculations for DNA bases surveyed across a multilayered graphene nanopore system to illustrate the advantages of the proposed geometry. A time-series analysis of the cross-correlation functions illustrates the potential of this method for enhancing the signal-to-noise ratio. This work constitutes a significant step forward in facilitating fingerprinting of single biomolecules using solid state technology.

The full paper can be found at http://iopscience.iop.org/0957-4484/25/12/125705/article

Research Corporation for Science Advancement Award goes to Dr. Adriana Banu!

Dr. Adriana Banu is one of the 2014 recipients of the Single-Investigator Cottrell College Science Award from the Research Corporation for Science Advancement to support her nuclear astrophysics research project entitled "Determination of Key Astrophysical Photonuclear Reaction Cross Section Towards Understanding the Origin of p-Nuclei". Several undergraduates from the Physics and Astronomy Department at JMU are heavily involved in the project!!!

Below is the abstract of the project:


The proposed research aims to contribute to enhancing the current state of fundamental knowledge on a forefront topic in nuclear astrophysics - the nucleosynthesis beyond iron of the rarest stable isotopes (the origin of the p-nuclei). More specifically, it is focused on constraining the origin of the p-nuclei through nuclear physics by investigating, as a first step, the cross section measurement of the ⁹⁴Mo(g,n)⁹³Mo reaction, a key photonuclear reaction for understanding the astrophysical p-process (the mechanism responsible for the origin of the p-nuclei). The experimentally unknown reaction cross section is proposed to be studied close to and above the neutron threshold with quasi-monochromatic photon beams at Duke University's High Intensity Gamma-ray Source (HIgS) facility, which is currently the most intense accelerator-driven g-ray source in the world. Total cross section measurements of the ⁹⁴Mo(g,n)⁹³Mo reaction with an energy threshold at 9.7 MeV will be performed at beam energies starting from above the neutron thresholds up to around 13 MeV in steps of 100 - 150 keV. A highly enriched target sample of the ⁹⁴Mo isotope is required. Neutrons from the (g,n) reaction will be detected using an assembly of 4pi ³He proportional counters developed at Los Alamos National Laboratories and presently available at HIgS-Triangle University Nuclear Laboratory (TUNL). 

CCTV Discussion Panel on the challenges for electric cars with Dr. Haraldsen

On Sunday February 16th 2014, Dr. Haraldsen (@JMU Physics) appeared on CCTV's World Insight to discuss the challenges that electric cars have to face. The major issues are cost, range, environmental savings. In the segment, it is discussed that, while the cost for some electric vehicles are becomes more reasonable for the average consumer, the range for the cheaper electric cars does not even come close to challenging conventional gasoline powered cars. Therefore, it is critical for research and development of more advanced battery technologies.

As for environmental savings, electric cars are highly dependent on the methods being used to produce electricity. Given that China, India, and the US are still very dependent on fossil fuels (coal, natural gas, and petroleum), the assertion that electric cars are zero emission is a fallacy. By charging your electric vehicle using coal and natural gas you are still producing massive amounts of carbon dioxide (CO2).

For example, the Tesla Model S ($70k - $100k) has the ability to travel around 255 miles on a single charge due to its large 85 kWh battery (initial charge). If you charge the Model S with electricity from coal (2.08 lbs. CO2/kWh), then you produce ~176 lbs. of CO2 and particulates. If you look at an average gasoline power vehicle with 30 mpg, then you use about 8.5 gallons of gasoline in a 255 mile trip. Given that gasoline, on average, produces 22 lbs. CO2/gallon, this gasoline powered vehicle will have released ~187 lbs of CO2 and particulates, which is about the same as the electric vehicle. If you have a Toyota Prius (~50 mpg), then that drops to 112 lbs. CO2 released. Furthermore, charging with natural gas (1.22 lbs. CO2/kWh) will help reduce the CO2 to 103 lbs., which puts it a slight bit better than the Prius. Therefore, if a country like China or the United States is serious about reducing carbon emissions, then there needs to be a planned move toward alternative, non-carbon producing power sources.

The main advantage of an electric car is that they are dependent on the source of electricity, and as the electric grid move toward more efficient and clearer energy sources, electric cars will become clearer as well.

Below are pictures from the discussion panel on CCTV News. Here is the video link for the discussion on electric cars.

Collaboration paper accepted to Journal of Physical Chemistry Letters!

Our first collaboration paper between Dr. Costel Constantin's group and Dr. Patrick Hopkins' group (from UVa) has been accepted into the Journal of Physical Chemistry Letters (see reference below). In this paper, we measured the thermal conductivity of solid, water insoluble thin films of bovine serum albumin and myoglobin proteins.  The measurements preformed in the temperature range 77 - 296 K indicate an anharmonic coupling of vibrations that is contributing to thermal conductivity.  Our own undergraduate, Chester Szwejkowski, is also a co-author on this work and he will join (as a graduate student!) Patrick's lab this Fall of 2014.  We wish him GOOD LUCK!

B. M. Foley, C. S. Gorham, J. C. Duda, R. Cheaito, C. J. Szwejkowski, C. Constanin, B. Kaehr, P. E. Hopkins. "Protein Thermal Conductivity Measured in the Solid State Demonstrates Anharmonic Interactions of Vibrations in a Fractal Structure". accepted in JPCL 2014. 

JMU Physics to host VA Soft Matter Workshop Feb. 11

JMU Physics is hosting the first Virginia Soft Matter Workshop on February 11th.  We invite faculty and students from Virginia and the region to join us for what promises to be an exciting meeting where ideas, techniques, and expertise in the areas of polymers, complex fluids, and biomaterials will be shared for the advancement of soft matter research in Virginia.

Soft Matter Workshop

Tuesday, February 11, 2014

9:00 AM – 4:30 PM

James Madison University

Festival Conference and Student Center

Highlands Room

Find more information and registration visit:

http://www.jmu.edu/research/softmatterworkshop.shtml

Holiday Party 2013

Another successful holiday party with lots of pizza and gift for everyone. More photos at this location.

COE Award for Improving Undergraduate Physics Education

As a following up on the previous post on this national recognition of our department, we now have the official statement of why we were chosen.  From the American Physical Society:

James Madison University sustains a thriving physics department that has grown significantly over the past 15 years. The Department of Physics & Astronomy has developed a culture of engaging students in the education process through an emphasis on undergraduate research experiences, personalized attention and advising, hiring for mission, recruiting and outreach efforts, and an ongoing move to research-based pedagogies and assessment.  Especially notable are the range of program offerings to serve a broad student population, including tracks in applied physics and technical communication, in addition to strong teacher education efforts as a PhysTEC site.

This week's amazing time-lapse video

Department Recognized

We received notice yesterday that Physics and Astronomy at JMU has been selected to receive the Improving Undergraduate Physics Education Award from the American Physical Society's Committee on Education.

The award will be announced at the APS April Meeting in Savannah, GA.  Along with the honor and a plaque, we will have recognition on the APS website, the AAPT eNNOUNCER and the APS Forum on Education Newsletter.

We are all very excited by this recognition. Previous recipients of this award are Colorado School of Mines, Kettering University, Massachusetts Institute of Technology, University of Wisconsin at LaCrosse, the Compass Project at UC Berkeley, Mount Holyoke College, University of Illinois at Urbana-Champaign, and Utah State University. This puts us in good company and we are proud to be among their number.

If you were looking for just one more reason to consider JMU as the place to come study physics, isn't this it?

Infrared power generation in an insulated compartment

Thermoelectric power generators can help harvesting infrared radiation from the sun and transform it into electricity.  These devices can produce a voltage difference linearly proportional to the temperature difference between the two junctions.  This phenomenon is known as the Seebeck effect.  JMU researchers lead by Dr. Scarel have found that, when infrared radiation activates a thermoelectric power generators, the Seebeck effect is violated.  The first results will soon be published in a paper accepted by Complexity:  Y. Schwab, H. S. Mann, B. N. Lang, J. L. Lancaster, R. J. Parise, A. J. Vincent-Johnson, and G. Scarel, “Infrared power generation in an insulated compartment”.  Complexity, in press (2013).  Undergraduate students played a key role in the research: Yosyp Schwab set up the data acquisition system and performed the data analysis, Harkirat Mann compared the data with those produced by the Seebeck effect, and finally Brian Lang explored diligently the literature to find similar and related experiments.  More is to come!

JMU undergraduates attending Conference Experience for Undergraduates (CEU13) in Newport News, VA

Bryan Isherwood (left) and Daniel Votaw (right) at the CEU13 poster presentation session

Every year in conjunction with the Fall meeting of the Division of Nuclear Physics of the American Physical Society takes place also the Conference Experience for Undergraduates (CEU). The goal of this event is to provide a "capstone" conference experience for undergraduates students who have conducted research in nuclear physics, by providing them the opportunity to present their research to the larger professional community and to one another. Additionally, it enables the students to converse with faculty and senior scientists from graduate institutions about graduate school opportunity.

This year the meeting took place 23-26 October 2013 in Newport News, VA, and JMU was represented by two of our physic majors, Bryan Isherwood (senior) and Daniel Votaw (junior), who do research in nuclear astrophysics under Dr. Adriana Banu's supervision. Moreover, both Bryan and Daniel have been awarded funding by the CEU13 review committee to attend the meeting for their high quality research accomplishments, which is remarkable taking into account the high number of applications (over 170) and a finite budget.

At what rate is work done by this machine?

In this video, there is an electric motor running at 200 rpm. It is connected to a series of gears each of which reduces the rotation rate by a factor of 50. After 12 such reductions, the last gear is turning at a rate of 1 rev/2.3 trillion years. Just for emphasis, this last gear is set in a block of concrete. 

So as an interesting exercise, at what rate is this machine doing work?

The Quest to Produce more Physics Teachers

Dr. Brian Utter  and colleagues have obtained a Physics Teacher Education Coalition (PhysTEC) grant to support, ultimately, the production of more well-qualified high school science teachers.  But this grant does more for our department and JMU students than encourage the production of much-needed teachers. It is giving our upperclassmen an opportunity to really learn physics by helping to teach it. It has spurred the reform of our introductory physics classes, making them more engaging and productive. It has brought a Teacher-in-Residence to the department to help connect our department to the College of Education, the prospective high school teachers, and give the TIR some experience outside the usual high school classroom.

The recent article in the Breeze give more details.

Physics Major Writes a Book

It isn't often that a freshman write a book that is published. It is even less often that this freshman is a physics major. Evan Meekins fits into this narrowly defined category.  He has written a young-adult fantasy novel called The Black Banner that will hit the stores nationwide next month. You can find more details on the Breeze.

More proof that physicists can do anything!

Time-lapse photography

This amazing time-lapse video is the result of the photographer, Shane Black, traveling over 13,000 miles and capturing over 10,000 photos. The results is remarkable. 

Producing More Physics Teachers

Dr. Utter and several of his colleagues in Physics, Psychology, and Education have been awarded aa $300,000 grant from the Physics Teacher Education Coalition. This grant is intended to make it possible for JMU to produce more qualified Physics teachers.  Along the way it is doing much more than simply generating more people interested in teaching physics. It is changing the way we teach physics in our department.

Check out the full article for all the details.

An example of a Heat Engine

A start-up company has designed and built a device to convert heat into electricity. By heating one end in a flame or over a burner and cooling the other end with a reservoir of water, a temperature difference is created by which electricity can be produced. Thermodynamics in action!

Amazing astronomy photos

The folks over at PetaPixel  held an astronomy photography contest and have now posted the winners. Above is the overall winner. The picture is described as

First up is the overall winner and winner of the Earth and Space category taken by Australian photographer Mark Gee and seen at the top. It’s called “Guiding Light to the Stars,” and it shows the Milky Way seemingly emerging from the light of a New Zealand lighthouse.

See the rest of the photos at Introducing the Winners of the Astronomy Photographer of the Year 2013 Contest

Truly larger than life

A. Einstein statue on the Washington mall.

One of the figures that looms larger than life in our nation's capitol is Albert Einstein. While we can't all be Einsteins, we can all make contributions to science and science education (in and out of the classroom). This photo was taken by Dean David Brakke.

Ever wonder what physicists do?

David Saltzberg, right, hosts his "Geek Of The Week," UCLA student Andrew Peck.

Professor David Saltzberg, UCLA has one of the cooler jobs in physics. He is the consultant for the award winning television show Big Bang Theory to make sure that all the science is correct. There is a great article about him and his role in the program on NPR today.

If you don't already have enough reasons to consider starting a career in physics JMU, maybe this helps.