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Undergraduate Physics Seminar: building a tower of balloons

Research Posters

Class time

A&S Fall Welcome 2011

Fall on MU campus

Physics Club trip at NASA

Teacher Academy - Physics First

A&S Fall Welcome 2011

Teacher Academy - Physics First

Honors Graduation 2012

MU seal on the East wall of the Physics Bldg.

Commencement 2007

Jesse Hall

Physics Bldg.

Life Sciences Bldg.

Sigma Pi Sigma - first chapter - 2011

Projects for MU Physics Research Experience for Undergraduates in Materials and Modeling

The selected applicants will be matched up with a faculty mentor, keeping in mind their research interests. We have preselected some typical projects keeping these guidelines in mind. Additional information on each faculty member’s research group can be found at

Faculty Mentor Project description Research
Dr. Shi-Jie Chen DNA and RNA structure dynamics Theoretical
Dr. Suchi Guha Charge transport in polymer-based transistors Experimental
Dr. Kattesh Katti Nanotechnology for Alternate Energy Sources Experimental
Dr. Gavin King Single molecule approaches to membrane proteins Experimental
Dr. Ioan Kosztin Molecular dynamics: water transport in channel proteins Theoretical
Dr. Peter Pfeifer Tunable single electron memory Experimental
Dr. Sashi Satpathy Computational condensed matter physics Theoretical
Dr. Angela Speck Modeling star dust formation Theoretical
Dr. Haskell Taub Neutron scattering studies of model membranes Experimental
Dr. Haojing Yan Galaxy evolution Theoretical

Project Descriptions

Dr. Chen: DNA and RNA structure and dynamics

Dr. Shi-Jie Chen has extensive experience with physics-based modeling of biomolecular structure and function, especially on the folding of DNA and ribonucleic acid (RNA) molecules.  Recently, his research group has made vigorous efforts in the theory development for the prediction of the structure, thermodynamic stability, and folding kinetics of RNA.  Advances in the results of the research are directly correlated to the understanding of gene regulation, early detection of disease, and rational design of therapeutic strategies.  The students would have an excellent opportunity to learn the biological significance of biophysics research. The major theories used in the research are thermodynamics and electrodynamics.  Through participation in the project, the student will receive rigorous training in both analytical theory development and computational programming.  The research projects involve close interactions with experimental biology labs in the medical school.  In summary, the combination of the above factors makes Chen’s lab an ideal host for the training of the undergraduate students.

What the undergraduate student intern will do:  The student involved in the REU project will participate in the development of the computational model for RNA all-atom structure prediction and folding kinetics, including the computational modeling and test/refinement of the model through comparisons with experimental results. The intern will perform simple analytical derivations and will work with others in the lab to develop a numerical algorithm, by writing computer code and performing numerical calculations using the state-of-the-art University of Missouri Bioinformatics Consortium computer cluster. The student will also participate in the processing of numerical results, presentation of these results at the conferences, and in preparation of publishable illustrations for the resulting papers.

Dr. Guha: Dynamic charge transport in polymer-based transistors

Prof. Guha’s current research interests are in the area of organic optoelectronics spanning all the way from optical spectroscopy of materials to devices. Her current research group includes four full-time PhD students, two undergraduate students, and a visiting faculty member. Her research utilizes (1) optical spectroscopic techniques such as Raman scattering, photoluminescence/absorption, modulation spectroscopy; (2) organic device fabrication (spincasting, thermal evaporation and modified pulsed laser deposition techniques); (3) electrical characterization techniques, which include current-voltage and capacitance measurements. Her current work, funded by the National Science Foundation, focuses on understanding charge transport mechanisms in organic field-effect transistors (FETs) and organic metal-insulator-semiconductor (MIS) diodes using various characterization techniques such as, current-voltage and capacitance measurements. An additional facet of this work includes vibrational spectroscopy from organic FETs and light-emitting-diodes under applied electric-fields. These studies elucidate the role of conformational changes in the molecules/polymers along with insights into the role of polarons/bipolarons in charge-transport.

What the undergraduate student will do — Typically the field-effect mobility in organic FETs is extracted from a measurement of the current-voltage characteristics made with DC or quasi-DC-measurements. Such measurements do not give any information on the drift mobility and velocity of the charge carriers at shorter time scales (tens of microseconds). The proposed REU project will involve dynamic charge carrier measurements from organic FETs based on both time-domain and frequency-domain characterization of FETs. These measurements will result in an accurate determination of the drift mobilities in organic FETs. The project will further develop a drift-diffusion-based theoretical model to simulate the experimental results in order to gain a deeper insight into electric-field and charge-density dependence of the carrier mobilities. The REU student will be trained both in the fabrication and characterization of organic FETs. The dynamic charge transport measurements will involve setting up a new experimental setup involving a voltage pulse generator and a fast oscilloscope. The student will also be trained in LabView programming for automating some of the experimental steps with the electrical measurements.

Prof. Guha has involved more than 15 undergraduate students in her research since 2000. These students have been supported by several external grants (NSF-REU supplement, Research Corporation, and Petroleum Research Fund). This has resulted in many research presentations at international meetings and peer-reviewed publications coauthored by her undergraduate/high school students.

Dr. Katti: Nanotechnology for Alternate Energy Sources

Dr. Katti’s research is focused on unraveling fundamentals of science and apply those principles and concepts to developing new chemical species at the macro and nano scales. In the nanodomain, he is interested in exploring chemical, biophysical, magnetic and photophysical properties, that are unique to specific nanoparticulates, toward the design and development of sophisticated diagnostic and therapeutic agents. Green nanotechnology is at the focal point of Dr. Katti’s approach to pursuing research in nanotechnology as he strongly believes in the total elimination of toxic chemicals either for the synthesis or as byproducts in the production of engineered nanoparticles. Toward this end, phytochemicals occluded within plants, herbs or from various sources from mother nature are being used in developing 100% green processes for the development of nano constructs for use in a plethora of medical, agricultural, hygienic and technological applications.

What the undergraduate intern will do: In this project, students will gain research experience on the application of Green Nanotechnology for the generation of alternate energy. Certain types of functionalized nanomaterials display unique photophysical, magnetic and electrical properties. Students will be trained to design and fabricate functionalized nanoparticles and test them in highly sophisticated electrochemical cells for splitting water—a means to generate excess energy through combination of electrochemical, photophysical and photovoltaic processes. Students will have opportunities for undertaking training on the design rationale, fabrication and characterization of nanoparticles and on how innovations in nanotechnology will provide new insights with potential applications in energy generation.

Dr. King: Precision single molecule approaches to the structure and dynamical properties of membrane proteins

The King lab addresses central questions in membrane biophysics by developing and applying a unique single molecule measurement apparatus, the ultra-stable atomic force microscope (US-AFM). Notwithstanding its many successful applications in biology, AFM performance is directly limited by unwanted mechanical drift between the probe tip and the sample. King’s US-AFM has achieved atomic-scale tip-sample stability over long time periods in ambient operating conditions, representing a 100-fold improvement over prior state-of-the-art [40]. Current projects aim to shed light on central questions in protein secretion and are designed to provide a more detailed understanding of this vital, but ill-understood phenomenon.

What the undergraduate student will do — Several undergraduate projects which are self-contained and achievable in approximately nine weeks of work are outlined. i) Exploring novel sample preparation protocols for functional adhesion of membrane bound proteins to surfaces: To exploit the full power of ultra-stable AFM lateral diffusion within the membrane needs to be suppressed. Experiments with the translocon complex (SecYEG) will utilize an existing library of cystine-tagged SecYEG complexes in conjunction with Au-coated substrates. The successful protocol will tether membrane-bound SecYEG to the substrate to prevent diffusion without denaturing the protein. ii) Data processing and data analysis algorithms for AFM images of membrane proteins: The student will develop and fine-tune particle identification algorithms which yield salient quantities such as volume, surface area, and height of individual features in an image. This analysis is critical to quantitatively assess the distribution of feature sizes, orientation and oligomeric state of the active translocon complex. iii) Tip selection and compatibility: With the US-AFM we have found that different AFM tips yield different optical signals, which alters sensitivity and precision. Here, the student will develop a database of commercial AFM tips’ compatibility with our novel optical stabilization technique. Creating a thorough database will guide our work (as well as others in the field) when selecting tips for specific future applications.

Dr. Kosztin: Molecular dynamics study of water transport through channel proteins

Dr. Kosztin’s group has extensive expertise in the computational and theoretical modeling of molecular and ion transport through channel proteins and artificial nanopores. These processes are inherently multiscale in nature because one needs to follow the dynamics of the transported molecules/ions on an atomic length scale (i.e., a few nanometers) during macroscopic time scales (milliseconds or more). In spite of the spectacular recent advances in massively parallel computing, the use of straightforward molecular dynamics (MD) simulations is not feasible to calculate the permeability of channel proteins. However, by assuming that the transported molecules undergo overdamped Brownian dynamics, this hurdle can be overcome by the following two-step approach: (1) determine the free energy profile U(x) and the underlying (position dependent) diffusion coefficient D(x) of the molecule along the axis of the channel, and (2) solve the appropriate stochastic equation of motion with U(x) and D(x) to calculate the desired physical observables (e.g., flux and channel permeability). This approach has been perfected in Dr. Kosztin’s group and successfully applied to several systems.

What the undergraduate intern will do – The intern will build a periodic system of four hexagonally packed, (6,6) armchair type, single walled carbon nanotubes (SWNT) by employing molecular modeling software VMD. Then, using VMD, pre-equilibrated (~20A thick) water layers will be added on both sides of the SWNTs. Next, the intern will use MD simulations, first to equilibrate the solvated SWNT system at room temperature and pressure, and then to record the diffusive dynamics of water molecules across the SWNTs. All MD simulations will be carried out with the parallel program NAMD. All computer modeling and simulations will be done on a multicore CPU laptop or desktop. The intern will analyze the obtained MD trajectories by: (1) counting the number of water molecules that crosses the SWNTs in both directions, and (2) determining the water distribution function and the corresponding free energy profile U(x). The intern will use these results to calculate the water flux, diffusion coefficient, and mean first passage time through a SWNT. To assist the intern in efficiently performing the above sequence of complex activities, Dr. Kosztin will provide a set of hands-on tutorials. The intern will complete the project by writing a comprehensive report in the style of a research paper.

Dr. Pfeifer: Alternative fuel technology (Pfeifer)

Dr. Pfeifer leads a research program, the “Alliance for Collaborative Research in Alternative Fuel Technology” (ALL-CRAFT,, which, since its inception in 2004 under a same-named NSF-PFI project (Partnerships for Innovation, 2004-07), has involved over 20 senior researchers, 20 Ph.D. students, and 40 undergraduates.  The program is a partnership of MU (lead institution), Midwest Research Institute in Kansas City, and other partners (domestic and abroad) to develop low-pressure, high-capacity storage technologies for natural gas (methane) and hydrogen as alternative fuels for advanced transportation. ALL-CRAFT has developed high-surface-area nanoporous carbons, with surface areas over 3000 m2/g-made from waste corncob, a low-cost raw material native to the Midwest (U.S. Patent #8,691,177 (2014)), and synthetic materials-which adsorb methane at the unprecedented capacity of over 130 g methane/liter carbon (200 times its own volume of natural gas, 110% of the DOE target) at ambient temperature and pressure of 35 bar, and also record amounts of hydrogen.  The immediate objective is to replace bulky, cylindrical compressed natural gas tanks in current natural gas vehicles by a lightweight, flat-panel (conformable), low-pressure tank, with storage as adsorbed natural gas, in the floor of next-generation natural-gas vehicles, and similarly for hydrogen vehicles.  The program is currently funded by DOE (BES and EERE), DOD (DLA), and the California Energy Commission.

What the undergraduate student will do —  A typical project for a summer intern is measurement and analysis of methane storage isotherms (methane uptake as a function of gas pressure) on a series of samples of interest, including determination of binding energies from isotherms, determination of surface areas, porosities, and pore-size distributions of samples (nitrogen adsorption at 77 K), interpretation of results as a function of physical/chemical structure and production conditions of samples, and recommendations for production of improved samples.  Students receive on-the-job training in the operation of state-of-the-art adsorption instruments, high- and low-pressure gas handling equipment, cryogenic equipment, sample preparation and characterization, and thermodynamics and statistical mechanics of adsorption and thin fluid films.

Dr. Satpathy: Computational condensed matter physics: dislocation states in semiconductors

Prof. Sashi Satpathy, is an expert in computational condensed matter physics, particularly on the electronic structure theory of solids, including ab initio density functional calculations. His group is involved in the studies of a variety of topics such as two-dimensional electron gas at the oxide interfaces, the RKKY interactions in graphene, Dynamical Jahn-Teller effect in vacancy systems, Kosterlitz-Thouless transition at the oxide interfaces, Skyrmion crystals, etc. Keeping in mind that this will be the first time that the student may be doing research, the objective of the REU project is to introduce to the student the elements of scientific computation, while at the same time applying the methods to a problem of current interest. The project will involve the solution of the defect states bound to the dislocations in semiconductors. There are two reasons why this is interesting. First, electronic properties in semiconductor applications are often controlled by the defect states, which are due to not just the extrinsic defects, but also intrinsic defects such as vacancies, grain boundaries, and dislocations. Second, from a fundamental point of view, these are one-dimensional systems, and defect electrons bound to the dislocations could be a novel realization of the Tomonaga-Luttinger liquid.

What the undergraduate student intern will do: The student will solve the one-particle Schrödinger equation for an electron bound to a model potential describing the dislocation strain field. First, the student will develop a variational wave function and obtain the ground-state energy by minimizing the expectation value of energy. This will be applied to several semiconductors. This in itself could potentially lead to a journal publication. If time permits, the second part of the project would involve an accurate solution of the Schrödinger equation by a numerical integration of the differential equation. The student will learn elementary Quantum Mechanics, computational techniques, as well as some simple semiconductor physics, with a reasonable expectation for a published paper.

Dr. Speck: radiative transfer modeling of star chemistry effect on dust formation

Professor Speck and her research group work on studying stardust – solid material generated by dying stars. Using a combination physics, chemistry, material science and geology we investigate the nature  (size, shape, composition and crystal structure) of dust grains around dying stars. While massive stars tend to explode and eject newly-formed elements violently, lower mass stars, like the sun end their lives more gently via approximately a million years of mass loss. This intensive mass loss characterizes the phase of a stars life known as the Asymptotic Giant Branch (AGB) phase and produces a circumstellar shell of dust, molecules and neutral gas. At the end of the AGB, mass loss stops (or at least decreases dramatically) and the circumstellar shell begins to drift away from the star. At the same time the central star begins to shrink and heat up from about 3000K until it is hot enough to ionize the surrounding gas, at which point the object becomes a planetary nebula (PN). Between the end of the AGB phase and the onset of ionization indicative of the PN phase is the post-AGB or proto-planetary nebula (PPN) phase.

What the undergraduate student intern will do: In order to understand the nature of the material that goes on to enrich the ISM, we need to understand dust and molecule formation and processing during the lifetime of a star, i.e. during the AGB, proto-planetary nebula (PPN) and PN phases. Our group investigates the nature of the circumstellar material around AGB stars PPNe and PNe from a variety of perspectives, including dust shell morphologies, relative locations of different molecular, ionized and dust species and the mineralogy of the dust. The REU project would involve using radiative transfer modeling to investigate how the chemistry of stars affects the dust formation.

Dr. Taub: Neutron scattering studies of model membranes

Professor Haskell Taub’s research group uses a variety of experimental techniques and computer simulations to study the physical properties of organic films as thin as a single molecular layer. Currently, his interest is focused on the structure, phase transitions, and dynamics of bilayer lipid membranes supported on a solid substrate. These systems are attractive models for more complex biological membranes that form the outer boundary of living cells. In order to understand the biological function of living cells, knowledge of the diffusive motion of water over and through these boundary membranes is necessary.

Dr. Taub’s lab primarily uses quasielastic neutron scattering as an experimental technique that allows them to investigate molecular motions, particularly hydrogen atoms, which occur on picosecond to nanosecond time scales. They use state-of-the-art neutron spectrometers at the Center for Neutron Research at the National Institute of Standards and Technology and at the newly constructed Spallation Neutron Source at Oak Ridge National Laboratory. Recently, the group’s experiments have demonstrated sufficient sensitivity to observe quasielastic neutron scattering from single bilayer membranes supported on a SiO2-coated silicon wafers such as used in the semiconductor electronics industry. These measurements offer promise of revealing how water is bound to the membrane and how the presence of the membrane affects the motion of associated water. In addition, they expect to follow the diffusive motion of hydrogen atoms within the membrane’s lipid molecules.

What the undergraduate intern will do: The undergraduate intern will participate in neutron reflectivity measurements at MURR and assist in the analysis of the membrane reflectivity measurements. Undergraduate students previously engaging in research in Taub’s lab have demonstrated that their study in introductory courses of interference effects with light scattered from thin films provides an adequate foundation for a conceptual understanding of a neutron reflectivity measurement. The project also reinforces their introduction to modern physics by giving them a first-hand experience with the wave-like properties of neutrons without their needing a detailed understanding of crystal structures and reciprocal space. The students have had little difficulty learning to manipulate the software available for fitting the reflectivity curves and are able to develop some independence in their modeling of them.

Dr. Yan: Galaxy Evolution

Our Extragalactic Astronomy Group studies galaxy formation and evolution. One key aspect is to investigate the star formation rate in galaxies, or in other words, how baryonic matter is turned into luminous matter. Star formation rate changes in different galaxies, and it has changed as a function of cosmic time.


We study star formation rate and stellar mass build-up in galaxies near and far, using various observations at different wavelengths to put together a comprehensive picture. A common method is to construct the spectral energy distributions (SEDs) of galaxies, and to fit the SEDs using theoretical models based on our understanding of the physical processes taking place, such as how stars that make up a galaxy should evolve, how the interstellar medium should be heated, and so on. This approach involves data taken over the entire electromagnetic spectrum, obtained by both ground-based and space-based facilities.