Current Members of the Bohn Research Group

POSTDOCTORAL RESEARCH ASSOCIATES

Dorothy Ahlf
dahlf@nd.edu

B.S., University of Evansville, 2007
Ph.D., Northwestern University, 2012

My current research is focused on developing correlated imaging platforms, specifically Confocal Raman and Imaging Mass Spectrometry for imaging 3D cell culture systems in colorectal and breast cancers. This work builds off fo my thesis project, which studied the phenomenon of chemotherapy-induced senescence, where a drug intended to cause cancer cell death instead causes the cell to go into a waiting state. Using cutting-edge mass spectrometry techniques initially developed for Top Down Proteomics to look at protein molecules in their entirety, I was able to track several known targets and new interesting ones during the onset, this "pausing" period of senescence, and also when the cells eventually escaped. The ultimate goal of this work is to correlate these findings to how cancers come out of remission and are able to resist therapeutics during secondary treatments.

Chaoxiong Ma
cma2@nd.edu

Ph.D. University of Utah, 2011

Single molecule electrochemical studies provide significant advantage over large scale measurements for investigating complex system and heterogeneous dynamics. The common method to observing a small number of electron transfer events involves amplifying the electron transferring reaction by repeatedly oxidized and reduced the reversibly redox molecules between two electrodes. An alternative strategy converts a non-fluorescent redox state into a highly fluorescent product reversibly and measures the electron transfer reaction by fluorescent spectroscopy. Recently, electrochemical correction has been demonstrated to be another technique that is sensitive to study the single molecule electro-transfer kinetics. One of my research goals is to combine these strategies by using the fluorescent correlation spectroscopy to investigate the electron transfer events in a nanoscale electrochemical cell, which allows cycling the redox molecules between fluorescent and non-fluorescent state. 

GRADUATE STUDENTS

Nameera Baig
nbaig@nd.edu

B.S. University of Houston

Raman imaging is a powerful label-free technique for studying dynamic biological systems. Microbial communities are ubiquitous and play an important role in geochemical cycles and diseases. My research deals with the study of chemically communicating microbial communities at the molecular level, using Confocal Raman microscopy.

Nick Contento
ncontent@nd.edu 

B.S. University of Florida

Our group seeks to use nanofluidics as a platform for continuous, high conversion heterogeneous chemical reactions. This is accomplished by fabricating nanochannels with embedded electrodes, which are then modified in situ to provide desirable characteristics for reactivity. The high aspect ratio of nanofluidic systems increases the rate of molecular interaction with reactive surfaces, thus enhancing reaction conversions even for only moderately reactive materials. Initially, the nanofluidic reactors are designed and characterized in lab-on-chip type devices, but the technology is amenable to eventual scale-up for practical applications in environmental remediation and chemical processing.

Erick Foster
efoster2@nd.edu 

B.S. University of Tennessee

Microscale fluidic devices offer unique advantages to traditional bench-top chemical analysis equipment including portability, low cost of fabrication, short analysis times, and minimal use of expensive reagents and biologically relevant molecular entities. Due to these advantages, lab-on-a-chip devices have garnered considerable interest in the field of medical diagnostics, where there is a need to carefully analyze mass-limited samples (biofluids). Using high precision electrokinetic flow strategies, it is possible to manipulate patient samples in a well-defined and predictable manner. Although substantial research has been conducted to address this need using aqueous formulations, many target analytes (biomarkers) used in the determination of neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease are hydrophobic, hence incompatible with aqueous-based processing schemes. My research is focused on understanding how electroosmotic flow is achieved using non-aqueous solvents in microfluidic devices.

Larry Gibson
lgibson1@nd.edu

B.S. Johns Hopkins University

Biomarkers are compounds produced by our bodies that correlate to disease states and provide physicians with substantial information regarding the progress of disease. Detection of these molecules in biofluids such as blood, urine, and cerebrospinal fluid is useful in determining patient susceptibility and in monitoring the link between stressors and disease outcome. One example is the link between oxidative stress and neuroinflammatory diseases, such as lupus, multiple sclerosis, and Niemann-Pick type C. Taking advantage of electrophoretic separation schemes, isolation and detection of biomarkers is performed in hybrid microfluidic/nanofluidic chips fabricated in our lab. These devices are a promising alternative to commercially available benchtop systems, because they are relatively inexpensive to fabricate and provide commensurable performance.

Dane Grismer
dgrismer@nd.edu

B.S. North Carolina State University

At the nanometer scale, many physical properties no longer behave as they normally do on the micrometer scale. Using rectangular horizontally-aligned nanochannels as reaction vessels is of particular interest because the container size (typically ~attoliter volume) is the same as important scaling lengths of the reactants, making these ideal structures to study the effects of confinement and crowding on macromolecular reactions. Additionally, their orientation allows for in situ observation of transport and reactions by techniques such as fluorescence correlation spectroscopy (FCS). Experimental measurements can be coupled with well-known plug-flow tubular reactor (PFTR) equations to model nanochannel systems. Three fundamental measurements of molecular transport at this scale are: (1) the average diffusion time from the bulk fluid to the nanochannel wall, (2) the average translocation time through a nanochannel, and (3) the rotational diffusion time for a molecule to rotate to the proper orientation to react with surface-bound partners on nanochannel walls.

Tai-Wei Hwang
thwang1@nd.edu

B.S. National Taiwan University

Nanostructured materials exhibit properties far different from macroscale materials. Metallic quantum wires and Atom-Scale Junctions (ASJs) are both attractive for chemical sensing applications. Each shows a conductance change due to adsorption that is sensitive enough to detect a single molecule. However, the stability of such small devices is relatively poor and the output signal is difficult to discriminate from the background noise. My interests include fabricating quantum wires, improving their stabilities, and using mathematical approaches to address the sensing signals.

Rachel Masyuko
rmasyuko@nd.edu

Raman microscopy and mass spectrometric imaging experiments like LDI and SIMS provide complementary information on the chemical composition of biological samples. Raman microscopy provides information on the spatial distribution of multiple constituents of the samples while mass spectrometric imaging has the ability to map the different chemical constituents on the surface of the sample along with chemical specificity. Biological samples are composed of multiple components such as lipids, carbohydrates, and proteins. As such, a Raman/mass spectrometric multi-modal imaging platform represents a powerful tool for probing biological systems. Our lab is working towards the development of a Raman/mass spectrometric imaging platform that is currently being used in two applications. (1) Chemically communicating microbial communities. Most bacteria readily form biofilms using their own self-driven motility, possess a cell-to-cell signaling mechanism via signaling molecules, and respond to external cues in concert. We seek to understand how bacterial communities respond to nitrogen changes in their environment at the cellular and multi-cellular level by characterizing their signaling molecules and the excreted metabolites during these changes. We are also interested in characterizing and identifying bacterial species in their planktonic and biofilm states in order to gain an understanding of the biological processes that occur within biofilms and during biofilm formation. (2) Exploration of how multicellular aggregates respond to different chemotherapeutics. By evaluating the distribution of drugs, lipids, and protein abundance changes, we can acquire useful information on understanding drug resistance.

Sneha Polisetti
spoliset@nd.edu

B.S. Jawaharlal Nehru Technological University
M.Tech. Jawaharlal Nehru Technological University

Molecular transport at the nanoscale is interesting because of the unique phenomena that arise at these length scales. I am interested in understanding how crowding and confinement effect molecular transport of biomacromolecules, in horizontal nanochannels. These studies are significant in the context of our group's interest in electrochemical and catalytic reaction kinetics under confinement. Single molecule diffusion, translocation, and rotation can be studied using Fluorescence Correlation Spectroscopy (FCS). I am also investigating the incorporation of plasmonic nanostructures to enhance single-molecule fluorescence signals in FCS.

Kayla Shaw
kreibel@nd.edu

B.S. Trine (Tri-State) University

There is great need for a quick, small, portable, easy-to-use water toxicity sensor to determine whether unknown water sources are safe for human consumption and utilization. My project seeks to meet this need through the development of a cell-based impedance biosensor. The biosensor consists of rainbow trout gill cells that are adhered to interdigitated electrodes. These cells respond to a wide variety of toxicants and remain viable when stored for long periods of time without maintenance. The interdigitated electrodes contain current close to the biosensor surface which allows the current to flow mostly through the cells attached to the surface rather than the bulk solution. In addition, the biosensor relies on impedance to measure the changes in the cell as it responds to the toxicant. In particular, my work uniquely utilizes Fourier Transform Electrical Impedance Spectroscopy (FT-EIS), which is capable of measuring large frequency spectrums in milliseconds as opposed to the common frequency scanning techniques which can take several minutes. FT-EIS will provide insight into cell behavior at difference frequencies and the mode of action of the toxicant.

Billy Wichert
wwichert@nd.edu

B.S. Michigan State University

Use of lab on a chip devices is constantly increasing, especially with the incorporation of sensors in tandem with micro- and nanofluidics. When military training facilities fire artillery and ammunition, heavy metals and other chemicals are given a direct route to contaminating ground water, affecting nearby communities. Consuming this contaminated water can potentially cause serious diseases affecting the circulatory, nervous, and immune systems. Sensors for micro- and nanofluidic devices have been developed for detection of heavy metals and other potentially hazardous chemicals in ground water and biological samples. Throughout experiments using this technology, biofilms have the potential to form on the sensors as well as the walls of these fluidic devices, leading to inaccurate readings of analyte concentration. Proteins can be one of the leading components in biofilm formation, making this a key area of research to find potential causes of biofouling under electrokinetic flow. Experimental variables responsible for biofouling under such electrokinetic environments include injection voltage, injection time, pH, protein concentration, and buffer concentration. Experiments looking into the effects of these variables are carried out in nanofluidic channels molded in a h-PDMS/PDMS mixture for fluorescence measurements using human fibrinogen tagged with Alexa Fluor 488 as a model protein.

Wei Xu
wxu@nd.edu 

B.S. Texas A&M University

With electrochemistry in lab-on-a-chip type devices, catalytic oxidation in nano spaces can be accomplished by electrochemical generation of reagents in nanofluidic architectures. The combined properties of fast diffusive transport and large surface-to-volume ratios make nanofluidic components an ideal candidate for high efficiency reactive processing and coupling with electrochemical sensors. Thus, my current work is exploring the use of nanochannels with embedded electrodes for electrochemical generation of reactive species.

Yang Yang
yyang3@nd.edu

B.S. University of Virginia

Localized surface plasmon resonance (LSPR) in metal nanoparticles can be utilized for sensing biological and chemical entities with high sensitivity. Our goal is to build a portable microfluidic diagnostic device which can rapidly detect and identify specific strains of bacteria. The device will make use of the inherently high selectivity that bacteria have for specific siderophores and will use label-free LSPR for detection.

Min Yu
myu@nd.edu

B.S. Wuhan University, P.R. China

Single molecule detection (SMD) allows researchers to detect specific particles or molecules at the individual level, which reveals information unobtainable in ensemble measurement. My goal is to fabricate nanostructures exhibiting excellent optical confinement, zero-mode waveguides (ZMWs), and apply them to single molecule analysis. Fluorescent molecules are immobilized in ZMWs and experiments are conducted using a wide-field microscope to observe the enzymes going through on- and off-time cycles. Real-time observation of the molecules is recorded and analyzed to provide kinetic information.

Larry Zaino
lzaino@nd.edu

B.S. University of North Carolina-Chapel Hill

At the nanometer scale, various properties change drastically in comparison to the millimeter or macro-scale. For example, nanometer scale electrodes exhibit much faster kinetics due to smaller time constants from smaller double layer capacitances. This is directly related to the decrease in electrode area. We intend to utilize the special properties of nanometer scale devices to amplify single electron transfer events. These devices will be characterized with electrochemically active fluorescent molecules using fluorescence correlation spectroscopy.

Jing Zhao
jzhao2@nd.edu

B.S. Tsinghua University, P.R. China

Zero mode waveguide (ZMW) structures, defined as metallic nanopores with a critical dimension less than the cutoff wavelength, strongly confine optical fields to zeptoliter volumes, in which binding/catalytic events can be observed at the single molecule level, even for molecules with Kd ≥1µM. The high signal-to-noise ratio and massive parallelism render ZMWs excellent devices for single molecule studies, including intrinsic single molecule behaviors not accessible with ensembles, such as static heterogeneity and dynamic disorder. In our lab, ZMWs are coupled with fluorescence microscopy to study the dynamics of oxidase enzymes, which play a critical role in the ability of cells to regulate metabolism. In addition, ZMWs open the way for systematic studies of the effect of molecular crowding on enzyme dynamics. Furthermore, the presence of an optically opaque metal may also be exploited for heterogeneous electron transfer.

Administrative Personnel:

Lauren Bohn, Lab/Program Manager
lbohn@nd.edu

325 Stinson-Remick Hall
Notre Dame, IN 46556
Phone: (574) 631-1260
Fax: (574) 631-8366

Owen, the Chemistry Dog

Responsibilities include: reading chemistry textbooks, begging for treats, looking cute, napping

Group activities pictures

Past group pictures

Lab moving pictures