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  Dr. Peter M. Frinchaboy
  Dr. William R.M. Graham
  Dr. Zygmunt (Karol) Gryczynski
  Dr. Doug R. Ingram
  Dr. Bruce N. Miller
  Dr. C.A. Quarles
  Dr. C. Magnus L. Rittby
  Dr. Yuri M. Strzhemechny
  Dr. T.W.Zerda
Dr. Hana Dobrovolny
Assistant Professor
Ph.D. (2008) Duke University


Computational Biophysics

My research uses mathematical models and computer simulations to understand and predict the behaviour of biological systems. I am particularly interested in studying disease processes and potential therapies or cures. The experiments and clinical trials used to study many diseases are very costly and time-consuming and the data we get are usually quite limited, so it's often difficult to get a clear picture of which biological processes are important in causing a disease. This also makes it difficult to study different treatment regimens. By the time a drug makes it to a clinical trial, usually only a couple of different dose/timing regimens are tested in humans; not because they were found to be the optimal regimens after a thorough examination of all the possibilities, but typically based on the educated guess of the researchers heading the trial. An accurate computer model of the disease can not only help us understand the underlying dynamics of the disease but will be extremely helpful in assessing potential treatments. Computers can simulate thousands of different dose/timing regimens and will help doctors choose optimal regimens to test in patients.



Influenza is a viral infection that affects millions of people every year. Most often, the illness is not serious and resolves on its own, but it has the potential to cause widespread illness and death during a pandemic. I use mathematical models of the infection process to study the causes of severe influenza, the emergence of drug resistance, the role of the immune response in clearing the infection, and antiviral treatment. The long-term goal of this research is to develop an accurate model of the infection in humans which can then be used to test a wide variety of drug treatment protocols and to simulate drug or vaccine treatment in high risk patients, reducing the risk to these patients.


H.M. Dobrovolny, Micaela B. Reddy, Mohamed A. Kamal, Craig R. Rayner, C.A.A. Beauchemin, `Current understanding of the immune response against influenza and the additional insights provided by mathematical models.' submitted to Journal of Virology.


H.M. Dobrovolny, R. Gieschke, B.E. Davies, N.L. Jumbe, C.A.A. Beauchemin (2011) `Neuraminidase inhibitors for treatment of human and avian strain influenza: A comparative modeling study.' J. Theor. Biol., 269:234-244.


H.M. Dobrovolny, M.J. Baron, R. Gieschke, B.E. Davies, N.L. Jumbe, and C.A.A. Beauchemin (2010) `Exploring cell tropism as a possible contributor to influenza infection severity.' PLOS One, 5(11):e13811. 


Cardiac Arrhythmia

In a healthy heart an electrical pulse from the sino-atrial node causes a single electrical wave to propagate uniformly across the heart. This wave initiates the contraction that pumps the blood through your body. In a heart experiencing an arrhythmia, the electrical pulse generates waves that spread non-uniformly or break up into multiple waves. This causes different parts of the heart to contract at different times making it difficult for the heart to pump blood efficiently. I use mathematical models to try to understand how a heart becomes arrhythmic so that we can predict which patients should be given medication to prevent arrhythmias. I also use models to assess the effect of different anti-arrhythmic drugs on electrical activity in the heart.

H.M. Dobrovolny, C.M. Berger, N.H. Brown, W. Krassowska Neu, D.J. Gauthier (2009) `Spatial Heterogeneity of Restitution Properties and the Onset of Alternans.' Proceedings of 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Sep. 6:4186-4189.


C.M. Berger, X. Zhao, D.G. Schaeffer, W. Krassowska, H.M. Dobrovolny, D.J. Gauthier (2007) `Period-doubling bifurcation to alternans in paced cardiac tissue: Crossover from smooth to border-collision characteristics.' Phys. Rev. Lett. 99:058101.


S.S. Kalb, H.M. Dobrovolny, E. Tolkacheva, S.F. Idriss, W. Krassowska, D.J. Gauthier (2004) `The restitution portrait: A new method for investigating rate-dependent restitution.' J. Cardiovasc. Electrophys. 15:698-709.


Dr. Peter M. Frinchaboy
Assistant Professor
Ph.D. (2006) University of Virginia



My primary research utilizes multi-wavelength observations (X-ray through mid-infrared) in the investigation of local stellar populations. Of particular interest is the use of star clusters and giant stars to probe the structure and evolution, chemical and dynamical, of the Milky Way and other Local Group galaxies. Related issues such as the role of environment and dark matter content of Miliky way satellite galaxies are also currently under study.



Understanding the structure of a galaxy from only one point of view is challenging, however being inside that galaxy makes it much more difficult. We understand more about other galaxies sturcture than we do for our own Milky Way. Using the Spitzer Space Telescope and Two Micron All-Sky Survey (2MASS) plus dynamical data, we are able to explore the Galaxy as never before. We are using Galactic stars clusters as dynamical probes to determine the structure and evolution of the Milky Way.

Galactic Chemical Evolution (SDSS-III/APOGEE)
In addition to the dynamical work on the Galaxy, I am also a leader of the Sloan Digital Sky Survey III/Apache Point Observatory Galactic Evolution Experiment (SDSS-III/APOGEE). SDSS-III/APOGEE will survey 100,000 stars in the galaxy to measure kinematics and provide detailed chemical analysis of 17 elements in these stars. Many of these stars will be in star clusters. Thus, we will have age-dated tracers with good distances and chemistry suitable for investigating the chemical evolution of the Galactic disk.


Stellar Populations
One way to recreate the history of a galaxy is by examining the stellar populations within that galaxy. The basis for understanding observations of other galaxies relies on a deep understanding of local stellar populations. The WIYN Open Cluster Study (WOCS), , aims to provide the most details stellar population study of key nearby star clusters.

My current WOCS research focuses on the infrared (near and mid-IR) properties of the WOCS clusters, which is being used to derive the lower end of the mass function, and binary star populations of the clusters. The primary facility for Mid-IR imaging is the Spitzer Space Telescope. Consisting of a 0.85-meter telescope and the cryogenically-cooled IRAC camera, Spitzer allows the WOCS clusters to be investigated by obtaining photometry at 3.6-8.0 microns. In addition to the WOCS optical data, we have obtained deep phtometry with the IRAC observations. Deep NIR (i.e., J,H,Ks) observation are being conducted with a number of ground bases facilities. Some of this work is done in collaboration with research groups at Texas A&M University and the University of Wisconsin.


Dark Matter and Local Group Galaxies
Cosmological Cold Dark Matter (CDM) models predict that a galaxy like the Milky Way should have 100's of satelite gallaxies filled with dark matter. The reality is that the Milky Way has tens of satellites and how much dark matter they have is not well determined. A major complication in measuring this is that many of these galaxies are also being torn apart by the Milky Way. The dynamics of dwarf galaxies and stellar streams is the key to understand the evolution of dark matter on small scales. I have worked on exploring the Milky Way dwarf satellites, including Sagittarius, the Magellanic Clouds, GASS, Carina, Leo I and II, Ursa Minor, and Sculptor, as well as, investigating star clusters associated with the Galactic Anticenter Stellar Structure "GASS", also know as the "Ring", that may be associated with the proposed "Argo" or "Canis Major" dwarf galaxy. Much of this work is done in collaboration with research groups at the University of Virginia.


Tombaugh 2: the first open cluster with a significant abundance spread or embedded in a cold stellar stream (with Marino, A. F.; Villanova, S.; Carraro, G.; Majewski, S. R.; Geisler, D.), MNRAS, 391, 39 (2008)


Open Clusters as Galactic Disk Tracers. I. Project Motivation, Cluster Membership, and Bulk Three-Dimensional Kinematics (with Majewski, S.R.), Astronomical J., 136, 188 (2008)


Photometry and Spectroscopy of Old, Outer Disk Star Clusters: vdB-Hagen 176, Berkeley 29, and Saurer 1 (with Munoz, R.R.; Phelps, R.L.; Majewski, S.R.; Kunkel, W.E.), Astronomical J., 131, 922 (2006)


Star Clusters in the Galactic Anticenter Stellar Structure and the Origin of Outer Old Open Clusters (with Majewski, S.R.; Crane, J.D.; Reid, I.N.; Rocha-Pinto, H.J.; Phelps, R.L.; Patterson, R.J.; Munoz, R.R.) Astrophys. J. Letters, 602, 21 (2004)


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Dr. William R.M. Graham
Ph.D. (1971) York University



Research in the Molecular Physics Laboratory is focused on the discovery and characterization of novel molecular species that are important to a wide variety of fundamental and applied problems in physics, chemistry and astrophysics. These range from the most basic, understanding the transition from molecular to bulk properties in materials and the identification of interstellar and circumstellar molecules, to practical applications in semiconductor fabrication and fuel combustion.

Experimental work includes Fourier transform spectroscopy, laser ablation of solids, preparation of condensed samples at cryogenic temperatures, and high vacuum techniques. A critical step is testing experimental conclusions about molecular spectra and structures against the predictions of density functional theory (DFT) calculations.


Carbon Chains and Rings
Carbon chains are the backbones of many interstellar molecules. Evidence suggests that the formation of fullerenes starts with the condensation of small cyclic carbon clusters or chains, which eventually form three-dimensional cage structures. Our Fourier transform infrared studies of small carbon clusters formed by laser ablation of graphite and trapped at ~10 K in inert solids have resulted in the first infrared measurements of vibrations for linear Cn (n≤12) chains, and the cyclic clusters, C6 and C8, generated by a novel laser ablation technique.


On the Identification of the Vibrational Spectrum of Cyclic C8 in Solid Ar, S.L. Wang, C.M.L. Rittby, and W.R.M. Graham, J. Chem. Phys. 112, 1457 (2000).


Fourier Transform Infrared Isotopic Study of the C12 Chain Trapped in Solid Ar, X.D. Ding, S.L. Wang, C.M.L. Rittby, and W.R.M. Graham, J. Chem. Phys. 112, 5113 (2000).


Transition Metal-Carbon Clusters
Transition metal-carbon clusters are of interest in the formation of novel nanomaterials, including metcars, and in the catalytic growth of carbon nanotubes. The discovery of simple diatomic molecules containing metals in the circumstellar shells of carbon-rich late stars in which Cn carbon chains have been identified is another reason for our interest in metal-carbon clusters MCn. FTIR experimental measurements coupled with DFT calculations have enabled the discovery of linear and fan-shaped carbon clusters containing Cr, Ti, Ni, Al, Co, and Sc.


Fourier transform infrared isotopic study of linear CrC3: Identification of the ν1(σ) mode, S.A. Bates, C.M.L. Rittby and W.R.M. Graham, J. Chem. Phys. 125, 74506 (2006).


Vibrational spectrum of cyclic TiC3 in solid Ar, R.E. Kinzer, Jr. C.M.L. Rittby, and W.R.M Graham, J. Chem. Phys. 125, 74513 (2006).


Fourier transform infrared observation of the ν1(σ) mode of linear CoC3 trapped in solid Ar, S.A. Bates, J.A. Rhodes, C.M.L. Rittby, and W.R.M. Graham, J. Chem. Phys. 127, 64506 (2007).


Fourier transform infrared observation of the ν3(σu) vibration of NiC3Ni in solid Ar, R.E. Kinzer, Jr., C.M.L. Rittby, and W.R.M. Graham, J. Chem. Phys. 128, 064312 (2008).


FTIR observation and DFT study of the AlC3 and AlC3Al linear chains trapped in solid Ar, S.A. Bates, C.M.L. Rittby, and W.R.M. Graham, J. Chem. Phys, 128, 234301 (2008).


Silicon-carbon Clusters
Mixed silicon-carbon clusters are important for their roles in the formation of interstellar grains and in the deposition of silicon-carbide films. The variety of their geometries also provides an important test for theoretical predictions.


Fourier-transform Infrared Observation of SiCn Chains. II. The ν1(σ) Mode of Linear SiC7 in Ar at 10 K, X.D. Ding, S.L. Wang, C.M.L. Rittby, and W.R.M. Graham, J. Phys. Chem. A, 104, 3712 (2000).


Semiconductor Clusters
Efforts to characterize the geometries and electronic structures of small semiconductor clusters have been fueled by their applications to semiconductors. These nanoscale systems also offer the possibility for exploring size dependent effects arising from changes in structure and electronic states.


Vibrational spectra of germanium-carbon clusters. II. GeC7 and GeC9, D.L. Robbins, K.C. Chen, C.M.L. Rittby, and W.R.M. Graham, J. Chem. Phys., 120, 4664 (2004).


Vibrational spectra of germanium-carbon clusters in solid Ar: Identification of the ν4(σu) mode of linear GeC5Ge, E. Gonzalez, C.M.L. Rittby, and W.R.M. Graham, J. Chem. Phys. 125, 44504 (2006).


FTIR identification of the 4(σu) and ν6(πu) modes of linear GeC3Ge trapped in solid Ar, E. Gonzalez, C.M.L. Rittby, and W.R.M. Graham, J. Phys. Chem., in press (2008).


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Dr. Zygmunt (Karol) Gryczynski
Professor - W. A. "Tex" Moncrief Jr. Chair in Physics
Ph.D. (1987) University of Gdansk

The major goal of the Biophysics Group is to merge optics and fluorescence with nanotechnology in order to create new research and developmental frontiers for modern medical diagnostics, biotechnology, genomics, and proteomics. The scope of our research is to explore biologically relevant processes at cellular and molecular levels. The range of technologies we utilize is very broad and includes basic fluorescence (time-resolved fluorescence/fluorescence microscopy, practical applications of Forster resonance energy transfer (FRET) as well as advanced fluorescence that include multi-photon fluorescence, fluorescence of nanoparticles, fluorescence probe development, and plasmonic fluorescence (molecular fluorescence stimulated/controlled by metallic nanostructures).
To fully exploit biomedical opportunities, we closely work and share instrumentation with the Center for Commercialization of Fluorescence Technologies (CCFT) at the University of North Texas Health Science Center just 10 minutes from TCU Campus. This fosters a very productive and collaborative environment and combines skills in biomedical sciences, spectroscopy, microscopy, chemistry, engineering, and nanotechnology.
Goals of modern preventive medicine include the development of new technologies for efficient diagnosis of diseases in their early stages and the detection of risk factors for a specific disease in an individual patient (personalized medicine). Furthermore, new and successful medical treatments will often require technologies capable of monitoring therapy progress at the cellular level using non-invasive or minimally invasive approaches. These requirements call for extremely sensitive diagnostic technologies and ultrasensitive non-invasive imaging technologies. Advanced fluorescence today is the leading technology for ultrasensitive non-invasive detection with ultimate sensitivity in the single molecule level.
Our facilities are equipped with state-of-the-art fluorescence instrumentation that only very few laboratories in the world have. We developed highly collaborative research model and our collaborators come from leading institutions in US and the World.

Basic Spectroscopy:  UV-Vis-NIR, Absorption, Fluorescence, Time-resolved Fluorescence Spectroscopy, Fluorescence Lifetimes, Multi-Photon Fluorescence, Circular Dichroism, Linear Dichroism.
These are basic optical technologies that we develop and we utilize for biomedical applications.


Fluorescent properties of antioxidant cysteine ABZ analogue (2011) Raut, S., Heck, A., Vishwanatha, J. K., Sarkar,  P., Mody, A., Luchowski, R., Gryczynski, Z., Gryczynski, I. J. Photochem. Photobiol. B: Biology, 102, 241-245.

Spectroscopic properties of curcumin: orientation of transition moments. Mukerjee A, Sørensen TJ, Ranjan AP, Raut S, Gryczynski I, Vishwanatha JK, Gryczynski Z. J Phys Chem B. 2010 Oct 7;114(39):12679-84.

Studies on solvatochromic properties of aminophenylstyryl-quinolinum dye, LDS798, and its application in studying submicron lipid based structure (2010) Sarkar, P., R. Luchowski, S. Raut, N. Sabnis, A. Remaley, A. G. Lacko, S. Thamake, Z. Gryczynski, I. Gryczynski. Biophys. Chem. 153, 61–69

Photophysical properties of novel fluorescein derivative and its applications for time-resolved fluorescence spectroscopy (2010) M. Szabelski, Z. Gryczynski, I. Gryczynski. Chem. Phys. Let. 493, 399–403.

Forster (Fluorescence) Resonance Energy Transfer (FRET). Macromolecular Structure/Dynamics.
FRET is probably the most utilized physical phenomenon to study molecular and cellular processes in-vivo and in-vitro.


Extending FRET Measurements Beyond 100 Å; with Commonly Used Organic Fluorophores: Enhanced Transfer in the Presence of Multiple Acceptors. (2012) Maliwal BP, Raut S, Fudala R, D’Auria S, Marzullo VM, Luini A, Gryczynski I, Gryczynski Z. Journal of Biomedical Optics; 17(1), 011006, doi:10.1117/1.JBO.17.1.011006.

Forster Resonance Energy Transfer Evidence for Lysozyme Oligomerization in Lipid Environment (2010) Trusova, V. M., G. P. Gorbenko, P. Sarkar, R. Luchowski, I. Akopova, L. D. Patsenker,  O. Klochko,  A. L. Tatarets, Y. O. Kudriavtseva,  E. A. Terpetschnig, I. Gryczynski,  and Z. Gryczynski. J. Phys. Chem. B, 114, 16773–16782

Ratiometric FRET-based detection of DNA and micro-RNA on the surface using TIRF detection. (2010), Matveeva, E.G., Gryczynski, Z., Stewart, D.R., Gryczynski, I. J. Luminescence 130, 698-702.

Basic of Fluorescence and FRET. Gryczynski, Z., I. Gryczynski and J.R. Lakowicz. In Molecular Imaging. FRET Microscopy and Spectroscopy (A. Periasami and R. N. Day Eds.). Oxford University Press. 2005, pp. 21-56.

Nanophotonics and Plasmonics.
 Recent developments in nanotechnology open new possibilities for many optical technologies. Fluorescence takes advantage of quantum-photonic interactions of fluorophores with surface plasmons in nanometer thin metallic films and nanostructures promoting new concepts for developing modular early detection devices for fast and reliable biochemical and biomedical detection and sensing.


Surface-Plasmon-Coupled Emission of Rhodamine 110 in a Silica Nanolayer. (2011) Rangelowa-Jankowska, S., Jankowski, D., Grobelna, B., Gryczynski, I., Gryczynski, Z., Bogdanowicz, R., Bojarski, P.: ChemPhysChem 12, 2449-2452.

Enhancement of Single-Molecule Fluorescence Signals by Colloidal Silver Nanoparticles in Studies of Protein Translation (2011) Bharill, S., Chen, C., Stvens, B., Kaur, J., Smilansky, Z., Mandecki, W., Gryczynski, I., Gryczynski, Z., Cooperman, B.S., Goldman, Y.E., ACS NANO 5, 399-407.

Single Molecule Immunoassay on Plasmonic Platforms. (2010) Luchowski, R., Matveeva, Stoyko,T., Sarkar, P., Patsnaker, L.D., Klochko, O.P., Terpetschnig, E.A., Borejdo, J., Akopova, I., Gryczynski, Z., Gryczynski, I. Curr. Pharm. Biotechn. 11, 96-102.

Surface Plasmon Coupled Emission - Novel Technology for Studying Thin Layers of BioMolecular Assemblies. Gryczynski, Z., E. G. Matveeva, N. Calander, J. Zhang, J. R. Lakowicz, and I. Gryczynsk. In: Surface plasmon Nanophotonics edition M.L. Brongersma and P.G. Kik. 2007 Springer, pp. 247-265.

Fluorescence Microscopy and Single Molecule Detection.
Fluorescence microscopy becomes a fundamental tool for studying molecular processes on cellular level. In combination with emerging advances in nontechnology and plasmonics we are developing new imaging methods to study biological processes.


Cross-bridge kinetics in myofibrils containing familial hypertrophic cardiomyopathy R58Q mutation in the regulatory light chain of myosin. (2011) Metticolla P., Calander, N., Luchowski, R., Gryczynski, I., Gryczynski, Z., Zhao, J., Szczesna-Cordaey, D., Borejdo, J.: J. Theor. Biol. 284, 71-81.


Evidence for Pre-and Post-Power Stroke of Cross-Bridges of Contracting Skeletal Myofibrils. Midde (2011) K., Luchowski, R., Das, H.K., Fedoric, J., Dumka, V., Gryczynski, I., Gryczynski, Z., Borejdo, J., Biophys. J. 100, 1024-1033.

Observing Cycling of a Few Cross-Bridges During Isometric Contraction of Skeletal Muscle. (2010), Mettikolla, P., Calander, N., Luchowski, R., Gryczynski, I., Gryczynski, Z., Borejdo, J. Cytoskeleton 67(6) 400-411

Single molecule kinetics in the familial hypertrophic cardiomyopathy D166V mutant mouse heart (2010) Muthu, P., Metticolla, P., Calander, N., Luchowski, R., Gryczynski, I., Gryczynski, Z., Szczesna-Cordary, D., Borejdo, J., J. Mol. Cell Cardio. 48, 989-998.

Detecting Physiological Markers. Cancer Detection.
Based on new technologies early reliable detection of physiological markers has the potential to significantly lower mortality related to ischemic heart disease, myocardial infarction, or cancer.


Fluorescence Detection of MMP-9. II. Ratiometric FRET-Based Sensing With Dually Labeled Specific Peptide. (2012) Fudala R, Rich R, Mukerjee A, Ranjan AP, Vishwanatha JK, Kurdowska AK, Gryczynski Z, Borejdo J, Gryczynski I. Current Pharmaceutical Biotechnology. Feb 20. [Epub ahead of print]

Fluorescence detection of hyaluronidase.(2011) Fudala, R., Mummert, M.E., Gryczynski,Z., Gryczynski,I. J.Photochem.Photobiol. B:Biology 104, 473-477.

Fluorescence Detection of MMP-9. I. MMP-9 Selectively Cleaves Lys-Gly-Pro-Arg-Ser-Leu-Gly-Lys Peptide (2011) Fudala, R., Ranjan, A.P., Mukerjee, A., Vishwanatha, J.K., Gryczynski, Z., Borejdo, J., Sarkar, P., Gryczynski, I. Curr. Pharm. Biotechn. 12, 834-838.

Enhanced Fluorescent Immunoassay on Silver Fractal-like Structures. (2008) Shtoyko, T., E.G. Matveeva, I.F. Chang, Z. Gryczynski, E. Goldys, I. Gryczynski. Ann. Chem., 80 (6), 1962-1966.

Photosynthetic Processes.
  Understanding the energy pathway in photosynthetic processes is not only crucial element for understanding plant physiology, but also may help in developing new efficient technologies for solar energy conversion.


Investigation of the molecular mechanism of the blue-light-specific excitation energy quenching in the plant antenna 
complex LHCII
(2011) Gruszecki, W. I., Zubik, M., Luchowski, R., Grudzinski, W., Gospodarek, M., Szurkowski, J., Gryczynski, Z., Gryczynski, I., J. Plant. Physiol. 168, 409-414.

Blue-light-controlled photoprotection in plants at the level of the photosynthetic antenna complex LHCII. (2010) Gruszecki, W.I., Luchowski, R., Zubik, M., Grudzinski, W., Janik, E., Gospodarek, M., Goc, J., Gryczynski, Z., Gryczynski, I., J. Plant. Physiol. 167, 69-73.

Photoprotective role of the xanthophyll cycle studied by means of modeling of xanthophyll-LHCII interactions, Gruszecki, W.I., Zubik, M., Luchowski, R. Janik. E., Grudzinski, W., Gospodarek, M., Goc, J., Fiedor, L., Gryczynski, Z., Gryczynski, I., (2010) Chem. Phys. 373(1-2) 122-128


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Dr. Doug R. Ingram
Ph.D. (1996) University of Washington



My main role at TCU is continuing development and improvement of undergraduate classes in both Physics and Astronomy, particularly the Astronomy labs and extra-curricular activities. We use an innovative new lab technique that utilizes Voyager software for the Mac, a planetarium simulator that is easily accessible to students. We also are implementing a shared database of Astronomy course material, such as lecture notes, labs, homework and exams on the Web in conjunction with several other Universities.



Observational Cosmology
We detect and catalogue lineemitting and starforming galaxies associated with damped Lyman alpha QSO absorption systems, using a broadband multicolor photometric technique combined with low resolution spectra to distinguish Primeval Galaxy candidates in the field near the absorbers. This yields integrals of the auto-correlation function of damped absorbers and high redshift proto-galaxies, which can then be used to constrain theories of cosmic structure formation. The spectral energy distributions can also be used to determine star formation histories and ages of the Primeval Galaxies, from which we can recover the evolutionary history of ordinary galaxies like our own.


Starlight Correlated with Damped Lyman-Alpha Absorbers, dissertation (1997).


Rotational Line Widths and the Size of M31 as a Distance Calibrator, Astronomical Journal 110, 634 (1995).


Cataclysmic Variables
Multicolor photometry and high resolution spectroscopy can be used to determine radial velocity solutions for eclipsing novae, which then yields mass estimates for the stellar components. The extent and morphology of the accretion disk in binary systems can also be determined, leading to a better understanding of the role magnetic fields play in mass transfer.


The Masses of V838 Herculis (Nova Herculis 1991) and QZ Aurigae, Astrophysical Journal 420, 830 (1994).


Photometry and Spectroscopy of Nova Herculis 1991, Pub. Astronomical Society of the Pacific 104, 402 (1992).


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Dr. Bruce N. Miller
Ph.D. (1969) Rice University



Quantum Localization and Self-trapping
The average deBroglie wave length of an itinerant electron or positron equilibrated in a fluid is usually much greater than the mean inter-atomic spacing, so either may simultaneously interact with many atoms. Consequently self-trapping may occur, where the light particle "digs" a potential well for itself in the fluid and localizes in the self-induced ground state. The stability of the trapped state depends sensitively on the thermodynamic properties of the fluid and is appreciable in the neighborhood of the critical point. Experimentally, localization alters the decay rates of the positron and positronium, and the mobility of electrons.

Starting in 1990 we employed the Feynman-Kacs path integral to explore the relation between the quantum states of the light particle and local fluctuations in the fluid. We used path integral Monte Carlo (PIMC) to study positron annihilation in fluids, and to develop simulated data that provides a benchmark for testing the predictions of various theories. We also derived a quantum virial expansion for the average properties of the particle at low density, and used PIMC to evaluate the coefficients. The method was used to study the temperature dependence of the positron lifetime in a dilute gas. Recently we have used PIMC to study self-trapping at the liquid-vapor critical point of a Lennard-Jones fluid.  We have also adapted the path integral method to represent a quantum particle on a lattice where, in principle, we can study both critical phenomena and Anderson Localization. This results in rapid convergence and permits us to test theories of localization over a wide parameter range. We plan to use the lattice model to study the influence of critical point fluctuations on quantum localization.


Quantum Particle on a Lattice, Journal of Statistical Physics 98, 347 (2000).

Path-integral Study of Positronium Decay in Xenon, Physical Review E 64, 061201 (2001).


Self-trapping at the liquid-vapor critical point: A path-integral study, Bruce N. Miller and Terrence L. Reese, Physical Review E 78, 061123 (1-10) (2008).


Nonlinear Dynamics

The fundamental assumption of statistical mechanics is that dynamical systems are “chaotic”. For decades physicists assumed that chaos occurs when a stable dynamical system is perturbed. However, simulations using the first vacuum tube computers broke the proverbial bubble by showing that most of the phase space remains stable under small perturbation. A breakthrough came in 1954 when three mathematicians were able to explain the structure of phase space and its separation into stable and chaotic regions. By studying accelerated billiards with discontinuous boundaries, we have found new sources of orbital instability. We developed a simple model, the wedge billiard, which exhibits the complete range of Hamiltonian chaos. The model has been used successfully as a teaching tool and formed the basis for some deep theorems on the ergodic properties of a many body system. Recently it has been studied experimentally using cold atoms. We have extended our approach with a hyperbolic boundary that can be continuously deformed into either a parabola or wedge. This is also a rich system that shows how nearly integrable behavior can be connected by chaotic regimes. Currently we are investigating a quantum mechanical version of the wedge billiard.


Numerical Study of a Billiard in a Gravitational Field, H. Lehtihet and B. N. Miller, Physica D. 21, 93 (1986).


Dynamics of a Pair of Spherical Gravitating Shells, CHAOS 7, 187 (1997).


Dynamics of a Gravitational Billiard with a Hyperbolic Lower Boundary, CHAOS,9, 841(1999).


Gravitational Evolution, Equilibrium, and Fractal Geometry
As a star ages, it radiates energy, heats up, and contracts, so its heat capacity is negative. In an ordinary physical system (e.g. a glass of water) this would not be possible. Because the gravitational force is purely attractive and of infinite range, the evolution and thermodynamic stability of astronomical objects such as galaxies and globular clusters is subtle and complex. In our group, we have used idealized models to study the nature of gravitational evolution in depth. Our studies of a system of parallel mass sheets have demonstrated weak chaos suggesting that stable regions in the phase space trap the system for long times. Relaxation to equilibrium was demonstrated for the first time in a planar system with two distinct populations. The evolution of a system of concentric mass shells approaches equilibrium much more rapidly than its planar counterpart. Mean field theory predicts that a phase transition occurs in this system at sufficiently low energy. This was verified for the first time by our group using dynamical simulation. We have also investigated how rotation influences core collapse. In other work, we have constructed a completely integrable cousin of an N-body gravitational system that, along with the energy, conserves an N dimensional generalization of angular momentum. Recently, by including the Hubble expansion in the evolution, we are studying the multifractal properties of clustering in models of a matter-dominated universe.


Angular Momentum Induced Phase Transition in a Spherical Gravitational Systems: N-Body Simulations, Phys. Rev. E, 65, 056127 (2002).


Influence of Expansion on Structure Formation, Phys. Rev. E, 65, 056121 (2002).


Incomplete Relaxation in a Two-mass One-dimensional Gravitating System, Phys. Rev. E 68 , Nov 1,2003.


Dynamical Simulation of Gravothermal Catastrophe, Peter Klinko and Bruce N. Miller, Physical Review Letters, 92 (2), 021102 (2004).


Exactly Integrable Analogue of a One Dimensional Gravitational System, Bruce N. Miller, Kenneth R. Yawn, and Bill Maier, Physics Letters A 346, 92-98 (2005).


Fractal Geometry in an expanding, one-dimensional, Newtonian universe, Bruce N. Miller, Jean-Louis Rouet, and Emmanuel Le Guirriec, Physical Review E 76 , 036705 (1-14) (2007).

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Dr. C. A. Quarles
Professor Emeritus, Distinguished Green Tutor
Ph.D. (1964) Princeton University



My current research focus is the characterization of materials using positron annihilation spectroscopy (PAS). PAS is a non-destructive nano-scale tool that is very useful in physics, chemistry and materials science. Materials of current interest include Zinc Oxide, tumor (cancer) cells and normal cells and other biological samples, rubber and rubber composites, polyimide and other porous polymer films, spherical and deformed magnetic alloy particles, and shale formation core and other samples of geological interest.


One recent Ph.D. graduate completed a variety of PAS studies of rubber-carbon black composites. A significant result has been to understand the behavior of rubber in composites as similar to a constrained viscous liquid. Other work includes investigation of vulcanization and cross link density, temperature measurements to below the glass transition of the rubber composite, correlation of PAS parameters with other physical properties of carbon black. Additionally, recent studies have included the investigation of Glioma brain tumor by comparing normal and tumor cells in a rat brain model.


Other recent research has included investigation of polarizational bremsstrahlung (PB). PB is distinct from ordinary bremsstrahlung. It occurs when an electron, passes by an atom, and the dynamic induced dipole moment causes the atom to radiate coherently with the accelerated electron. Two somewhat conflicting experimental results have recently been obtained : (1) the first observations of a PB contribution in experiments with 25 - 50 keV electrons on rare gas targets; (2) a measurement of bremsstrahlung from gold solid films of various thicknesses for which there is no observed PB contribution. Thus an essential theoretical problem is to explain why PB is seen from free atoms, but not from atoms in a solid lattice.


Absolute bremsstrahlung yields for 53 keV electrons on gold film targets, Scott Williams and C. A. Quarles, Physical Review A 78, 062703 (2008).


Positron study of carbon black parameters: Structure and Surface Area, J. Wang, V. O. Jobando, and C. A. Quarles, Materials Science Forum  607 (2009) 186-188.


Application of Positron Doppler Broadening Spectroscopy to the Measurement of the uniformity of Composite Materials,  C. A. Quarles, Thomas Sheffield, Scott Stacy and Chun Yang, CP1099 Applications of Accelerators in Research and Industry: 20th International Conference, edited by F.D. McDaniel and B.L Doyle, 2009 American Institute of Physics, pp 940-943.


Positron Spectroscopy Investigation of Normal Brain Section and Brain Section with Glioma Derived from a Rat Glioma Model,   SH. Yang, C. Ballmann and C. A. Quarles, CP1099 Applications of Accelerators in Research and Industry: 20th International Conference, edited by F.D. McDaniel and B.L Doyle, 2009 American Institute of Physics, pp 948-951.


Positron Annihilation Lifetime Studies of ZnO Nanopowders,  Raul M Peters, J. A. Paramo, C. A. Quarles, Y. M. Strzhemechny, CP1099 Applications of Accelerators in Research and Industry: 20th International Conference, edited by F.D. McDaniel and B.L Doyle, 2009 American Institute of Physics, pp 965-969.


Positron annihilation lifetime and Doppler broadening correlations for a variety of polymers, cross linked rubbers and organic liquids, C. A. Quarles , Vincent Jobando, Paul Arpin, Nuclear Instruments and Methods in Physics Research B261 (2007) 875, doi:10.1016/j.nimb.2007.03.048.
Target thickness dependence of 50 keV electron bremsstrahlung, Scott Williams, Keith Hayton and C. A. Quarles, Nuclear Instruments and Methods in Physics Research B261 (2007) 184.
Positron Lifetime Studies on the free volume changes during curing of Rubber- Carbon Black Composites, V.O. Jobando and C.A. Quarles, physica status solidi (c) 4 (2007) 3763-3766.
Effect of Cross-Linking on the Free-Volume Properties of Natural Rubber studied by Positron Annihilation Lifetime Spectroscopy, V.O. Jobando and C.A. Quarles, physica status solidi (c) 4 (2007) 3759-3762.
Positron Lifetime Studies on the free volume changes during deformation of Rubber- Carbon Black Composites, V.O. Jobando and C.A. Quarles, physica status solidi (c) 4 (2007) 3767-3770.
Forward to the Special Issue on Bremsstrahlung, C. A. Quarles and R. H. Pratt, Radiation Physics and Chemistry 75 (2006) 1113-1114.


Review of absolute doubly differential cross section experiments and cross section ratios for electron bremsstrahlung from rare gas atom and thin-film targets, C. A. Quarles and Sal Portillo, Radiation Physics and Chemistry 75 (2006) 1187-1200.
Target thickness dependence of bremsstrahlung from solid films, Scott Williams, Ryan Haygood and C. A. Quarles, Radiation Physics and Chemistry 75 (2006) 1707-1710.
Bremsstrahlung from gas atom targets: study of background processes, Ryan Haygood, Scott Williams and C. A. Quarles, Radiation Physics and Chemistry 75 (2006) 1688-1692.
Absolute doubly differential cross sections for electron bremsstrahlung from rare gas atoms at 28 and 50 keV, S. Portillo and C. A. Quarles, Physical Review Letters 91, 173201 (2003).


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Dr. C. Magnus L. Rittby
Associate Professor
Ph.D. (1985) University of Stockholm



The research in the group is focused on the development and application of quantum theoretical techniques for the study of atomic and molecular systems. Projects range from the study of the structure and properties of molecular clusters to the development of new theoretical and computational techniques as well as more fundamental questions regarding the interpretation of quantum theory.


Molecular Clusters
Pure and mixed molecular clusters of carbon, silicon, and germanium atoms provide an interesting and challenging group of molecular systems to a theorist. Sufficiently high-level theoretical methods have to be employed to provide accurate data to be used in conjunction with the analysis of experimental data.


In these theoretical studies we employ state-of-the-art computational techniques to solve the quantum mechanical many-body electron problem in the Born-Oppenheimer approximation. These techniques includes the so called coupled cluster methods where the electronic wave-function is essentially expressed in an infinite sum with certain constraints that lead to a finite computational scheme. Relatively recently, an alternative approach, the density functional method (DFT), has been developed for the description of electronic ground states. Here, instead of attempting to describe the electronic wave function, the focus is on calculating the electron density. Such DFT techniques can provide very accurate information at a very modest computational cost and enable us to study and describe large molecular clusters more accurately.


Although advanced software is available for electronic structure calculations an additional challenge is to provide results to experimentalists that are meaningful in that they come with some type of “error bars” to facilitate in the comparison with real experimental results. One of the major goals in the group is to develop and employ techniques in a way to facilitate the resolution of experimental spectra. As a result a number of new theoretical techniques that serve as interfaces between theory and experiment have been developed.


Fourier Transform Infrared Observation of the Vibrational Spectrum of the Linear SiCCH Radical in Ar at 10 K (with D.S. Han and W.R.M. Graham), J. Chem. Phys. 106, 6222 (1997).


Detection of Cyclic Carbon Clusters I: Isotopic Study of the v4(eu) Mode of Cyclic C6 in Solid Ar (with S.L. Wang and W.R.M. Graham), J. Chem. Phys. 107, 632 (1997).


Detection of Cyclic Carbon Clusters II: Isotopic study of the v12(eu) Mode of Cyclic C8 in Solid Ar, (with S.L. Wang and W.R.M. Graham), J. Chem. Phys. 107, 725 (1997).


Electronic Structure Methods
Quantum theoretical and computational methods are developed and refined in order to perform efficient calculations of the electronic structure of atoms and molecules. Our main interest has been in coupled cluster methods and the closely related many-body perturbation theoretical techniques.


Photoelectron Spectroscopic and Theoretical Study of Ketene Imine CH2=C=NH and Ketene N-Methylimine CH2=C=NCH3, (with H.W. Kroto, G.Y. Matti, R.J. Suffolk, J. Watts, and R.J. Bartlett), J. Am. Chem. Soc. 112, 3779 (1990).


Fock Space Multireference Coupled-Cluster Theory for General Single Determinant Reference Functions, (with J.F. Stanton and R.J. Bartlett), J. Chem. Phys. 97, 5560 (1992).


Fundamental Quantum Theory
Quantum theory is a well-established theory which provides a highly accurate description of microcosmic phenomena. Although developed in the early part of the 20th century several problems concerning the interpretation of quantum theory still remain. Ongoing projects involve the study of the structure of the theory in the complex energy plane using complex scaling techniques as well as investigations of new and alternative descriptions of the quantum theory measurement.


Generalized Green's Functions and Spectral Densities in the Complex Energy Plane, (with E. Engdahl, E. Brändas, and N. Elander), J. Math. Phys. 27, 2629 (1986).


Resonances and Background. A Decomposition of Scattering Information, (with E. Engdahl, E. Brändas, and N. Elander), Phys. Rev. A 37, 3777 (1988).


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Dr. Yuri M. Strzhemechny
Associate Professor
Ph.D. (2000) City University of New York



Focus of Research
Despite the fact that ZnO has been a widely and efficiently employed for centuries as a material of choice in many areas, its new promising applications became apparent only recently, with the advent of novel growth techniques producing bulk ZnO crystals of a very high quality. This translated into a high potential for optoelectronics, spintronics, and high-temperature, high-power microelectronics.


For many of these applications, and especially for the nanoscale-based, the condition of the surface and the subsurface region is a key performance-defining factor. Because of the large surface/volume ratio in ZnO nanostructures, device performance is determined essentially by the surface and near-surface properties. Current understanding of the relationship between the morphology of the ZnO nanostructures and their defect properties is still largely incomplete. The nature of the surface and sub-surface defect states is still ambiguous and only in a small number of studies in the past few years attempts were made to correlate properties of these states with the morphology of the nanocrystals themselves on the one hand and on the other hand to modify these states in a controllable fashion. In our studies we investigate a number of different ZnO systems, for which studies of surface/interface defect properties of ZnO may yield a significant outcome. In particular, a distinct class of surface/interface processes of interest for us is the influence of defects on the optolelectronic phenomena and structural properties in various ZnO nanostructures. We aim to extend our understanding of the fundamental mechanisms in such systems and their influence on the valuable applied properties.


Due to its potential optoelectronic applications (lasers and light emitters, planar waveguide devices, flat panel displays, etc.), the rare earth (Er, Tm, Tb, Dy) doping of semiconductors, and ZnO in particular, is an important field of study. In such materials, the shielded 4f levels of the rare earth (RE) ions produce narrow optical transitions. Despite the fact that the rear earth ions are excellent candidates for luminescent centers, their matrix environment often limits the luminescence efficiency. It is important to elucidate the optimum conditions for high-efficiency luminescence of those materials, and ZnO is one of the most important representatives. In addition, the rare earth ion dopant can serve as a sensitive probe of the chemistry and structure of its host. We are interested in addressing numerous problems and unresolved issues in this area such as difficulties with incorporating the RE ions into the host ZnO lattice, unknown mechanisms of energy transfer from the matrix to the RE species, almost unidentified relationship between their structural and optical properties. There is no clear model of the upconversion transitions in the RE-doped ZnO systems.


Experimental Facilities
Experimental instrumentation available at our lab includes: photoluminescence (PL) spectroscopy, Raman spectroscopy, and a high-vacuum (HV) analysis/processing multi-chamber setup. One of the main advantages of this multifunctional HV system is a versatile combination of in situ processing and characterization tools. It includes remote plasma treatment simultaneous with resistive annealing and ability to accommodate a number of subsurface-sensitive and surface-specific spectroscopic probes such as surface photovoltage (SPV) spectroscopy and Auger electron spectroscopy (AES).


We employ remote plasma as a tool for tailoring surface and sub-surface properties. Remote plasma processing refers to the arrangement, in which the surface-plasma contact occurs outside the plasma-generating region. The main advantage of using remote plasma follows from the fact that the chemically driven changes at the surface occur without significant temperature variations. This allows a separate control of the temperature at the surface of a specimen. In our research we demonstrated that well-defined remote-plasma treatment procedures allow control and qualitative improvement of key performance parameters of the studied surfaces.


SPV is known for its ability to detect surface states and distinguish their charge sates and donor- vs. acceptor-like nature. It is based on a vibrating Kevlin probe positioned near the surface of the sample of interest. Light of a variable frequency generates transitions from/to the gap states, modifies the population of the surface states, and induces changes in the surface barrier heights. This translates into the variation of the surface potential detected by the Kelvin probe. The SPV technique offers notable advantages: identification of conduction vs. valence band nature of the deep level transitions and the deep level positions within the band gap; ability to measure surface defect densities less than 1010 cm-2 as well as their cross sections. Additional information can be deduced from the SPV transient measurements. The adjacent AES probe provides surface-specific information about surface stiochiometry and contamination.


Complementary to the in vacuo spectroscopic probes, we have in our lab a multi-purpose optical bench setup allowing PL and Raman studies in a wide range of temperatures (6K – 320K), polarizations, and geometries, as well as several laser beams: ultraviolet and visible continuous wave HeCd and ultraviolet pulsed nitrogen. This facility provides information about optoelectronic, structural and chemical properties of the studied systems.


   1. Shallow donor generation in ZnO by remote hydrogen plasma, Y. M. Strzhemechny, H. L. Mosbacker, S. H. Goss D. C. Look, D. C. Reynolds, C. W. Litton, N. Y. Garces, N. C. Giles, L. E. Halliburton, S. Niki, and L. J. Brillson., Journal of Electronic Materials. 34, 399, (2005).
   2. Role of near-surface states in ohmic-Schottky conversion of Au contacts to ZnO, H. L. Mosbacker, Y. M. Strzhemechny, B.D. White, P. E. Smith, D. C. Look, D. C. Reynolds, C. W. Litton, and L. J. Brillson, Appl. Phys. Lett. 87, 012102 (2005).
   3. The role of defects at nanoscale ZnO and Cu(In,Ga)Se2 semiconductor interfaces, Y. M. Strzhemechny, J. Vac. Sci. Technol., A. 24, 1233 (2006).
   4. Dominant effect of near-interface native point defects on ZnO Schottky barriers, L. J. Brillson, H. L. Mosbacker, M. J. Hetzer, Y. Strzhemechny, D. C. Look, G. H. Jessen, G. Cantwell, J. Zhang, and J. J. Songe, Appl. Phys. Lett., 90, 102116 (2007).
   5. Interface and defect states at ultrathin SiO2-HfO2-SiO2-Si junctions, Y. M. Strzhemechny, M. Bataiev, S. P. Tumakha, S. H. Goss, C. L. Hinkle, C. C. Fulton, G. Lucovsky, and L. J. Brillson, J. Vac. Sci. Technol. B, 26, 232 (2008).
   6. Correlation between morphology and defect luminescence in precipitated ZnO nanorod powders, M. Bitenc, P. Podbršček, Z. Crnjak Orel, M. A. Cleveland, J. A. Paramo, R. M. Peters, Y. M. Strzhemechny, submitted to Crystal Growth & Design.


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Ph.D, D.Sc. (1983) Silesian University



Raman Micro-imaging
Raman micro-imaging is a new technique and its potentials have not been fully explored. It allows for quick, non-destructive measurements that require very little sample preparation. Raman signal can be obtained from a specimen at a remote location, simply by having a microscope objective connected via an optical fiber with a spectrometer. Our laboratory has recently built a Raman microscopy system with the spatial resolution of 0.5 micron in the horizontal plane and 2 microns along the optical axis of the confocal microscope. By advancing a sample in small steps of 0.2 micron we can obtain three-dimensional distribution of components within the specimen. To reduce fluorescence, laser lines ranging from 488 nm to 785 nm can be selected. The system has been extensively tested and applied to study distribution of polymers and fillers in blends, phase transitions and interfaces in hydrogels, and distribution of strain in crystals.


Surface stress distribution in diamond crystals in diamond-silicon carbide composites, Diamond and Related Materials 17, 84 (2008); doi:10.1016/j.diamond.2007.10.035


Spatial distribution of residual stress in diamond-silicon carbide composites, J. Phys.: Conf. Ser. 121 062007 doi: 10.1088/1742-6596/121/6/062007


Solid State Physics
Carbon structures. The goal of this project is the understanding of the structure and properties of various carbon materials, including combustion engine deposits, carbon nanotubes, graphitic structures on diamond, nanodiamonds, and carbon blacks to be used in tires. In this research gas adsorption technique, atomic force microscopy, X-ray, neutron scattering, and Raman are employed.

Some interesting results include the discovery of nanosize cavities in engine deposits, onion-like structures formed during graphitization of nanosize diamonds, oriented growth of graphite on large diamond crystals, determination of fractal dimension of carbon blacks, modeling of spatial distribution of particles in carbon blacks aggregates, and characterization of sizes and strains in carbon nanocrystallites.


Size and shape of crystallites and internal stresses in carbon blacks, Composites A. Applied Science., 36, 431- 436 (2005); doi:10.1016/j.compositesa.2004.10.017


Graphitization of small diamond cluster – molecular dynamics simulation, Diamond Related Materials, 15, 1818-1821 (2006), doi:10.1016/j.diamond.2006.06.002


The Structural Influence of Erbium Centers on Silicon Nanocrystal Phase Transitions, Phys. Rev. Lett. 93, 175502 (2004); DOI: 10.1103/PhysRevLett.93.175502


Diamond-SiC Composites
We manufacture diamond SiC composites under high pressure and high temperature conditions. The composites are very hard and exhibit unusually high abrasive resistance, much higher than, for example, tungsten carbides. They find applications in drill bits used in gas/oil exploration. I am holding two drill bits in the photo on the left.


The mechanism of the reaction that results in diamond crystals being chemically bonded to SiC and the structure and properties of the final product are the main goal of our research. The reaction takes place at high temperature, T>1500 K, and is controlled by diffusion rate of carbon atoms through a layer of SiC formed on diamonds. At low hydrostatic pressures diamond spontaneously transforms into graphite and this process may affect properties of the composites. At high pressures graphitization process is suppressed and silicon may react only with diamonds.


Reaction kinetics of nanostructured silicon carbide, J. Phys. Condens. Mat. 20 325216 (2008); doi: 10.1088/0953-8984/20/32/325216

Structure of diamond-silicon carbide nanocomposites as a function of sintering temperature at 8 GPa, Materials Science Engineering A, 487, 180 (2008); doi:10.1016/j.msea.2007.10.006


Origin of macro- and microstrains in diamond-SiC nanocomposites based on the core-shell model, J. Appl. Phys, 102, 074303 (2007); DOI:10.1063/1.2785025

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