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Sidney Perkowitz. Physics.
Phone: 404-727-4321
Email: physp@emory.edu
Institution: Emory
Location: Other
Availability: Spring,Summer,Fall
Lab Positions: 0
Project Description: Projects in science writing and science journalism that might include reporting about scientific research, interpreting the meaning of scientific efforts, the ethical and social implications of science, the history of science, and other facets of explaining science and scientists to the general public.
Student Requirements: Junior/senior level status in any science major; evidence of writing ability; an interest in developion a career in science communication, journalism, or writing.
Techniques used in this lab: How to communicate science to experts and non-experts in ways that are both accurate and accessible.
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Eric Weeks. Physics.
Phone: 404-727-4479
Email: weeks@physics.emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: We study squishy materials like pastes and foams and gels. How do their microscopic properties relate to their macroscopic squishyness? For example, foams can support some weight without significant deformation. How does the microscopic structure of foam result in this, and what needs to be done to make the foam stronger? Overall, we use microscopy to take pictures of squishy materials and study their properties. We have a variety of specific projects related to squishy materials, email Dr. Weeks for more details.
Student Requirements: at least one year of college-level physics; nothing more is required.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) "Squishy materials", P Habdas, ER Weeks, & DG Lynn, The Physics Teacher 44, 276-279 (May 2006)
(2) "Colloidal glass transition observed in confinement", CR Nugent, KV Edmond, HN Patel, and ER Weeks, Phys. Rev. Lett. 99, 025702 (2007)
(3) "Particle migration in pressure-driven flow of a Brownian suspension", M Frank, D Anderson, ER Weeks, and JF Morris, J. Fluid Mech. 493, 363 (2003).
(4) "Forced motion of a probe particle near the colloidal glass transition", P Habdas, D Schaar, AC Levitt, and ER Weeks, Europhys. Lett. 67, 477 (2004).
(5) "Correlations of structure and dynamics in an aging colloidal glass," GC Cianci, RE Courtland, and ER Weeks, Solid State Communications 139, 599-604 (2006).
Techniques used in this lab: confocal microscopy, image analysis, chemical handling and sample preparation, general optical microscopy
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Ivan Rasnik. Physics.
Phone: 404-727-4039
Email: irasnik@physics.emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: In our lab we study biological systems using single molecule techiques. Currently we are studying several proteins that interact with DNA trying to understand their molecular mechanisms. For example we are looking at a helicase ( a protein that separates DNA or RNA strands) from the Hepatitis C virus, that is essential for virus replication. We are also looking at mismatch repair proteins, that correct errors during the replication process that if go uncorrected may result in cancer and other genetic disorders. By looking at the function of proteins, one at a time we can look at details that are impossible to observe looking at average behavior.
Additional Project Information: We will work towards the development of new approaches to formation of supported lipid bilayers. Present techniques rely on the bilayer formation on a surface, this approach has severe limitations in the applicability of this artificial membranes for membrane protein studies. We will start by exploring the possibilities of patterned surfaces to create lipid bilayers with minimal surface interaction. The physical properties of the lipid bilayers will be studied by single molecule fluorescnce studies of lipids and protein difussion.
Student Requirements: All the techniques we use can be learn if there is dedication and willing to learn. Undergraduate students start working with posdocs or graduate students till they master the technqiues and become independent.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Rasnik, I., S. Myong, W. Cheng, T. M. Lohman and T. Ha (2004). Journal of Molecular Biology 336(2): 395-408
(2) Murphy, M. C., I. Rasnik, W. Cheng, T. M. Lohman and T. J. Ha (2004). Biophysical Journal 86(4): 2530-2537
(3) Ha, T., I. Rasnik, W. Cheng, H. P. Babcock, G. H. Gauss, T. M. Lohman and S. Chu (2002). Nature 419(6907): 638-41.
(4) Rasnik, I., McKinney, S. A., Ha T., Accounts of Chemical Research 38 (7): 542-548.
(5) S. Myong, I. Rasnik, C. Joo, T. M. Lohman and T. Ha . In Press, Nature (October 2005).
Techniques used in this lab: Our lab is highly interdisciplinary, the students will be exposed to a variety of techniques, depending on their specific interests they will use a substet of: fluorescence, spectrophotometry, gel purification, general chemistry lab procedures (buffer preparations etc.), surfaces cleaning protocols for single moelcule experiments, covalently polymer coating of glass surfaces, preparation of unilamelar vesicles, formation of supported lipid bilayers, single molecule fluorescence techniques (confocal, total internal reflection), programming (data acquisition, Labview, C++), programming (data analyses, IDL, Matlab, C++)
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Stefan Boettcher. Physics.
Phone: 404-727-4298
Email: sboettc@physics.emory.edu
Institution: Emory University
Location: On Campus (Emory main campus)
Availability: Summer
Lab Positions: 1
Project Description: Simulation of disordered materials (spin glasses), combinatorial optimization problems, and dynamics of complex systems. (Requires knowledge of C or C++, Unix/Linux.)
Additional Project Information: Applied math: derivation of asymptotic forms for various statistical problems. (Requires knowledge of typical course on mathematical methods for scientists, special functions, etc.)
Student Requirements: Experience in C, C++, or Java programming in Unix/Linux environment
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Stiffness of the Edwards-Anderson Model in all Dimensions,
S. Boettcher, Physical Review Letters 95, 197205 (2005).
http://uk.arxiv.org/abs/cond-mat/0508061.
(2) Optimizing at the Ergodic Edge,
S. Boettcher and M. Frank, Physica A (in press), http://uk.arxiv.org/abs/physics/0509001.
(3) Exact Enumeration of Ground States in the Sherrington-Kirkpatrick Spin Glass, S. Boettcher and T. M. Kott, Physical Review B 72, 212408 (2005). http://uk.arxiv.org/abs/cond-mat/0506780.
(4) Tetris Model for Granular Drag, T. M. Kott and S. Boettcher, Europhysics Letters (submitted), http://uk.arxiv.org/abs/cond-mat/0510413.
(5) Obtaining Stiffness Exponents from Bond-diluted Lattice Spin Glasses, S. Boettcher and S. E. Cooke, Physical Review B 71, 214409 (2005), http://uk.arxiv.org/abs/cond-mat/0501547.
Techniques used in this lab: Understanding the dynamics of complex systems. Theory, modeling and simulation of physical systems, evaluation of statistical data. Program development, data structures and visualization methods.
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James Kindt. Chemistry.
Phone: 404-712-1817
Email: jkindt@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 1
Project Description: The goal of our research is to understand and predict the self-assembly behavior of molecules, macromolecules, and nanoparticles into interesting structures: membranes, disks, chains, networks, rings, and vesicles, to name a few. We use several different types of computer simulation as well as the theory of statistical thermodynamics. A student working in the group over the summer would typically run simulations of mixed lipid bilayer membranes with the goal of understand how the molecular properties of lipids influence their distribution in biological membranes. Along the way, he or she would learn some general skills in computational science, and have the chance to learn to write some simple programs or apply any existing programming expertise.
Student Requirements: Should have completed a year of physics and a year of organic chemistry. Physical chemistry (thermodynamics) or equivalent is useful but not required.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) J. de Joannis, Y. Jiang, F. Yin, and J. T. Kindt, 2006. "Equilibrium distributions of dipalmitoyl phosphatidylcholine and dilauroyl phosphatidylcholine in a mixed lipid bilayer: Atomistic semigrand canonical ensemble simulations." J. Physical Chemistry B, 110, 25875-25882.
(2) J. de Joannis, F. Y. Jiang, and J. T. Kindt, 2006. "Coarse-grained model simulations of mixed-lipid systems: Composition and line tension of a stabilized bilayer edge." Langmuir, 22, 998-1005.
(3) K. Khanna, T. T. Chang, and J. T. Kindt. 2006 "Complementarity and clustering in a simple model mixed bilayer." Journal of Chemical Physics, 124, 036102.
(4) Xinjiang Lu and J. T. Kindt, 2004 "Monte Carlo simulation of the self-assemble and phase behavior of semiflexible equlibrium polymers." J. Chem. Phys. 120, 10328-10338
(5) F. Y. Jiang, Y. Bouret, and J. T. Kindt, 2004. "Molecular dynamics simulations of the lipid bilayer edge." Biophysical Journal, 87, 182-192
Techniques used in this lab: Molecular dynamics and/or Monte Carlo simulation, molecular graphics and animation, Unix/Linux operating system.
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Keith Berland. Physics.
Phone: 404 712 9061
Email: kberland@physics.emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: A wide variety of undergraduate research opportunities are available in the biophotonics lab, ranging from the development of novel optical instrumentation to the application of high-sensitivity fluorescence measurements to investigate protein dynamics and interactions in living cells. Many of our research projects are highly interdisciplinary, and appropriate for students interested in physics, biophysics, biochemistry, and even cell biology. Students interested in instrumentation can participate in designing and building new optical devices, or in writing software for instrument control and data analysis. Interested students should contact the PI about specific current opportunities.
Student Requirements: Preferable to have a strong math background and or computer programming skills, but not specifically required. Molecular biology skills are also useful.
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Observation Volumes and Gamma Factors in Two-Photon Fluctuation Spectroscopy. Biophysical Journal. Vol. 89, 2077-2090
(2) Characterizing Observation Volumes and the Role of Photophysical Dynamics in One-Photon Fluorescence Fluctuation Spectroscopy. Journal of Biomedical Optics Vol 10(4). 044015, 1-9
(3) Saturation Modified Point Spread Functions in Two-Photon Microscopy. Microscopy Research and Technique. Vol. 64, 135-141.
(4) High Sensitivity Detection of Specific DNA Molecules Using Dual-Color Two-Photon Fluorescence Correlation Spectroscopy. Journal of Biotechnology. Vol. 108, 127-136.
(5) Fluorescence Correlation Spectroscopy: A New Tool for Quantification of Molecular Interactions , Protein-Protein Interactions: Methods and Protocols (ed. H. Fu), Humana Press. Pp. 383-397.
Techniques used in this lab: Some reserach tools you may learn about and use in the lab include: Fluorescence Microscopy, Fluctuation Spectroscopy, Laser Physics, Two-photon microscopy, Nuclear Localization Signal Biophysics, Protein Conjugation, Amyloid Peptide Self-assembly, Biophysics of the Intracellular Environment
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Stephan Koehler. Physics.
Phone: 1 404 727 0873
Email: skoehler@physics.emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Summer
Lab Positions: 2
Project Description: Swimming in granular media
Student Requirements: programming skills, basic mechanics
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Journal of Fluid Mechanics (2003) 490 15-25
(2) Europhysics Letters (2005) 72 137-143
Techniques used in this lab: programming, robotic control and design
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Michael Heaven. Chemistry.
Phone: 404 727 6617
Email: mheaven@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: We are studying the structure, bonding and reactivity of chemical intermediates (radicals and ions) using electronic spectroscopy. These species are examined in the gas phase and in low-temperature rare-gas solids.
Student Requirements:
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) J. Merritt, J. Han, and M. C. Heaven, J. Chem. Phys. 128, 084304/1-084304/8 (2008)
Spectroscopy of the UO2+ cation and the delayed ionization of UO2
(2) J. Han, M. C. Heaven, U. Schnupf, and M. H. Alexander, J. Chem. Phys. 128, 104308/1-104308/12 (2008)
Experimental and theoretical studies of the CN-Ar van der Waals complex
(3) Md. H. Kabir, V. N. Azyazov and M. C. Heaven, J. Phys. Chem. A, 111 10062 (2007)
Quenching of I(2P1/2) by NO2, N2O4, and N2O
(4) W. M. Fawzy and M. C. Heaven, J. Chem. Phys. 126, 154311 (2007)
Ab initio investigation of the NH(X)-N2 van der Waals complex
Techniques used in this lab: Students will introduced to pulsed laser technology, vacuum systems, fast detection electronics and molecular spectroscopy
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Connie Roth. Physics.
Phone: 404-727-4083
Email: cbroth@emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: We study the physical and dynamical properties of polymers. How polymer molecules are perturbed by their surroundings and how these effects can be used to create polymer materials with unique properties. Research focuses on fundamental understanding that will lead to innovations for new technological applications.
Student Requirements: at least one year of college-level physics; nothing more is required.
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Giant molecules: Here, and There, and Everywhere, A. Y. Grosberg and A. R. Khokhlov, Academic Press, San Diego, 1997.
(2) Polymer Physics, M. Rubinstein and R. H. Colby, Oxford University Press, New York, 2003.
(3) C.B. Roth and J.R. Dutcher, "Glass transition and chain mobility in thin polymer films", Journal of Electroanalytical Chemistry 584, 13 - 22 (2005).
(4) C.B. Roth, K.L. McNerny, W.F. Jager, and J.M. Torkelson, "Eliminating the Enhanced Mobility at the Free Surface of Polystyrene: Fluorescence Studies of the Glass Transition Temperature in Thin Bilayer Films of Immiscible Polymers," Macromolecules 40, 2568 - 2574 (2007).
(5) C.B. Roth, A. Pound, S.W. Kamp, C.A. Murray, and J.R. Dutcher, "Molecular weight dependence of the glass transition temperature of freely-standing poly(methyl methacrylate) films", European Physical Journal E 20, 441 - 448 (2006).
Techniques used in this lab: ellipsometry, fluorescence, chemical handling and sample preparation, polymer synthesis, graphing and data analysis
Additional Comments: Undergraduate students will have an opportunity to participate in current research projects often working closely with a particular graduate student in the group. All efforts will be made to find research projects that are sufficiently self-contained as to come to some form of conclusion at the end of the research term, but the nature of research is that you will be trying something new. The undergraduate student will be considered an integral member of the group, thus gaining a feel for the graduate school experience.
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EUGENE DEMCHUK. Division of Toxicology.
Phone: 770-488-3327
Email: edemchuk@cdc.gov
Institution: CDC/ATSDR
Location: Off-campus (personal vehicle required, carpool possible but not guaranteed)
Availability: Spring,Summer,Fall
Lab Positions: 2
Project Description: Autism Spectrum Disorder (ASD) is an increasingly common developmental disability in industrial nations. ASD is thought to result from gene-environment interactions. Despite research progress in identifying candidate genes associated with ASD, no clear etiology or causative marker has been found. If and when a genetic predisposition is identified, the next research question will be: What environmental trigger is responsible for the development or manifestation of the clinical phenotype? To address this question we develop a rapid-screening computational toxicology methodology which can be applied to large numbers of environmental pollutants (ligands) and a known or suspected biological target for autism. Starting with a model database of hypothesized chemical triggers and a set of critical-pathway genes, we screen the chemicals against known genetic variants using state-of-the-art molecular docking techniques. Top scored gene/chemical combinations potentially offer an educated choice for further in-depth analysis of gene-environment interactions using laboratory and/or epidemiological methods.
Additional Project Information: The Agency for Toxic Substances and Disease Registry (ATSDR) Computational Toxicology and Method Development Laboratory implements the full range of methods in support of ATSDR mission to protect human populations from exposure to environmental contaminants. These include benchmark dose, chemical-specific adjustment factor, physiologically-based pharmacokinetic, quantitative structure-activity relationship (QSAR), genetic-susceptibility- and meta-analysis modeling, and modeling the toxicity of chemical mixtures. Computational toxicology methods are used as an integrated systematic approach in the development of ATSDR Minimal Risk Levels to be used as health guidance values to protect populations exposed to toxic chemicals at hazardous waste sites. These methods are also used in the development of ATSDR Toxicological Profiles, to support environmental health consultations and prioritization of environmental chemical hazards, when experimental information is insufficient, and to improve study design, when filling the priority data needs as mandated by the Congress. Also, the Laboratory is engaged in the development of response strategies to new emerging chemical threats. We develop methods for assessing toxicological effects of potentially hazardous chemicals from their chemical structure alone. A need for analysis of this type is especially imminent during the times of emergencies, whether it is an accidental chemical release, major natural disaster, or terrorist threat in all situations when time is a critical element of public health response.
Student Requirements: chemistry, toxicology and/or physiology, statistics, biochemistry, basic understanding of principles in physics, basic math
Accepts 1st year students? Y
Accepts 2nd year students? Y
Suggested Reading (References):
(1) Demchuk, E.; Ruiz, P.; Wilson, J.D.; Scinicariello, F.; Pohl, H.R.; Fay, M.; Mumtaz, M.; Hansen, H.; De Rosa, C.T. Computational toxicology methods in public health practice . Toxicol. Mech. Method. 2008, 18, 119135.
(2) Snyder, J.A.; Demchuk, E.; McCanlies E.C.; Schuler, C.R.; Kreiss, K.; Frye, B.; Ensey, J.; Stanton, M.; Weston, A. Impact of negatively charged patches on the surface of MHC class II antigen-presenting proteins on risk of chronic beryllium disease . J. R. Soc. Int. 2008, 5, 749758.
(3) Demchuk, E.; Albin, B.C.; Fay, M.; Garrett, R.M.; Hansen, H. Structure-activity analysis of chemical health guidance values . Toxicologist (Suppl. to Toxicol. Sci.) 2006, 90, 186.
(4) Demchuk, E.; Yucesoy, B.; Johnson, V.J.; Weston, A.; Germolec, D.; De Rosa, C.T.; Luster, M.I. A statistical model to assess genetic susceptibility as a risk factor in multifactorial diseases: Lessons from occupational asthma . Environ. Health Persp. 2007, 115, 231234.
(5) Hnizdo, V.; Darian, E.; Fedorowicz, A.; Demchuk, E.; Li, S.; Singh, H. Nearest-neighbor nonparametric method for estimating the configurational entropy of complex molecules . J. Comp. Chem. 2007, 28, 655668.
Techniques used in this lab: Students may learn various computational toxicology techniques, including benchmark dose modeling, chemical-specific adjustment factor modeling, physiologically-based pharmacokinetic/pharmacodynamic modeling, (quantitative) structure-activity relationship -- (Q)SAR modeling, genetic-susceptibility- and meta-analysis modeling, modeling the toxicity of chemical mixtures and chemical-chemical interactions, molecular docking, protein homology structure modeling, and other.
Additional Comments: A brief description of the ATSDR Computational Toxicology lab can be found at http://www.atsdr.cdc.gov/dtem/programs/comptox/index.html
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Horace Dale III. Physics.
Phone: 404-273-6827
Email: hdale@physics.emory.edu
Institution: Emory
Location: On Campus (Emory main campus)
Availability: Summer,Fall
Lab Positions: 1
Project Description: We analyze stellar variability of both eclipsing binary stars and pulsating variables. We model these systems by applying well understood laws of physics that lead us to a better understanding of our universe.
Student Requirements: Junior or seior level Physics and Astronomy majors
Suggested Reading (References):
(1) J. Coughlin, H. Dale, R. Williamon. 2008. Long-term Photometric Analysis of the Active W UMa-type System TU Bootis. The Astronomical Journal.
Techniques used in this lab:
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