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Tung Le
Graduate Research Assistant
Education
PhD in Biophysics, Georgia Institute of Technology, May 2015 (expected)
Bachelor in Physics, Hanoi National University of Education, Hanoi, Vietnam
Research Interests

I am a graduate student working under the supervision of Dr. Harold Kim in School of Physics at Georgia Tech. My focus is on experimental single-molecule biophysics using FRET technique. I am also interested in applying simple theoretical models and simulations to explain experimental data. I am actively looking for a postdoc position in single-molecule biophysics labs for further interesting problems.

Research Experience

Georgia Institute of Technology, supervised by Dr. Harold Kim, September 2010 − present

- Developed an agent-free single-molecule Fluorescence Resonance Energy Transfer (smFRET) looping assay to study looping of double-stranded (ds) DNA with different intrinsic curvatures and lengths

- Developed a PCR-based protocol to prepare dsDNA molecules free of mismatches for the DNA looping and unlooping experiments

- Developed a smFRET unlooping assay to study the bendability of DNA in the strong bending condition

- Performed coarse-grained simulations using Gaussian and Monte Carlo (MC) sampling methods to obtain the conformational distributions of linear DNA and DNA minicircles in thermal equilibrium

- Implemented the Peyrard–Bishop–Dauxois (PBD) model and the two-state model to calculate the melting profile of dsDNA sequence

Georgia Institute of Technology, supervised by Dr. Toan Nguyen, August 2009 – September 2010

- Performed coarse-grained simulations on the counterion-mediated reentrant behavior of dsDNA molecules to form DNA aggregate

Technical Skills

1. Experimental skills

 

- Microscopy: Fluorescence microscopy (objective-type TIR)

- Molecular biology: Polymerase Chain Reaction (PCR), gel electrophoresis, oligo labeling, E. coli transformation, site-directed mutagenesis, DNA ligation, nucleosome reconstruction by salt dialysis

2. Software

- MATLAB for data collection, data analysis, and computer simulation

- Visual C++ for equipment control and data acquisition

- Microsoft Word, LaTex for manuscript preparation  

3. Simulation

- MC simulation including the umbrella sampling technique

Teaching and Extracurricular activities

Teaching Assistant at Georgia Institute of Technology: graded homework, quizzes, and exams; coordinated Introductory Physics Labs, August 2009 – August 2011

- Moderator of the Physics of Living System (PoLS) Lunch and Learn talk series at Georgia Institute of Technology: invited speakers, coordinated and directed talks, January 2014 – April 2014

Honors and Awards:
Molecular Biophysics Senior Student Award, College of Science, Georgia Institute of Technology, 2013 – 2014
Amelio Research Award for Excellence in Research by a Graduate Student, Georgia Institute of Technology, 2014
Certificate of Merit to students graduating with the best result of Physics Department, Hanoi National University of Education, 2008
Odon Vallet Scholarship for undergraduate students, 2007
Papers:

Peer-reviewed Publications

1. Le, T.T. and Kim, H.D. (2014) Probing the elastic limit of DNA bending, Nucleic Acids Research, 42 (16), 10786-10794

2. Le, T.T. and Kim, H.D. (2014) Studying DNA Looping by Single-Molecule FRET. Journal of Visualized Experiments, (88), e51667

3. Le, T.T. and Kim, H.D. (2013) Measuring Shape-Dependent Looping Probability of DNA. Biophysical Journal, 104, 2068–2076

4. Lee, S., Le, T.T. and Nguyen, T.T. (2010) Reentrant Behavior of Divalent-Counterion-Mediated DNA-DNA Electrostatic Interaction. Physical Review Letters, 105, 248101

Oral and Poster Presentations

1. Le, T.T. and Kim, H.D. A single-molecule study of sharp DNA bending. Presented at Molecular Biophysics Research Review, 2014 (oral).

 2. Le, T.T. and Kim, H.D. Measuring energetics of sharp DNA bending from breakage kinetics of small DNA loops. Presented at the Biophysical Society 58th Annual Meeting, 2014 (poster).

3. Le, T.T. and Kim, H.D. Using small DNA loops to study energetics of DNA kinking. Presented at Lunch and Learn (Physics of Living Systems seminars), 2014 (oral).

4. Le, T.T. and Kim, H.D. Measuring energetics of sharp DNA bending from breakage kinetics of small DNA loops. Presented at Atlanta Area Molecular and Cellular Biophysics Symposium, 2013 (poster).

5. Le, T.T. and Kim, H.D. Measuring energetics of sharp DNA bending from breakage kinetics of small DNA loops. Presented at Lunch and Learn (Physics of Living Systems seminars), 2013 (oral).

6. Le, T.T. and Kim, H.D. Single-molecule studies on dynamics of short DNA duplexes: looping and denaturing. Presented at CPLC Summer School at UIUC, 2013 (poster).

7. Le, T.T. and Kim, H.D. Single molecule FRET study on the spontaneous repositioning of nucleosomes. Presented at The 7th Southeast Meeting on Soft Materials, 2013 (oral).

8. Le, T.T. and Kim, H.D. Catch-bond like behavior of DNA duplex under shear. Presented at Biophysical Society 57th Annual Meeting, 2013 (poster).

9. Le, T.T. and Kim, H.D. Single molecule FRET study on the spontaneous repositioning of nucleosomes. Presented at The 7th Southeast Meeting on Soft Materials, 2013 (oral).

10. Le, T.T. and Kim, H.D. Measuring looping kinetics of short double-stranded DNA. Presented at Lunch and Learn (Physics of Living Systems seminars), 2012 (oral).

11. Le, T.T. and Kim, H.D. Catch-bond like behavior of DNA duplex under shear. Presented at The 2012 Physics of Living Systems (PoLS) annual meeting, 2012 (oral).

12. Le, T.T. and Kim, H.D. Catch-slip transition in DNA duplex under shear stress. Presented at The 6th Southeast Meeting on Soft Materials, 2012 (oral).

13. Le, T.T. and Kim, H.D. Measuring sequence-dependent DNA looping kinetics. Presented at Biophysical Society 56th Annual Meeting, 2012 (poster).

14. Le, T.T. and Kim, H.D. Sequence dependent DNA bending. Presented at Atlanta Colloid & Soft Matter Bag Lunch Seminar, 2011 (oral).

15. Le, T.T. and Kim, H.D. DNA looping dynamics. Presented at Georgia Tech Biology Graduate Student Symposium, 2011 (poster).

16. Le, T.T. and Kim, H.D. Dynamics of sequence-dependent DNA bending. Presented at The 5th Southeast Workshop on Soft Materials, 2011 (oral).

17. Lee, S., Tran, V.C., Le, T.T. and Nguyen, T.T. DNA ejection from bacteriophage in the presence of Mg2+ counterions, reentrant DNA condensation by multivalent counterions. Presented at Integrative BioSystems Institute IBSI, Second community-wide poster session, 2010 (poster).

18. Le, T.T. and Nguyen, T.T. Reentrant DNA condensation by multivalent counterions. Presented at The 4th Southeast Meeting on Soft Materials, 2010 (oral).

Memberships and Committees:
Biophysical Society (2010-current)
Moderator of the Physics of Living System (PoLS) Lunch and Learn talks (Spring 2014).