Krishnakumar Mayuram Ravikumar Contact Education Department of Physics University of California, Davis 402 Physics Building, Davis, CA 95616 USA Web: www.kmravikumar.com Cell: 979 204 5014 E-mail: [email protected] Ph.D., Biomedical Engineering (2008-2011) M.S., Biomedical Engineering (2005-2008) Texas A&M University, College Station, TX, USA Adviser: Wonmuk Hwang • Dissertation : Computational study of the role of hydration in in the assembly of collagen and other bio-filaments B.E., Mechanical Engineering (2000-2004) University of Madras, Chennai, India Research Experience Postdoctoral Scholar (2014 - Present) Department of Physics, University of California, Davis CA Advisors: Daniel Cox and Rajiv Singh • Worked as a part of multi-department research team to engineer controlled self-assembly of biopolymers. • Analyzed the binding energy of biopolymers using Molecular Dynamics simulations on GPUs (Graphical Processing Unit). • Worked closely with experimentalists to design and validate the binding interfaces in vitro. • Mentored and supervised two undergraduates working in the lab. Postdoctoral Scholar (2011 - 2014) Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland OH Advisor: Sichun Yang • Developed coarse-grained model for computationaly studying protein-protein interactions. • Developed an enhanced sampling technique for exhaustive sampling of proteinprotein conformations. • Implemented a rapid theoretical small-angle X-ray scattering (SAXS) method for protein, DNA, RNA and their complexes (Fast-SAXS-pro available for download). • Worked in a two member team with an experimentalist to understand the binding interface of estrogen receptor ligand and DNA binding domains using both computational and experimental methods (ongoing project). • High throughput small molecule docking of biomolecules - as part of research in the University Hospitals, Cleveland. • Supervised an undergraduate working in the lab to implement a structure based clustering protocol. 1 of 5 • Published seven papers (three as first author), two of which featured as cover articles. Graduate Research Assistant (2005 - 2011) Department of Biomedical Engineering, Texas A&M University, College Station TX Advisor: Wonmuk Hwang • Research involved understanding the role of hydration and hydration forces in biomolecular assembly. • Implemented a grid based method to study the structure and dynamics of water around protein surfaces. • Measured and analyzed the magnitude and the origin of hydration forces involved in assembly of collagen, and amyloid peptides. • Worked with a experimental group to elucidate the molecular mechanism of optical clearing in collagenous tissue. • Managed a custom built computational cluster in the lab. • Published four papers (three as first author). Teaching & Mentoring Experience Guest Lectures Thermodynamics and Statistical Mechanics (PHYS 112, Fall 2014) • Handled a lecture on transport theory for upper level undergraduate students Statistical Mechanics (PHYS 219B, FALL 2014) • Handled a lecture on H-theorem, phase flow, and Poincar´e recurrence for graduate students Electricity and Magnetism (PHY 009, FALL 2014) • Handled a lecture on conductors in an electric field Mentoring Students mentored during postdoctoral tenure • Leonard Heinz (Visiting undergraduate summer student from Heidelberg University, Germany) Guided him in learning and implementing Molecular Dynamics simulations to study the mechanical properties of biofilaments and writing a journal publication. • Colin Chin (Undergraduate summer student from Electrical Engineering, Case Western Reserve University) Guided him to implement a distance based clustering protocol to group structurally similar protein conformations. • Shengqiao Luo (Undergraduate research student in Physics at University of California, Davis) Guided her in learning python and implementing fourier analysis to analyze vibrational modes of biofilaments. 2 of 5 Volunteer Tutor, Community College (Spring 2013) • Math tutoring on weekends at Cuyahoga Community College (East Campus) on Calculus and Algebra Graduate Teaching Assistant Biomeasurements Lab (Spring 2007) • Supervised lab exercises on gel electrophoresis, thermal gravimetric analysis, rheometer for senior undergraduate students • Graded assignments and final exams. Leadership & Professional Activities President - SPICMACAY-TAMU Student organization (2008-2009) (Society for promotion of Indian Classical Music and Culture among Youth, Texas A&M chapter) • Coordinated a group of 20 volunteers to organize Indian classical music and dance concerts for College Station community at no cost. Journal Reviewer • Biophysical Journal and European Journal of Medicinal Chemistry Publications Journal Publications 1. K M Ravikumar, R R P Singh, & D L Cox, Mapping the force-field for linear assembly of β-solenoid proteins (in preparation) 2. L Heinz, K M Ravikumar, & D L Cox, In silico measurements of twist and bend moduli for β-solenoid protein self-assembly units (in preparation) 3. M D R Peralta, A Karsai, A Ngo, C Sierra, K Fong, R N Hayre, N Mirzaee, K M Ravikumar, A J Klubernder, X Chen, G-y Liu, M D Toney, R R P Singh, & D L Cox, Engineering Amyloid Fibrils from β-solenoid Proteins for Biomaterials Applications ACS Nano (in review). 4. K M Ravikumar, W Huang, C Chin, & S Yang, A pipeline to study protein-protein conformational landscape: Modeling, extensive sampling, and orientational clustering (in preparation). 5. W Huang, K M Ravikumar, M Chance, & S Yang, Protection factors for synchrotron oxidation of proteins Biophys. J. (in review). 6. W Huang, K M Ravikumar & S Yang, A new found cancer-activating mutation reshapes the energy landscape of estrogen-binding domain J. Chem. Theo. Comput. 2014, 10 (8), 2897–2900. 7. W Huang, K M Ravikumar & S Yang, Cross-talk between the ligandand DNA-binding domains of estrogen receptor Proteins 2013, 81 (11), 1900–1909. Featured as cover article 8. S Yang, K M Ravikumar & H Levine, Energy evaluation of β-strand packing in a fibril-forming SH3 domain J. Phys. Chem. B 2013, 117 (42), 13051–13057. 3 of 5 9. K M Ravikumar, W Huang & S Yang, Fast-SAXS-pro: A unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes J Chem. Phys. 2013, 138 (2), 024112. Fast-SAXS-pro web server 10. K M Ravikumar, W Huang & S Yang, Coarse-grained simulations of protein-protein association: An energy landscape perspective Biophys. J. 2012, 103, 1–9. Featured as cover article 11. K M Ravikumar & W Hwang, Role of hydration shell in the selfassembly of collagens and amyloid steric zipper filaments J. Am. Chem. Soc. 2011, 133 (30), 11766–11773. 12. J Hirshburg, K M Ravikumar, W Hwang & A Yeh, Molecular basis for optical clearing of collagenous tissue J. Biomed. Opt. 2010, 15, 055002. 13. K M Ravikumar & W Hwang, Region-specific role of water in collagen unwinding and assembly Proteins, 2008, 72, 1320–1332. 14. K M Ravikumar, J D Humphrey & W Hwang, Spontaneous unwinding of a labile domain in a collagen triple helix J. Mech. Matl. Struc. 2007, 2, 999–1010. Selected Presentations 1. K M Ravikumar, W Huang, S Yang, Fast-SAXS-pro: A unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes, Biophysical Society Meeting 2013, Philadelphia. 2. K M Ravikumar & W Hwang, Role of water in mediating interactions between collagens, Biophysical Society Meeting 2010, San Francisco. 3. K M Ravikumar & W Hwang, Hydration forces direct collagen self-assembly, BMES Meeting 2009, Pittsburgh. 4. K M Ravikumar & W Hwang, Role of water in conformational behavior and assembly of collagen molecules, Biophysical Society Meeting 2008, Long Beach. 5. K M Ravikumar & W Hwang, Water mediated stabilization and microunfolding of the collagen triple helix, Society of Engineering Science 2007, College Station. Selected for student paper competition. 6. K M Ravikumar & W Hwang, Sequence-specific role of water in spontaneous local unwinding of collagen, ASME Summer Bioengineering Conference 2007, Keystone. Other Publications Swaras - Android app • Co-authored a predictive pattern matching algorithm which generates Carnatic (South Indian classical) music phrases based on first and second order Markov chains (> 18500 downloads with rating 4.3). 4 of 5 References Daniel Cox, Distinguished Professor, Department of Physics, University of California, Davis Phone: (415) 867 4992 Email: [email protected] Rajiv Singh, Professor, Department of Physics, University of California, Davis Phone: (530) 752-4710 Email: [email protected] Wonmuk Hwang, Associate Professor, Department of Biomedical Engineering, Texas A&M University, College Station Phone: (979) 458 0178 Email: [email protected] Sichun Yang, Assistant Professor, Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland Phone: (216) 368 5793 Email: [email protected] 5 of 5
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