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: kmravikumar@ucdavis.edu
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 graduate and undergraduate students 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
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based clustering protocol.
• 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 Poincaré 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.
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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. 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).
3. L Heinz, K M Ravikumar, & D L Cox, In silico measurements of twist
and bend moduli for β-solenoid protein self-assembly units Nano Lett.
2015. (in review)
4. 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 2015, 9 (1), pp 449463.
5. W Huang, K M Ravikumar, M Chance, & S Yang, Quantitative mapping
of protein structure by hydroxyl radical footprinting mediated structural
mass spectrometry: A protection factor analysis Biophys. J. 2015, 8 (1)
107115.
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
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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.
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 back-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.
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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).
References
Daniel Cox,
Distinguished Professor,
Department of Physics,
University of California, Davis
Phone: (415) 867 4992
Email: cox@physics.ucdavis.edu
Rajiv Singh,
Professor,
Department of Physics,
University of California, Davis
Phone: (530) 752-4710
Email: singh@physics.ucdavis.edu
Wonmuk Hwang,
Associate Professor,
Department of Biomedical Engineering,
Texas A&M University, College Station
Phone: (979) 458 0178
Email: hwm@tamu.edu
Sichun Yang,
Assistant Professor,
Center for Proteomics and Bioinformatics,
Case Western Reserve University, Cleveland
Phone: (216) 368 5793
Email: sichun.yang@case.edu
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