Reading (photo by Amber Labelle)


Coming from a theoretical physics and mathematics background, my current research interests include integration of energy conversion processes in bioenergetic systems at protein-, organelle-, and cell-scale using on atomic detail structural models.

My work develops structural and functional models of cellular compartments from photosynthetic bacteria and plants in close collaboration with experimental scientists, particularly with Neil Hunter Lab providing AFM, EM, mass spectrometry, and optical spectroscopy data. These data-driven models describe the primary processes of energy conversion from excitation transfer kinetics to ATP production, derive Physics-based evolutionary constraints inherent to natural bioenergetic systems, determine principles of robustness and optimality under environmental perturbations, and provide performance comparisons to artificial and bio-inspired solar energy solutions in order to establish design criteria.

I am also regularly involved in outreach activities to bring the excitement of science and discovery to everyone, including public lectures and demonstrations for lay audiences and design of interactive museum exhibits featuring molecular machines of life and their evolution.

Ph. D. in Physics Stony Brook University. Title: Universality in Random Matrix Models of Quantum Chromodynamics.

Publications

Contact Information

Research and Outreach Highlights

The following highlights are mostly non-technical and should be accessible to general audiences. See publications for in-depth information.

A visual summary of some my recent work on light-harvesting in bacteria can be found in the following video, which has won the the Best Movie award in the Supercomputing 2014 Visualization Showcase. More information can be found in this publication.


chromotophore vesicle - the Death Star view


The sun is not only the author of visibility in all visible things, but of generation and nourishment and growth.
    - Plato (quoted by Govindjee )



Photosynthetic chromatophore vesicles found in purple bacteria are essentially biological solar cells built from light-harvesting proteins. Shown are approximately two hundred proteins assembled in silico by combining AFM, NMR, EM, crystallography, mass spectrometry, and optical spectroscopy data containing 3,000 chlorophylls ( more information).

* 'Life's Solar Battery' A (pseudo-)organelle made of light-harvesting proteins is constructed combinining AFM, NMR, EM, crystallography, and spectroscopy data as atomic detail model, revealing how efficient energy harvesting is achieved through a quantum mechanical process across a 70~nm vesicle containing up to four thousand chlorophylls.
* 'Evolution Shaped by Physics' How biological networks evolve and how physical constraints that act upon their dynamics shape this evolution is poorly understood. A glimpse of insight can be gained by a comparison of energy transfer networks from related species as presented in this 'Tale of Two Photosystems'.
* 'Finding the Path' A novel method is presented for finding representative reaction paths for biological processes based on mean first passage times.
* 'Unbreakable Biological Solar Cell' "If it ain't broke, don't fix it!" By observing the network topology of excitation migration pathways in a massive light harvesting assembly and comparing it to alternative configurations we uncovered signs of robustness and optimality in chlorophyll network architecture.
* 'Exciting Biology and Hot Physics Meet' Thermal disorder is an ever-present challenge for all organisms - and the scientists who model them. Quantum field theory tools come to the rescue of modelling thermal effects in electronically excited bioenergetic systems.
* Organization of energy transfer networks in photosynthesis. Lessons learned on robustness and optimality from photosynthetic proteins.
* Tale of two photosystems. A glimpse at evolutionary history by comparing the same protein, photosystem I, from cyanobacteria and plants.

The supramolecular models featured here were built mainly using Mathematica.

Cover Work

BJ cover BJ cover


Publications

* Overall energy conversion efficiency of a photosynthetic vesicle. Melih Sener, Johan Strumpfer, Abhishek Singharoy, C. Neil Hunter, and Klaus Schulten. eLife, 10.7554/eLife.09541, 2016. (30 pages). (PMC: PMC5001839)
* Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing. John E. Stone, Melih Sener, Kirby L. Vandivort, Angela Barragan, Abhishek Singharoy, Ivan Teo, Joao V. Ribeiro, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C. Phillips, Craig MacGregor-Chatwin, Matthew P. Johnson, Lena F. Kourkoutis, C. Neil Hunter, and Klaus Schulten Parallel Computing, 55:17-27, 2016. (PMC: PMC4890717)
* Visualization of energy conversion processes in a light harvesting organelle at atomic detail. Melih Sener, John E. Stone, Angela Barragan, Abhishek Singharoy, Ivan Teo, Kirby L. Vandivort, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C. Phillips, Lena F. Kourkoutis, C. Neil Hunter, and Klaus Schulten. In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, SC '14. IEEE Press, 2014.
* Integration of energy and electron transfer processes in the photosynthetic membrane of Rhodobacter sphaeroides. Michael L. Cartron, John D. Olsen, Melih Sener, Philip J. Jackson, Amanda A. Brindley, Pu Qian, Mark J. Dickman, Graham J. Leggett, Klaus Schulten, and C. Neil Hunter. Biochimica et Biophysica Acta - Bioenergetics, 1837:1769-1780, 2014.
* Light harvesting by lamellar chromatophores in Rhodospirillum photometricum. Danielle Chandler, Johan Strumpfer, Melih Sener, Simon Scheuring, and Klaus Schulten. Biophysical Journal, 106:2503-2510, 2014. (PMC: PMC4052275)
* How Quantum Coherence Assists Photosynthetic Light Harvesting. Johan Strumpfer, Melih Sener, and Klaus Schulten. Journal of Physical Chemistry Letters. 3:536-542, 2012.
* Forster energy transfer theory as reflected in the structures of photosynthetic light harvesting systems. Melih Sener, Johan Strumpfer, Jen Hsin, Danielle Chandler, Simon Scheuring, C. Neil Hunter, and Klaus Schulten. ChemPhysChem, 12:518-531, 2011.
* The light-harvesting apparatus in purple photosynthetic bacteria: introduction to a quantum biological device. Johan Strumpfer, Jen Hsin, Melih Sener, Danielle Chandler, and Klaus Schulten. In Benoit Roux, editor, Molecular Machines, chapter 2, pp. 19-48. World Scientific Press, 2011.
* Energy transfer dynamics in an RC-LH1-PufX tubular photosynthetic membrane. Jen Hsin, Johan Strumpfer, Melih Sener, Pu Qian, C. Neil Hunter, and Klaus Schulten. New Journal of Physics, 12:085005, 2010. (19 pages).
* Photosynthetic vesicle architecture and constraints on efficient energy harvesting. Melih Sener, Johan Strumpfer, John A. Timney, Arvi Freiberg, C. Neil Hunter, and Klaus Schulten. Biophysical Journal, 99:67-75, 2010.
* Self-assembly of photosynthetic membranes. Jen Hsin, Danielle E. Chandler, James Gumbart, Christopher B. Harrison, Melih Sener, Johan Strumpfer, and Klaus Schulten. ChemPhysChem, 11:1154-1159, 2010.
* From Forster resonance energy transfer to coherent resonance energy transfer and back. Robert M. Clegg, Melih Sener, Govindjee. In Optical Biopsy VII, edited by Robert R. Alfano, Proceedings of SPIE, Vol. 7561, paper number: 7561-12; article CID Number 75610C, 21 pages, 2010.
* Structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter sphaeroides. Melih K. Sener, Jen Hsin, Leonardo G. Trabuco, Elizabeth Villa, Pu Qian, C. Neil Hunter, and Klaus Schulten. Chemical Physics, 357:188-197, 2009.
* From atomic-level structure to supramolecular organization in the photosynthetic unit of purple bacteria. Melih K. Sener and Klaus Schulten. In C. Neil Hunter, Fevzi Daldal, Marion C. Thurnauer, and J. Thomas Beatty, editors, The Purple Phototrophic Bacteria, volume 28 of Advances in Photosynthesis and Respiration, pp. 275-294. Springer, 2008.
* Atomic level structural and functional model of a bacterial photosynthetic membrane vesicle. Melih K. Sener, John D. Olsen, C. Neil Hunter, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 104:15723-15728, 2007.
* Comparison of the light harvesting networks of plant and cyanobacterial photosystem I. Melih K. Sener, Craig Jolley, Adam Ben-Shem, Petra Fromme, Nathan Nelson, Roberta Croce, and Klaus Schulten. Biophysical Journal, 89:1630-1642, 2005.
* Physical principles of efficient excitation transfer in light harvesting. Melih Sener and Klaus Schulten. In David L. Andrews, editor, Energy Harvesting Materials, pp. 1-26. World Scientific, Singapore, 2005.
* Excitation migration in trimeric cyanobacterial photosystem I. Melih K. Sener, Sanghyun Park, Deyu Lu, Ana Damjanovic, Thorsten Ritz, Petra Fromme, and Klaus Schulten. Journal of Chemical Physics, 120:11183-11195, 2004.
* Reaction paths based on mean first-passage times. Sanghyun Park, Melih K. Sener, Deyu Lu, and Klaus Schulten. Journal of Chemical Physics, 119:1313-1319, 2003.
* Robustness and optimality of light harvesting in cyanobacterial photosystem I. Melih K. Sener, Deyu Lu, Thorsten Ritz, Sanghyun Park, Petra Fromme, and Klaus Schulten. Journal of Physical Chemistry B, 106:7948-7960, 2002.
* A general random matrix approach to account for the effect of static disorder on the spectral properties of light harvesting systems. Melih Sener and Klaus Schulten. Physical Review E, 65:031916, 2002. (12 pages).
* Universality in Random Matrix Models of Quantum Chromodynamics. Ph.D. Thesis. Melih K. Sener, Stony Brook, August 1999.
* Universality in Chiral Random Matrix Theory at beta =1 and beta =4. Melih K. Sener and Jacobus J. M. Verbaarschot. Physical Review Letters, 81:248-251,1998.
* Universality of Correlation Functions in Random Matrix Models of QCD. Andrew D. Jackson, Melih K. Sener, and Jacobus J.M. Verbaarschot. Nuclear Physics B, 506:612-632,1997.
* Finite volume partition functions and Itzykson-Zuber integrals. Andrew D. Jackson, Melih K. Sener, and Jacobus J. M. Verbaarschot Physics Letters B, 387:355-360,1996.
* Universality near zero virtuality. Andrew D. Jackson, Melih K. Sener, and Jacobus J. M. Verbaarschot Nuclear Physics B, 479:707-726,1996.

Contact information

address: Beckman Institute, 405 N. Mathews, Urbana, IL 61801.
tel: 217-244 1612   fax: 217-244 6078
email: (my first name) at ks.uiuc.edu

Personal snippets

* Of Bread, Words, and Motion. Musings on dance and poetry, mostly.
* The Writer's Almanac. Has many a hidden gem in the way of poems and biographical tidbits.
* '... the colors and the lines that trace the past will in the semi-darkness form a face ...' If I were to pick only one poem for the end of time...