• +1 865.574.6308

Loukas Petridis

Staff Scientist, Biosciences Division, ORNL
Joint Faculty, BCMB Department, University of Tennessee, Knoxville

Email: petridisl@ornl.gov
Work: 865.576.2576 
https://www.ornl.gov/staff-profile/loukas-petrids

Address:
Oak Ridge National Laboratory
E340, Bldg. 2040
1 Bethel Valley Rd.
Oak Ridge, TN 37831-6309

 

 

 Biography

 I am a biophysicist that combines computational methods and neutron scattering to understand the molecular-level properties of biosystems. I obtained my PhD in theoretical physics from the University of Cambridge, U.K. in 2005. I have been part of a multidisciplinary team that has established, from the ground up, a new research approach of employing computer simulation and experiments to elucidate the molecular-scale processes that drive the deconstruction of plant biomass to fuels and materials. The impact of our research is demonstrated by the substantial increase in use of Molecular Dynamics (MD) simulation and neutron scattering in studying biomass. I am also interested in biomolecular flexibility -manifested as transitions among multiple states accessible to a macromolecular system-, applying polymer theory to biological systems, the interactions of organic matter with metal oxides, nanoparticles for plant therapeutics and the computational discovery of molecules for human health.

 

 

Research Interests

Bioenergy
Deconstruction of Lignocellulose

Protein Flexibility
Intrinsic disorder, multi-domain complexes and flexible linkers

Nanoparticles
Electronic properties of metal oxides
and their interactions with organic molecules

Plant Cell Walls
Structure and formation of plant cell walls

Supercomputing
MD simulation of multi-million atom systems

Drug Discovery
Lead molecules for FGF23 


Group Members

Michelle Aranha

Postdoctoral Research Associate
Nanomaterials

Marcella Berg

Postdoctoral Research Associate
Bioenergy

Shih-Hsien Liu

Postdoctoral Research Associate
Nanomaterials; bioenergy; drug discovery

Takat B. Rawal

Postdoctoral Research Associate
Nanomaterials; bioenergy

Utsab Shrestha

Postdoctoral Research Associate
Protein flexibility; plant cell wall structure

Micholas Dean Smith

Postdoctoral Research Associate
Bioenergy; nanomaterials

Derya Vural

Visiting Professor
Bioenergy

Madhulika Gupta
Postdoctoral Research Associate
Plant cell wall structure

 

Publications

Google Scholar: https://scholar.google.com/citations?user=Fg3oNxwAAAAJ&hl=en

  1. Shrestha, U. R.; Juneja, P.; Zhang, Q.; Gurumoorthy, V.; Borreguero, J. M.; Urban, V.; Cheng, X.; Pingali, S. V.; Smith, J. C.; O’Neill, H. M.; Petridis, L., Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation. Proc Natl Acad Sci USA 2019, 116 (41), 20446.
  2. Liu, S.-H.; Rawal, T. B.; Soliman, M.; Lee, B.; Maxwell, T.; Rajasekaran, P.; Mendis, H. C.; Labbé, N.; Santra, S.; Tetard, L.; Petridis, L., Antimicrobial Zn-Based “TSOL” for Citrus Greening Management: Insights from Spectroscopy and Molecular Simulation. J Agric Food Chem 2019, 67 (25), 6970–6977.
  3. Rawal, T. B.; Ozcan, A.; Liu, S.–H.; Pingali, S. V.; Akbilgic, O.; Tetard, L.; O’Neill, H.; Santra, S.; Petridis, L., Interaction of Zinc Oxide Nanoparticles with Water: Implications for Catalytic Activity. ACS Appl. Nano Matter. 2019, 2 (7), 4257–4266.
  4. Patri, A. S.; Mostofian, B.; Pu, Y.; Ciaffone, N.; Soliman, M.; Smith, M. D.; Kumar, R.; Cheng, X.; Wyman, C. E.; Tetard, L.; Ragauskas, A. J.; Smith, J. C.; Petridis, L.; Cai, C. M., A Multifunctional Cosolvent Pair Reveals Molecular Principles of Biomass Deconstruction. J Am Chem Soc 2019, 141 (32), 12545–12557.
  5. Mostofian, B.; Petridis, L.; Cai, C. M., Exploring Molecular Mechanisms of Cosolvent Enhanced Biomass Deconstruction: An Overview of Recent Progress. In Understanding Lignocellulose: Synergistic Computational and Analytic Methods, American Chemical Society: 2019; Vol. 1338, pp 103–117.
  6. Demerdash, O.; Shrestha, U. R.; Petridis, L.; Smith, J. C.; Mitchell, J. C.; Ramanathan, A., Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins. Front. Mol. Biosci. 2019, 6 (64).
  7. Shrestha, U. R.; Smith, S.; Pingali, S. V.; Yang, H.; Zahran, M.; Breunig, L.; Wilson, L. A.; Kowali, M.; Kubicki, J. D.; Cosgrove, D. J.; O’Neill, H. M.; Petridis, L., Arabinose substitution effect on xylan rigidity and self-aggregation. Cellulose 2019, 26 (4), 2267–2278.
  8. Vermaas, J. V.; Petridis, L.; Ralph, J.; Crowley, M. F.; Beckham, G. T., Systematic parameterization of lignin for the CHARMM force field. Green Chem. 2019, 21 (1), 109–122.
  9. Yang, H.; Watts, H. D.; Gibilterra, V.; Weiss, T. B.; Petridis, L.; Cosgrove, D. J.; Kubicki, J. D., Quantum Calculations on Plant Cell Wall Component Interactions. Interdisciplinary Sciences: Computational Life Sciences 2019, 11 (3), 485–495.
  10. Borreguero, J. M.; Islam, F.; Shrestha, U. R.; Petridis, L., idpflex: Analysis of Intrinsically Disordered Proteins by Comparing Simulations to Small Angle Scattering Experiments. J. Open Source Softw. 2018, 3 (32), 1007.
  11. Tan, P.; Fu, Z.; Petridis, L.; Qian, S.; You, D.; Wei, D.; Li, J. L.; Hong, L., A Two-Fold Structural Classification Method for Determining the Accurate Ensemble of Protein Structures. Commun. Comput. Phys. 2018, 25 (4), 1010–1023.
  12. Petridis, L; Smith, J.C.. “Molecular-level driving forces in the assembly of lignocellulosic biomass and its deconstruction for biofuels and bioproducts.” Nat. Rev. Chem. 2018, 2 (11), 382–389.
  13. Vural, D.; Smith, J. C.; Petridis, L., Dynamics of the lignin glass transition. Phys. Chem. Chem. Phys. 2018, 20 (31), 20504-20512.
  14. Vural, D., Gainaru, C.,  O’Neill, H., Pu, Y., Smith, M. D., Pingali, S. V., Mamontov, E., Davison, B. H.,  Sokolov, A. P., Ragauskas, A. J., Smith, J. C., Petridis, L. “Impact of hydration and temperature history on the structure and dynamics of lignin.” Green Chemistry 2018, 20 (7), 1602-1611.       
  15. Smith, M.D., Cai, C.M., Cheng, X., Petridis, L. & Smith, J.C. Temperature-dependent phase behaviour of tetrahydrofuran-water alters solubilization of xylan to improve co-production of furfurals from lignocellulosic biomass. Green Chemistry 2018, 20, 1612-1620.
  16. Smith, J. C.; Tan, P.; Petridis, L.; Hong, L., Dynamic Neutron Scattering by Biological Systems. Annu. Rev. Biophys. 2018, 47 (1), 335-354.
  17. Kumar, R.; Bhagia, S.; Smith, M. D.; Petridis, L.; Ong, R.; Cai, C. M.; Mittal, A.; Himmel, M. E.; Balan, V.; Dale, B. E.; Ragauskas, A.; Smith, J. C.; Wyman, C. E., Cellulose-Hemicellulose Interactions at Elevated Temperatures Increase Cellulose Recalcitrance to Biological Conversion. Green Chemistry 2018, 20 (4), 921-934.
  18. Yang, H.; Watts, H. D.; Gibilterra, V.; Weiss, T. B.; Petridis, L.; Cosgrove, D. J.; Kubicki, J. D., Quantum Calculations on Plant Cell Wall Component Interactions. Interdisciplinary Sciences: Computational Life Sciences 2018.
  19. Moyer, P.; Smith, M. D.; Abdoulmoumine, N.; Chmely, S. C.; Smith, J. C.; Petridis, L.; Labbe, N., Relationship between lignocellulosic biomass dissolution and physicochemical properties of ionic liquids composed of 3-methylimidazolium cations and carboxylate anions. Physical Chemistry Chemical Physics 2018, 20 (4), 2508-2516.
  20. Smith, M. D.; Cheng, X.; Petridis, L.; Mostofian, B.; Smith, J. C., Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis. Scientific Reports 2017, 7 (1), 14494.
  21. Yang, H.; Wang, T.; Oehme, D.; Petridis, L.; Hong, M.; Kubicki, J. D., Structural factors affecting 13C NMR chemical shifts of cellulose: a computational study. Cellulose 2018, 25 (1), 23-36.
  22. O’Neill, H.; Pingali, S. V.; Petridis, L.; He, J.; Mamontov, E.; Hong, L.; Urban, V.; Evans, B.; Langan, P.; Smith, J. C.; Davison, B. H., Dynamics of water bound to crystalline cellulose. Scientific Reports 2017, 7 (1), 11840.
  23. Polimeni, M.; Petridis, L.; Smith, J. C.; Arcangeli, C., Dynamics at a Peptide–TiO2 Anatase (101) Interface. The Journal of Physical Chemistry B 2017, 121 (38), 8869-8877.
  24. Petridis, L.; Smith, J. C., Conformations of Low-Molecular-Weight Lignin Polymers in Water. ChemSusChem 2016, 9 (3), 289-295.
  25. Mostofian, B.; Cai, C. M.; Smith, M. D.; Petridis, L.; Cheng, X.; Wyman, C. E.; Smith, J. C., Local Phase Separation of Co-solvents Enhances Pretreatment of Biomass for Bioenergy Applications. J. Am. Chem. Soc. 2016, 138 (34), 10869-10878.
  26. Smith, M. D.; Mostofian, B.; Cheng, X.; Petridis, L.; Cai, C. M.; Wyman, C. E.; Smith, J. C., Cosolvent pretreatment in cellulosic biofuel production: effect of tetrahydrofuran-water on lignin structure and dynamics. Green Chem. 2016, 18 (5), 1268-1277.
  27. Vandavasi, V. G.; Putnam, D. K.; Zhang, Q.; Petridis, L.; Heller, W. T.; Nixon, B. T.; Haigler, C. H.; Kalluri, U.; Coates, L.; Langan, P.; Smith, J. C.; Meiler, J.; O’Neill, H., A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers. Plant Physiol. 2016, 170 (1), 123-135.
  28. Smith, M. D.; Petridis, L.; Cheng, X.; Mostofian, B.; Smith, J. C., Enhanced sampling simulation analysis of the structure of lignin in the THF-water miscibility gap. Phys. Chem. Chem. Phys. 2016, 18 (9), 6394-6398.
  29. Smith, M. D.; Mostofian, B.; Petridis, L.; Cheng, X.; Smith, J. C., Molecular Driving Forces behind the Tetrahydrofuran–Water Miscibility Gap. J. Phys. Chem. B 2016, 120 (4), 740-747.
  30. Sangha, A. K.; Petridis, L.; Cheng, X.; Smith, J. C., Relative Binding Affinities of Monolignols to Horseradish Peroxidase. J. Phys. Chem. B 2016, B 120 (31), 7635-7640
  31. Lindner, B.; Petridis, L.; Langan, P.; Smith, J. C., Determination of cellulose crystallinity from powder diffraction diagrams. Biopolymers 2015, 103 (2), 67-73.
  32. Carmona, C.; Langan, P.; Smith, J. C.; Petridis, L., Why genetic modification of lignin leads to low-recalcitrance biomass. Phys. Chem. Chem. Phys. 2015, 17 (1), 358-364.
  33. Vermaas, J. V.; Petridis, L.; Qi, X.; Schulz, R.; Lindner, B.; Smith, J. C., Mechanism of lignin inhibition of enzymatic biomass deconstruction. Biotechnol. Biofuels 2015, 8 (1), 1-16.
  34. Johnson, Q.; Lindsay, R.; Petridis, L.; Shen, T., Investigation of Carbohydrate Recognition via Computer Simulation. Molecules 2015, 20 (5), 7700-7718.
  35. Langan, P.; Petridis, L.; O’Neill, H. M.; Pingali, S. V.; Foston, M.; Nishiyama, Y.; Schulz, R.; Lindner, B.; Hanson, B. L.; Harton, S.; Heller, W. T.; Urban, V.; Evans, B. R.; Gnanakaran, S.; Ragauskas, A. J.; Smith, J. C.; Davison, B. H., Common processes drive the thermochemical pretreatment of lignocellulosic biomass. Green Chem. 2014, 16, 63-68.
  36. Pingali, S.; O’Neill, H.; Nishiyama, Y.; He, L.; Melnichenko, Y.; Urban, V.; Petridis, L.; Davison, B.; Langan, P., Morphological changes in the cellulose and lignin components of biomass occur at different stages during steam pretreatment. Cellulose 2014, 21 (2), 873-878.
  37. Hong, L.; Petridis, L.; Smith, J. C., Biomolecular Structure and Dynamics with Neutrons: The View from Simulation. Isr. J. Chem. 2014, 54 (8-9), 1264-1273.
  38. Petridis, L.; O’Neill, H. M.; Johnsen, M.; Fan, B.; Schulz, R.; Mamontov, E.; Maranas, J.; Langan, P.; Smith, J. C., Hydration Control of the Mechanical and Dynamical Properties of Cellulose. Biomacromolecules 2014, 15 (11), 4152-4159
  39. Erler, J.; Zhang, R.; Petridis, L.; Cheng, X.; Smith, Jeremy C.; Langowski, J., The Role of Histone Tails in the Nucleosome: A Computational Study. Biophys. J. 2014, 107 (12), 2911-2922.
  40. Mayes, M.; Jagadamma, S.; Ambaye, H.; Petridis, L.; Lauter, V., Neutron reflectometry reveals the internal structure of organic compounds deposited on aluminum oxide. Geoderma 2013, 192, 182-188.
  41. Sawada, D.; Nishiyama, Y.; Petridis, L.; Parthasarathi, R.; Gnanakaran, S.; Forsyth, V. T.; Wada, M.; Langan, P., Structure and dynamics of a complex of cellulose with EDA: insights into the action of amines on cellulose. Cellulose 2013, 20 (4), 1563-1571.
  42. Lindner, B.; Petridis, L.; Schulz, R.; Smith, J. C., Solvent-Driven Preferential Association of Lignin with Regions of Crystalline Cellulose in Molecular Dynamics Simulation. Biomacromolecules 2013, 14 (10), 3390-3398.
  43. Petridis, L.; Ambaye, H.; Jagadamma, S.; Kilbey, S. M.; Lokitz, B. S.; Lauter, V.; Mayes, M. A., Spatial Arrangement of Organic Compounds on a Model Mineral Surface: Implications for Soil Organic Matter Stabilization. Environ. Sci. Technol. 2013, 48 (1), 79-84.
  44. Sangha, A. K.; Petridis, L.; Smith, J. C.; Ziebell, A.; Parks, J. M., Molecular simulation as a tool for studying lignin. Environ. Prog. Sustainable Energy 2012, 31 (1), 47-54.
  45. Langan, P.; Evans, B. R.; Foston, M.; Heller, W. T.; O’Neill, H.; Petridis, L.; Pingali, S. V.; Ragauskas, A. J.; Smith, J. C.; Urban, V. S., Neutron technologies for bioenergy research. Ind. Biotechnol. 2012, 8 (4), 209-216.
  46. Smith, J. C.; Krishnan, M.; Petridis, L.; Smolin, N., Integration of neutron scattering with computer simulation to study the structure and dynamics of biological systems. In Dynamics of Biological Macromolecules by Neutron Scattering, 2011; pp 99-108.
  47. Petridis, L.; Pingali, S. V.; Urban, V.; Heller, W. T.; O’Neil, H. M.; Foston, M.; Ragauskas, A.; Smith, J. C., Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation. Phys. Rev. E 2011, 83 (6), 061911.
  48. Petridis, L.; Schulz, R.; Smith, J. C., Simulation Analysis of the Temperature Dependence of Lignin Structure and Dynamics. J. Am. Chem. Soc. 2011, 133 (50), 20277-20287.
  49. Pingali, S. V.; O’Neill, H. M.; McGaughey, J.; Urban, V. S.; Rempe, C. S.; Petridis, L.; Smith, J. C.; Evans, B. R.; Heller, W. T., Small Angle Neutron Scattering Reveals pH-dependent Conformational Changes in Trichoderma reesei Cellobiohydrolase I IMPLICATIONS FOR ENZYMATIC ACTIVITY. J. Biol. Chem. 2011, 286 (37), 32801-32809.
  50. Petridis, L.; Xu, J.; Crowley, M. F.; Smith, J. C.; Cheng, X., Atomistic simulation of lignocellulosic biomass and associated cellulosomal protein complexes. In ACS Symposium Series, 2010; Vol. 1052, pp 55-73.
  51. Schulz, R.; Lindner, B.; Petridis, L.; Smith, J., Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer. J. Chem. Theory Comput. 2009, 5 (10), 2798-2808.
  52. Petridis, L.; Smith, J. C., A Molecular Mechanics Force Field for Lignin. J. Comput. Chem. 2009, 30 (3), 457-467.
  53. Petridis, L.; Smith, J.; Stevens, R., Cellulosic ethanol: progress towards a simulation model of lignocellulosic biomass – art. no. 012055. 2008; 125, p 12055-12055.
  54. Petridis, L.; Terentjev, E. M., Quenched disorder and spin-glass correlations in XY nematics. J. Phys. A: Math. Gen. 2006, 39 (31), 9693.
  55. Petridis, L.; Terentjev, E. M., Nematic-isotropic transition with quenched disorder. Phys. Rev. E 2006, 74 (5).

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