Abhishek Singharoy

Assistant Professor
Faculty
TEMPE Campus
Mailcode
1604
Associate Faculty
Faculty
TEMPE Campus
Mailcode
1604

Biography

Abhishek Singharoy is an Assistant Professor in the School of Molecular Sciences at Arizona State University. His research is at the confluence of statistical mechanics, molecular biology, hybrid modeling and large-scale computer simulations.

The unified theme of Singharoy laboratory’s research is to combine rigorous statistical mechanical methodologies with state-of-the-art computational approaches for capturing cell-scale biological responses with atomic precision. Many of the high-throughput computations essential for approaching this grand challenge are pioneered in the group's past and ongoing work on molecular dynamics, free energy and kinetic modeling methods. Spanning multiple spatio-temporal scales ranging from that of single proteins to complexes up to the whole cell, these computations have led to discoveries in voltage-sensing and ion transport mechanisms of Ci-VSP and NRAMP proteins, ribosomal insertion pathways via YidC and holotranslocon complexes, allosteric networks controlling immunogenicity of Human Papilloma virus, and the bioenergetics of bacterial membranes. The laboratory's most recent endeavors focus on dissecting the evolutionary design principles of mitochondrial respiration, in particular, through investigation of an outer membrane-embedded supercomplex called the respirasome. This study brings to light a couple of cutting-edge biomedical applications, namely, determination of the molecular origins of cellular ageing and programmed cell death, and creation of a novel computer-aided pipeline pertaining to intricate pathology of the respiratory network. To put together large-scale membrane systems in atomic detail requires theoretical advances in terms of fitting/refining structural data from experiments. To address this need, group members have been developing and applying an array of flexible-fitting tools that derive high-resolution molecular models from low-resolution experimental data, such as from X-ray crystallography, electron microscopy, quantitative mass-spectrometry and chemical cross-linking. 

Some recent research highlights are provided here:  

http://ascr-discovery.science.doe.gov/2018/06/cellular-energy-crisis/

https://www.olcf.ornl.gov/2017/05/09/assembling-lifes-molecular-motor/

https://www.olcf.ornl.gov/2017/06/27/annual-user-meeting-spotlights-titan-summit-and-deep-learning/

https://beckman.illinois.edu/news/2016/08/singharoy

https://beckman.illinois.edu/news/2015/08/cyanostar-atomic-structure

https://www.olcf.ornl.gov/2018/02/07/new-discoveries-within-sight/

Google Scholar

Publications

  • Ali, Md. E.; Singharoy, A.; Datta, S.N. Molecular Tailoring and Prediction of Strongly Ferromagnetically Coupled Trimethylenemethane-Based Nitroxide Diradicals J. Phys. Chem. A 2007, 111, 5523.
  • Singharoy, A.; Yesnik, A.; Ortoleva, P. J. Multiscale Analytic Continuation Approach to Nanosystem Simulation: Applications to Virus Electrostatics J.Chem. Phys. 2010, 132, 174112 (Reviewed in Virtual Journals in Science and Technology).
  • Singharoy, A.; Cheluvaraja, S.; Ortoleva, P. J. Order Parameters for Macromolecules: Application to Multiscale Simulation J. Chem. Phys. 2011, 134, 044104 (Reviewed in Virtual Journals in Science and Technology).
  • Joshi, H.; Singharoy, A.; Sereda, Y.; Cheluvaraja, S.; Ortoleva, P. J. Multiscale Simulation of Microbe Structure and Dynamics Prog. Biophys. Mol. Biol. 2011, 107, 200.
  • Singharoy, A. ; Joshi, H.; Ortoleva, P.J.; Miao, Y. Space Warping Order Parameters and Symmetry: Application to Multiscale Simulation of Macromolecular Assemblies J. Phys. Chem. B 2012, 116, 8423 .
  • Singharoy, A.; Sereda, Y.; Ortoleva, P. J. Hierarchical Order Parameters for Macromolecular Assembly Simulation I: Construction and Dynamical Properties of Order Parameters J. Chem. Theor. Comput. 2012, 8, 1379 .
  • Pankavich, S.; Singharoy, A. ; Ortoleva, P.J. Hierarchical Multiscale Modeling of Macromolecules and their Assemblies Soft Matter 2013, 9, 4319.
  • Joshi, H.; Lewis, K.; Singharoy, A. ; Ortoleva, P.J. Epitope Engineering and Molecular Metrics of Immunogenicity: A Computational Approach to VLP-based Vaccine DesignVaccine 2013, 31, 4841.
  • Singharoy, A.* ; Polavarapu, A.*; Joshi, H.; Baik, M.; Ortoleva, P. J. Epitope Fluctuation in the Human Papillomavirus are under Dynamic Allosteric Control:a Computational Evaluation of a New Vaccine Design Strategy J. Am. Chem. Soc. 2013, 135, 18458.
  • Li, Q.; Wanderling, S.; Paduch, M.; Medovoy, D.; Singharoy, A. ; Mcgreevy, R.; Villalba-Galea, C.; Hulse, R.E.; Roux, B.; Schulten, K.; Kossaikoff, A.; Perozo, E. Structural mechanism of Voltage-dependent Gating in an Isolated Voltage-sensing Domain Nat. Struct. Chem. Biol. 2014, 21, 244.
  • Wickles, S.; Singharoy, A. ; Andreani, J.; Seemayer, S.; Bischoff, L.; Berninghausen, O.; Soeding, J.; Schulten, K.; Van der Sluis, E. O.; Beckmann, R. A Structural Model of the Active Ribosome-bound Membrane Protein Insertase YidCi eLife 2014, 3, e03035 .
  • Mcgreevy, R.*, Singharoy, A.* ; Li, Q.; Zhang, J.; Xu, D.; Perozo, E.; Schulten, K. xMDFF: Molecular dynamics flexible fitting of low-resolution X-Ray structures Acta. Cryst. D 2014, 70, 2344.
  •  Singharoy, A.* ; Venkatakrishnan, B.*; Liu, Y.*; Mayne, C.; Lee, S.; Chen, C.; Zlotnick, A.; Schulten, K.; Flood, A. Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles J. Am. Chem. Soc. 2015, 137, 8810.
  • Singharoy, A.* ; Liu, Y.*; Mayne, C.*; Sengupta, A.; Raghavachari, A.; Schulten, K.; Flood, A. Flexibility Coexists with Shape-Persistence in Cyanostar Macrocycles J. Am. Chem. Soc. 2016, 138, 4843.
  • Sener, M.; Strumpher, J.; Singharoy, A. ; Hunter, N.; Schulten, K. Overall energy conversion efficiency of a photosynthetic vesicle eLife 2016, 5, e09541.
  • Singharoy, A. ; Teo, I.; Mcgreevy, R.; Stone, J.; Jhao, J.; Schulten, K. Molecular dynamics-based refinement and validation with Resolution Exchange MDFF for sub-5 Å cryo-electron microscopy maps eLife 2016, 5, e16105.
  • Bozzi, A.; Bane, L.; Singharoy, A. ; Chipot, C.; Schulten, K.; Gaudet, R. Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters PNAS 2016, 113, 10310.
  • Singharoy, A. ; Barragan, A.; Thangapandian, S.; Tajkhorshid, E.; Schulten, K. Binding site recognition and docking dynamics of a single electron transport protein: revisiting cytochrome c2 J. Am. Chem. Soc. 2016, 138, 12077.
  • 24. Singharoy, A. ; Moradi, M.; Chipot, C.; Schulten, K. Chemomechanical coupling in hexameric protein-protein interfaces harness energy within V- type ATPases J. Am. Chem. Soc 2017, 139, 293.

Courses

Fall 2018
Course NumberCourse Title
CHM 113General Chemistry I
Spring 2018
Course NumberCourse Title
CHM 113General Chemistry I