Publications
After joining Syracuse University
Bold: ACompChemLab member. | * Corresponding authors
27. D. Sil, E. Osmanbasic, S. C. Mandal, A. Acharya, and C. Dutta.
Variable Non-Gaussian Transport of Nanoplastic on Supported Lipid Bilayers in Saline Conditions.
Submitted
26. S. Maity and A. Acharya*
Many roles of carbohydrates: A computational spotlight on the coronavirus S protein binding.
25. V. G. Lui, M. Hoenig, B. Cabrera-Martinez, R. M. Baxter, J. E. Garcia-Perez, A. Acharya, K. Lundquist, J. Capera, P. Matusewicz, F. A. Hartl, M. D’Abramo, J. Alba, E.-M. Jacobsen, D. Niewolik, M. Lorenz, U. Pannicke, A. S. Schulz, K.-M. Debatin, W. W. Schamel, S. Minguet, J. C. Gumbart, M. L. Dustin, J. C. Cambier, K. Schwarz, E. W.Y. Hsieh
A partial human LCK defect causes a T cell immunodeficiency with intestinal 2 inflammation.
24. S. Sarkar*, A. Shil, S. Maity, Y. L. Jung, M. Dai, A. Acharya*, and K. H. Ahn*
A General Strategy Toward pH-Resistant Phenolic Fluorophores for High-Fidelity Sensing and Bioimaging Application.
23. Y. Li, A. Acharya, L. Yang, J. Liu, E. Tajkhorshid, H. I. Zgurskaya, M. Jackson, and J. C. Gumbart
Insights into substrate transport and water permeation in the mycobacterial transporter MmpL3.
Biophys. J. 2023, 122, 2342-2352
22. Y. T. Pang, A. Acharya, D. L. Lynch, A. Pavlova, J. C. Gumbart; first authorship shared
SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact.
Before joining Syracuse University
21. C. Stevens, S. Babii, A. N. Pandya, W. Li, Y. Li, J. Mehla, R. Scott, P. Hegde, P. K. Prathipati, A. Acharya, J. Liu, J. C. Gumbart, J. North, M. Jackson, and H. I. Zgurskaya.
Proton transfer activity of the reconstituted Mycobacterium tuberculosis MmpL3 is modulated by substrate mimics and inhibitors.
Proc. Nat. Acad. Sci. USA. 2022, 119, e2113963119
Press: Phys.org, ThePrint, Hindustan Times, and Times Now
20. B. Yu, M. R. Choudhury, X. Yang, S. L. Benoit, E. Womack, K. V. M. Lyles, A. Acharya, A. Kumar, C. Yang, A. Pavlova, M. Zhu, Z. Yuan, J. C. Gumbart, D. W. Boykin, R. J. Maier, Z. Eichenbaum, and B. Wang
Restoring and enhancing the potency of existing antibiotics against drug-resistant Gram-negative bacteria through the development of potent small-molecule adjuvants.
19. P. J. Dahl, S. M. Yi, Y. Gu, A. Acharya, C. Shipps, J. Neu, J. P. O’Brien, U. N. Morzan, S. Chaudhuri, M. J. Guberman-Pfeffer, D. Vu, S. E. Yalcin, V. S. Batista, and N. S. Malvankar
A 300-fold conductivity increase in microbial cytochrome nanowires due to temperature-induced restructuring of hydrogen bonding networks.
Press: ErekAlert, Phys.org, SciTechDaily, ChemEurope, Bioengineer, and Yale News
18. A. Acharya, D. Yi, A. Pavlova, V.A. Agarwal, and J. C. Gumbart
Resolving the hydride transfer pathway in oxidative conversion of proline to pyrrole.
17. A. Acharya*, D. L. Lynch, A. Pavlova, Y. T. Pang, and J. C. Gumbart; *co-corresponding author.
ACE2 glycans preferentially interact with SARS-CoV-2 over SARS-CoV.
16. A. Pavlova, Z. Zhang, A. Acharya, D. L. Lynch, Y. T. Pang, Z. Mou, J. M. Parks, C. Chipot, and J. C. Gumbart;
Machine learning reveals the critical interactions for SARS-CoV-2 spike protein binding to ACE2
15. D. Yi, A. Acharya, J. C. Gumbart, W. Gutekunst, and V. Agarwal
Gatekeeping ketosynthases dictate initiation of assembly line biosynthesis of pyrrolic polyketides.
14. Z. Zhang, D. Ryoo, C. Balusek, A. Acharya, M. O. Rydmark, D. Linke, And J. C. Gumbart
Resolving the relationships between sequence, shape, and size of β-barrel membrane proteins.
13. A. Pavlova, D. L. Lynch, I. Daidone, L. Zanetti-Polzi, M. D. Smith, C. Chipot, D. W. Kneller, A. Kovalevsky, L. Coates, A. A. Golosov, C. J. Dickson, C. Velez-Vega, J. S. Duca, J. V. Vermaas, Y. T. Pang, A. Acharya, J. M. Parks, J. C. Smith, and J. C. Gumbart.
Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease.
12. A. Acharya, R. Agarwal, M. B. Baker, J. Baudry, D. Bhowmik, S. Boehm, K. G. Byler, S. Y. Chen, L. Coates, C. J. Cooper, O. Demerdash, I. Daidone, J. D. Eblen, S. Ellingson, S. Forli, J. Glaser, J. C. Gumbart, J. Gunnels, O. Hernandez, S. Irle, D. W. Kneller, A. Kovalevsky, J. Larkin, T. J. Lawrence, S. LeGrand, S.-H. Liu, J.C. Mitchell, G. Park, J.M. Parks, A. Pavlova, L. Petridis, D. Poole, L. Pouchard, A. Ramanathan, D. M. Rogers, D. Santos-Martins, A. Scheinberg, A. Sedova, Y. Shen, J. C. Smith*, M. D. Smith, C. Soto, A. Tsaris, M. Thavappiragasam, A. F. Tillack, J. V. Vermaas, V. Q. Vuong, J. Yin, S. Yoo, M. Zahran, and L. Zanetti-Polzi
Supercomputer-based ensemble docking drug discovery pipeline with application to Covid-19.
J. Chem. Inf. Model. 2020, 60, 5832–5852
Press: ScienMag, Bioengineer.org, Phys.org, EurekAlert, and Observer.
11. S. E. Yalcin, J. P. O’Brien, Y. Gu, K. Reiss, S. M. Yi, R. Jain, V. Srikanth, P. Dahl, W. Huynh, D. Vu, A. Acharya, S. Chaudhuri, T. Varga, V. S. Batista, and N. S. Malvankar
Electric field stimulates production of highly conductive microbial OmcZ nanowires
Nat. Chem. Biol. 2020, 16, 1136-1142
News and Views, Press: Yale press release, Scientific American, Phys.org, ErekAlert, Live Science, Oxford Instruments, NBC-SYFY, American Society of Microbiology (podcast @16:30), greenreport (italy), SciTechDaily, and SpaceDaily. In 98th percentile across all journals.
10. A. Acharya, J. Stockmann, L. Beyer, A. Nabers, J. C. Gumbart, K. Gerwert, and V. S. Batista
The effect of (-)-epigallocatechin-3-gallate on the amyloid-ß secondary structure.
9. K. W. East, J. C. Newton, U. N. Morzan, Y. Narkhede, A. Acharya, E. Skeens, G. Jogl, V. S. Batista, G. Palermo, G. P. Lisi
Allosteric motions of the CRISPR-Cas9 HNH nuclease probed by NMR and molecular dynamics.
8. T. Sen, A. V. Mamontova, A. V. Titelmayer, A. M. Shakhov, A. A. Astafiev, A. Acharya, K. A. Lukyanov, A. I. Krylov, and A. M. Bogdanov
Influence of the first chromophore-forming residue on photobleaching and oxidative photoconversion of EGFP and EYFP.
7. S. Chaudhuri, A. Acharya, E. T. J. Nibbering, and V. S. Batista
Regioselective ultrafast photoinduced electron transfer from naphthols to halocarbon solvents.
6. J. A. Christensen, B. T. Phelan, S. Chaudhuri, A. Acharya, V. S. Batista, and M. R. Wasielewski
Phenothiazine radical cation excited states as super-oxidants for energy-demanding reactions.
5. A. Acharya*, S. Chaudhuri, and V. S. Batista; * co-corresponding author.
Can TDDFT describe excited electronic states of naphthol photoacids? A closer look with EOM-CCSD.
4. A. Acharya, A. M. Bogdanov, B. L. Grigorenko, K. B. Bravaya, A. V. Nemukhin, K. A. Lukyanov, and A. I. Krylov
Photoinduced chemistry in fluorescent proteins: Curse or blessing?
3. P. K. Gurunathan, A. Acharya, D. Ghosh, D. Kosenkov, I. Kaliman, Y. Shao, A. I. Krylov, and L. V. Slipchenko; first authorship shared.
The extension of the effective fragment potential method to macromolecule.
2. A. M. Bogdanov, A. Acharya, A. Titelmayer, A. V. Mamontova, K. B. Bravaya, A. B. Kolomeisky, K. A. Lukyanov, and A. I. Krylov; first authorship shared.
Turning on and off photoinduced electron transfer in fluorescent proteins by pi-stacking, halide binding, and Tyr145 mutations.
1. D. Ghosh, A. Acharya, S.C. Tiwari, and A.I. Krylov
Towards understanding the redox properties of model chromophores from the green fluorescent protein family: An interplay between conjugation, resonance stabilization, and solvent effects.
PERSPECTIVE
1.B. Rudshteyn, A. Acharya, and V. S. Batista
Is the supporting information the venue for reproducibility and transparency?
J. Phys. Chem. A 2017, 121, 968. Link To Article
J. Phys. Chem. B 2017, 121, 11425. Link To Article
J. Phys. Chem. C 2017, 121, 28212. Link To Article