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Publications

#co-first author  *corresponding author

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  • ​Liang R*, Guan L* (2024) Atomic-Level Free Energy Landscape Reveals Cooperative Symport Mechanism of Melibiose Transporter. bioRxiv:2024.2008.2021.608993. DOI:10.1101/2024.08.21.608993.

  • Xu T, Wang Y, Jin S, Rahman AU, Yan X, Yuan Q, Liu H, Wang J-Y, Yan W, Jiao Y, Liang R*, Li G* (2024) Amino Turbo Chirality and Its Asymmetric Control. Research 7:0474. (PDF)

  • Hariharan P, Bakhtiiari A, Liang R*, Guan L* (2024) Distinct roles of the major binding residues in the cation-binding pocket of the melibiose transporter MelB. J. Biol. Chem. 300(7):107427. (PDF)

  • Pandey A, Poirier B*, Liang R*. (2024) Development of Parallel On-the-Fly Crystal Algorithm for Global Exploration of Conical Intersection Seam Space. J. Chem. Theory Comput. DOI: 10.1021/acs.jctc.4c00292 (PDF)

  • Hariharan P, Shi Y, Katsube S, Willibal K, Burrows ND, Mitchell P, Bakhtiiari A, Stanfield S, Pardon E, Kaback RH, Liang R, Steyaert J, Viner R, Guan L*. (2024)  Mobile barrier mechanisms for Na+-coupled symport in an MFS sugar transporter. eLife. DOI: https://doi.org/10.7554/eLife.92462.3 (Peer-reviewed and accepted research article)

  • Costa G. J, Egbemhenghe A, Liang R* Computational Characterization of the Reactivity of Compound I in Unspecific Peroxygenases. J. Phys. Chem. B.  DOI: https://doi.org/10.1021/acs.jpcb.3c06311 (PDF)

  • Costa G. J, Liang R* (2023) Understanding the multifaceted mechanism of Compound I formation in unspecific peroxygenases through multiscale simulations. J. Phys. Chem. B.  DOI: https://doi.org/10.1021/acs.jpcb.3c04589 (PDF)

  • Bakhtiiari A, Costa G. J, Liang R* (2023) On the Simulation of Thermal Isomerization of Molecular Photoswitches in Biological Systems. J. Chem. Theory Comput. 19 (18), 6484–6499 (PDF)

  • Liang R.*, Bakhtiiari, A. (2022) Multiscale simulation unravels the light-regulated reversible inhibition of dihydrofolate reductase by phototrexate. J. Chem. Phys. 156 (24), 245102. (PDF)

  • Katsube S, Liang R,* Amin A, Hariharan P, & Guan L* (2022) Molecular basis for the cation selectivity of Salmonella typhimurium melibiose permease. J. Mol. Biol.:167598. (PDF)

  • Liang R* & Bakhtiiari A (2022) Effects of Enzyme–Ligand Interactions on the Photoisomerization of a Light-Regulated Chemotherapeutic Drug. J. Phys. Chem. B 126:2382-2393. (PDF)

  • Liang R,* Das D & Bakhtiiari A (2021) Protein confinement fine-tunes the aggregation-induced emission in the human serum albumin. Phys. Chem. Chem. Phys. 23, 26263-26272. (PDF)

  • Liang R* (2021) First-principles non-adiabatic dynamics simulation of azobenzene photodynamics in solutions. J. Chem. Theory Comput. 17 (5), 3019-3030. (PDF)

  • Liang R, Yu JK, Meisner J, Liu F, & Martinez TJ* (2021) Electrostatic Control of Photoisomerization in Channelrhodopsin 2. J. Am. Chem. Soc. 143, 5425-5437.

  • Pinney MM, Mokhtari D, Akiva E, Yabukarski F, Sanchez DM, Liang R, Doukov T, Martinez TJ, Babbitt PC, & Herschlag D (2021) Parallel Molecular Mechanisms for Enzyme Temperature Adaptation. Science. 371, eaay2784

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Before joining Texas Tech University in 2020

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  • Yu JK, Bannwarth C, Liang R, Hohenstein EG, Martínez TJ* (2020) Nonadiabatic Dynamics Simulation of the Wavelength-Dependent Photochemistry of Azobenzene Excited to the nπ* and ππ* Excited States. J. Am. Chem. Soc. 142 (49), 20680-20690.

  • Yu JK, Liang R, Liu F, & Martínez TJ* (2019) First-Principles Characterization of the Elusive I Fluorescent State and the Structural Evolution of Retinal Protonated Schiff Base in Bacteriorhodopsin. J. Am. Chem. Soc. 141(45):18193-18203.

  • Watkins LC, Liang R, Swanson JMJ, DeGrado WF, & Voth GA* (2019) Proton Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel. J. Am. Chem. Soc. 141(29):11667-11676.

  • Liang R, Liu F, & Martínez TJ* (2019) Nonadiabatic Photodynamics of Retinal Protonated Schiff Base in Channelrhodopsin 2. J. Phys. Chem. Lett. 10(11):2862-2868.

  • Liang R,# Cotton SJ,# Binder R,# Hegger R, Burghardt I,* & Miller WH* (2018) The symmetrical quasi-classical approach to electronically nonadiabatic dynamics applied to ultrafast exciton migration processes in semiconducting polymers. J. Chem. Phys. 149(4):044101. (Editor’s Pick, Cover Article)

  • Cotton SJ, Liang R, & Miller WH* (2017) On the adiabatic representation of Meyer-Miller electronic-nuclear dynamics. J. Chem. Phys. 147:064112. (Editor’s Choice)

  • Pinney MM, Natarajan A, Yabukarski F, Sanchez DM, Liu F, Liang R, Doukov T, Schwans JP, Martinez TJ, & Herschlag D* (2018) Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein. J. Am. Chem. Soc. 140(31):9827-9843.

  • Liang R, Swanson JMJ*, Wikström M, & Voth GA* (2017) Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase. Proc. Natl. Acad. Sci. U. S. A. 114:5924-5929.

  • Liang R, Swanson JMJ, Madsen JJ, Hong M, DeGrado WF,* & Voth GA* (2016) Acid activation mechanism of the influenza A M2 proton channel. Proc. Natl. Acad. Sci. U. S. A. 113:E6955-E6964.

  • Liang R, Swanson JMJ, Peng Y, Wikström M, & Voth GA* (2016) Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase. Proc. Natl. Acad. Sci. U. S. A. 113(27):7420-7425.

  • Lee S,# Liang R,# Voth GA, & Swanson JMJ* (2016) Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins. J. Chem. Theory Comput. 12(2):879-891.

  • Liang R, Li H, Swanson JMJ, & Voth GA* (2014) Multiscale simulation reveals a multifaceted mechanism of proton permeation through the influenza A M2 proton channel. Proc. Natl. Acad. Sci. U. S. A. 111(26):9396-9401.

  • Liang R, Swanson JMJ, & Voth GA* (2014) Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel. J. Chem. Theory Comput. 10(1):451-462.

  • Choi TH,# Liang R,# Maupin CM, & Voth GA* (2013) Application of the SCC-DFTB Method to Hydroxide Water Clusters and Aqueous Hydroxide Solutions. J. Phys. Chem. B 117(17):5165-5179.

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