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Madushanka Manathunga
Madushanka Manathunga
Research Associate, Department of Chemistry, Michigan State University
Verified email at msu.edu
Title
Cited by
Cited by
Year
Amber 2021
DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ...
University of California, San Francisco, 2021
51502021
AmberTools
DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, ...
Journal of chemical information and modeling 63 (20), 6183-6191, 2023
1042023
Probing the photodynamics of rhodopsins with reduced retinal chromophores
M Manathunga, X Yang, HL Luk, S Gozem, LM Frutos, A Valentini, ...
Journal of Chemical Theory and Computation 12 (2), 839-850, 2016
512016
Design, synthesis, and dynamics of a green fluorescent protein fluorophore mimic with an ultrafast switching function
M Paolino, M Gueye, E Pieri, M Manathunga, S Fusi, A Cappelli, ...
Journal of the American Chemical Society 138 (31), 9807-9825, 2016
502016
Engineering the vibrational coherence of vision into a synthetic molecular device
M Gueye, M Manathunga, D Agathangelou, Y Orozco, M Paolino, S Fusi, ...
Nature communications 9 (1), 313, 2018
462018
An average solvent electrostatic configuration protocol for Qm/mm free energy optimization: Implementation and application to rhodopsin systems
Y Orozco-Gonzalez, M Manathunga, MDC Marín, D Agathangelou, ...
Journal of chemical theory and computation 13 (12), 6391-6404, 2017
352017
Impact of electronic state mixing on the photoisomerization time scale of the retinal chromophore
M Manathunga, X Yang, Y Orozco-Gonzalez, M Olivucci
The Journal of Physical Chemistry Letters 8 (20), 5222-5227, 2017
352017
Parallel implementation of density functional theory methods in the quantum interaction computational kernel program
M Manathunga, Y Miao, D Mu, AW Götz, KM Merz Jr
Journal of Chemical Theory and Computation 16 (7), 4315-4326, 2020
342020
Open-source multi-GPU-accelerated QM/MM simulations with AMBER and QUICK
VWD Cruzeiro, M Manathunga, KM Merz Jr, AW Götz
Journal of Chemical Information and Modeling 61 (5), 2109-2115, 2021
252021
Quantum–classical simulations of rhodopsin reveal excited-state population splitting and its effects on quantum efficiency
X Yang, M Manathunga, S Gozem, J Léonard, T Andruniów, M Olivucci
Nature chemistry 14 (4), 441-449, 2022
242022
ReaxFF/AMBER—a framework for hybrid reactive/nonreactive force field molecular dynamics simulations
A Rahnamoun, MC Kaymak, M Manathunga, AW Götz, ACT Van Duin, ...
Journal of chemical theory and computation 16 (12), 7645-7654, 2020
232020
Electronic State Mixing Controls the Photoreactivity of a Rhodopsin with all-trans Chromophore Analogues
M Manathunga, X Yang, M Olivucci
The journal of physical chemistry letters 9 (21), 6350-6355, 2018
232018
Harnessing the power of multi-GPU acceleration into the quantum interaction computational kernel program
M Manathunga, C Jin, VWD Cruzeiro, Y Miao, D Mu, K Arumugam, ...
Journal of Chemical Theory and Computation 17 (7), 3955-3966, 2021
202021
On the transition from a biomimetic molecular switch to a rotary molecular motor
M Paolino, T Giovannini, M Manathunga, L Latterini, G Zampini, R Pierron, ...
The Journal of Physical Chemistry Letters 12 (16), 3875-3884, 2021
172021
Quantum mechanics/molecular mechanics simulations on NVIDIA and AMD graphics processing units
M Manathunga, HM Aktulga, AW Götz, KM Merz Jr
Journal of Chemical Information and Modeling 63 (3), 711-717, 2023
162023
Computer-aided drug design, quantum-mechanical methods for biological problems
M Manathunga, AW Götz, KM Merz Jr
Current Opinion in Structural Biology 75, 102417, 2022
132022
Computational and spectroscopic characterization of the photocycle of an artificial rhodopsin
M Manathunga, AJ Jenkins, Y Orozco-Gonzalez, A Ghanbarpour, ...
The journal of physical chemistry letters 11 (11), 4245-4252, 2020
62020
Free Energy Computation for an Isomerizing Chromophore in a Molecular Cavity via the Average Solvent Electrostatic Configuration Model: Applications in Rhodopsin and Rhodopsin …
DM Nikolaev, M Manathunga, Y Orozco-Gonzalez, AA Shtyrov, ...
Journal of Chemical Theory and Computation 17 (9), 5885-5895, 2021
52021
Torsionally broken symmetry assists infrared excitation of biomimetic charge-coupled nuclear motions in the electronic ground state
G Chatterjee, A Jha, A Blanco-Gonzalez, V Tiwari, M Manathunga, ...
Chemical Science 13 (32), 9392-9400, 2022
42022
Geometry Optimization: A Comparison of Different Open-Source Geometry Optimizers
A Shajan, M Manathunga, AW Götz, KM Merz Jr
Journal of Chemical Theory and Computation 19 (21), 7533-7541, 2023
12023
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