Dr. Muhamed Amin
Ph.D Physics
I use and implement computer algorithms including machine learning models to study biochemical/biophysical reactions in proteins. These interactions include ligand-protein binding, DNA-protein interactions, proton and electron transfer, photosynthesis, laser alignment of protein and imaging proteins with free electron lasers.
2024
Amin,
M., Kaur, D., Brudvig, G. W., & Brooks, B. R. (2024).
Mapping the Oxygens in the Oxygen-Evolving Complex of
Photosystem II by Their Nucleophilicity Using Quantum
Descriptors. Journal of Chemical Theory and
Computation, 20(3), 1414–1422. https://doi.org/10.1021/acs.jctc.3c00926
2023
Kapuścińska,
K., Dukała, Z., Doha, M., Ansari, E., Wang, J., Brudvig, G.
W., Brooks, B., & Amin, M. (2024). Bridging
the Coordination Chemistry of Small Compounds and Metalloproteins
Using Machine Learning. Journal of chemical
information and modeling, 64(7), 2586-2593. https://doi.org/10.1021/acs.jcim.3c01564
Ranepura,
G. A., Mao, J., Vermaas, J. V., Wang, J., Gisriel, C. J., Wei, R.
J., Ortiz-Soto, J., Uddin, M. R., Amin, M., Brudvig,
G. W., & Gunner, M. R. (2023). Computing the Relative
Affinity of Chlorophylls a and b to Light-Harvesting Complex
II. Journal of Physical Chemistry B,
127(51), 10974-10986. https://doi.org/10.1021/acs.jpcb.3c06273
Abdelmouleh,
M., Amin, M., Lalande, M., Schlathölter,
T., & Poully, J.-C. (2023). Ionizing radiation
induces cross-linking of two noncovalently-bound collagen mimetic
peptide triple helices in the absence of molecular
environment. PPCP : Physical Chemistry Chemical
Physics, 25(42), 29249-29256. https://doi.org/10.1039/D3CP03264G
Gisriel,
C. J., Shen, G., Flesher, D. A., Kurashov, V., Golbeck, J. H.,
Brudvig, G. W., Amin, M., & Bryant, D. A. (2023).
Structure of a dimeric photosystem II complex from a
cyanobacterium acclimated to far-red light.
Journal of Biological Chemistry,
299(1), Article 102815. https://doi.org/10.1016/j.jbc.2022.102815
2022
Ali,
A., Basuni, M., Shams-Eldin, R., Pilz, L., Hashem, T., Heinle, M.,
Nefedov, A., Amin, M., Tsotsalas, M., Drazic, G.,
Hassanien, A., & Alkordi, M. H. (2023). Engineering of
Molybdenum Sulfide Nanobunches on MWCNTs: Modulation of Active
Sites and Electronic Conductivity via Controllable Solvothermal
Deposition. ACS Applied Nano
Materials, 6(5), 3627–3636. https://doi.org/10.1021/acsanm.2c05311
Amin,
M. (2023). Predicting the oxidation states of Mn ions
in the oxygen-evolving complex of photosystem II using supervised
and unsupervised machine learning. Photosynthesis
Research, 156, 89–100. https://doi.org/10.1007/s11120-022-00941-8
Ali,
F., Shafaa, M. W., & Amin, M. (2022).
Computational Approach for Probing Redox Potential for
Iron-Sulfur Clusters in Photosystem I.
Biology, 11(3), Article 362. https://doi.org/10.3390/biology11030362
Hashim,
S., Farooq, S., Syriopoulos, E., Cremer, K. D. L. L., Vogt, A., de
Jong, N., Aguado, V. L., Popescu, M., Mohamed, A.
K., & Amin, M. (2022). Machine Learning
Model for Predicting Number of COVID-19 Cases in Countries with Low
Number of Tests. Open Bioinformatics
Journal, 15, Article e187503622208290. https://doi.org/10.2174/18750362-v15-e2208290
Goher,
S. S., Ali, F., & Amin, M. (2022). The Delta
variant mutations in the receptor binding domain of SARS-CoV-2 show
enhanced electrostatic interactions with the ACE2.
Medicine in Drug Discovery, 13,
Article 100114. https://doi.org/10.1016/j.medidd.2021.100114
2021
Welker,
S., Amin, M., & Küpper, J. (2022).
CMInject: Python framework for the numerical simulation of
nanoparticle injection pipelines. Computer Physics
Communications, 270, Article 108138. https://doi.org/10.1016/j.cpc.2021.108138
Semchonok,
D. A., Mondal, J., Cooper, C. J., Schlum, K., Li, M., Amin,
M., Sorzano, C. O. S., Ramírez-Aportela, E., Kastritis,
P. L., Boekema, E. J., Guskov, A., & Bruce, B. D.
(2022). Cryo-EM structure of a tetrameric photosystem I from
Chroococcidiopsis TS-821, a thermophilic, unicellular,
non-heterocyst-forming cyanobacterium. Plant
Communications, 3(1), Article 100248. https://doi.org/10.1016/j.xplc.2021.100248
Ibrahim,
M., & Amin, M. (2021). Predicting the
Oxidation States of Mn ions in the Oxygen Evolving Complex of
Photosystem II Using Supervised and Unsupervised Machine
Learning. arXiv.
Ali,
F., Kasry, A., & Amin, M. (2021). The new
SARS-CoV-2 strain shows a stronger binding affinity to ACE2due to
N501Y mutant. Medicine in Drug
Discovery, 10, Article 100086. https://doi.org/10.1016/j.medidd.2021.100086
Ali,
F., Kasry, A., & Amin, M. (2021). The
New SARS-CoV-2 Strain Shows a Stronger Binding Affinity to ACE2 Due
to N501Y Mutation. (ArXiv). arXiv.
Amin,
M., Kaur, D., Gunner, M. R., & Brudvig, G. W. (2021).
Toward understanding the S2-S3 transition in the Kok cycle of
Photosystem II: Lessons from Sr-substituted structure.
Inorganic Chemistry Communications,
133, Article 108890. https://doi.org/10.1016/j.inoche.2021.108890
2020
Ali,
F., Elserafy, M., Alkordi, M. H., & Amin, M.
(2020). ACE2 coding variants in different populations and
their potential impact on SARS-CoV-2 binding affinity.
Biochemistry and Biophysics Reports,
24, Article 100798. https://doi.org/10.1016/j.bbrep.2020.100798
Amin,
M., Sorour, M. K., & Kasry, A. (2020). Comparing
the binding interactions in the receptor binding domains of
SARS-CoV-2 and SARS-CoV. The Journal of Physical
Chemistry Letters, 11(12), 4897–4900. https://doi.org/10.1021/acs.jpclett.0c01064
Samanta,
A. K., Amin, M., Estillore, A. D., Roth, N., Worbs,
L., Horke, D. A., & Küpper, J. (2020). Controlled
beams of shock-frozen, isolated, biological and artificial
nanoparticles. Structural dynamics,
7(2), Article 024304. https://doi.org/10.1063/4.0000004
Roth,
N., Amin, M., Samanta, A. K., & Küpper, J.
(2020). Microscopic force for aerosol
transport. (ArXiv). arXiv. https://arxiv.org/abs/2006.10652
Ali,
F., Medhat, S. W., & Amin, M. (2020).
Probing redox potential for Iron sulfur clusters in
photosystem I. (ArXiv). Cornell University Press. https://doi.org/10.48550/arXiv.2009.11681
Safy,
M. E. A., Amin, M., Haikal, R. R., Elshazly, B., Wang,
J., Wang, Y., Wöll, C., & Alkordi, M. H. (2020).
Probing the Water Stability Limits and Degradation Pathways
of Metal-Organic Frameworks (MOFs).
Chemistry, 26(31), 7109-7117. https://doi.org/10.1002/chem.202000207
Amin,
M., & Küpper, J. (2020). Variations in
Proteins Dielectric Constants.
Chemistryopen, 9(6), 691-694. https://doi.org/10.1002/open.202000108
2019
Etman,
N., Said, A. M. A., Atia, K. S. R., Sultan, R., Hameed, M. F.
O., Amin, M., & Obayya, S. S. A. (2019).
Quantum Effects In Imaging Nano-Structures Using
Photon-Induced Near-Field Electron Microscopy.
Scientific Reports, 9, Article 6139.
https://doi.org/10.1038/s41598-019-42624-w
Kaur,
D., Szejgis, W., Mao, J., Amin, M., Reiss, K. M.,
Askerka, M., Cai, X., Khaniya, U., Zhang, Y., Brudvig, G. W.,
Batista, V. S., & Gunner, M. R. (2019). Relative
stability of the S2 isomers of the oxygen evolving complex of
photosystem II. Photosynthesis
Research, 141(3), 331-341. https://doi.org/10.1007/s11120-019-00637-6
Amin,
M., Samy, H., & Kuepper, J. (2019). Robust and
Accurate Computational Estimation of the Polarizability Tensors of
Macromolecules. JOURNAL OF PHYSICAL CHEMISTRY
LETTERS, 10(11), 2938-2943. https://doi.org/10.1021/acs.jpclett.9b00963
Amin,
M., Kaur, D., Yang, K. R., Wang, J., Mohamed, Z., Brudvig,
G. W., Gunner, M. R., & Batista, V. (2019).
Thermodynamics of the S2-to-S3 state transition of the
oxygen-evolving complex of photosystem II. PPCP :
Physical Chemistry Chemical Physics, 21(37),
20840-20848. https://doi.org/10.1039/c9cp02308a
Ibrahim,
A. H., El-Mehalmey, W. A., Haikal, R. R., Safy, M. E. A.,
Amin, M., Shatla, H. R., Karakalos, S. G., & Alkordi, M.
H. (2019). Tuning the Chemical Environment within the
UiO-66-NH2 Nanocages for Charge-Dependent Contaminant Uptake and
Selectivity. Inorganic Chemistry,
58(22), 15078-15087. https://doi.org/10.1021/acs.inorgchem.9b01611
2018
Amin,
M., Mohamed, Z., El-Sayed, M., Samy, A., Sultan, A.,
Bassuoni, M., & Alkordi, M. H. (2018). Combined QM/MM and
Monte Carlo study for redox leveling in Mn and Fe superoxide
dismutase. Journal of biological inorganic
chemistry, 23(2), 285-293. https://doi.org/10.1007/s00775-017-1530-8
2017
Mandal,
M., Askerka, M., Banerjee, G., Amin, M., Brudvig, G.
W., Batista, V. S., & Gunner, M. R. (2017).
Characterization of ammonia binding to the second
coordination shell of the oxygen-evolving complex of photosystem
II. Dalton Transactions,
46(46), 16089-16095. https://doi.org/10.1039/c7dt03901h
Chierotti,
M. R., Amin, M., Hassan, Y. S., Haikal, R. R., Garino,
C., & Alkordi, M. H. (2017). Combined Solid-State NMR and
Computational Approach for Probing the CO2 Binding Sites in a
Porous-Organic Polymer. Journal of Physical
Chemistry C, 121(16), 8850-8856. https://doi.org/10.1021/acs.jpcc.7b00660
Fuller,
F. D., Gul, S., Chatterjee, R., Burgie, E. S., Young, I. D.,
Lebrette, H., Srinivas, V., Brewster, A. S., Michels-Clark, T.,
Clinger, J. A., Andi, B., Ibrahim, M., Pastor, E., de Lichtenberg,
C., Hussein, R., Pollock, C. J., Zhang, M., Stan, C. A., Kroll, T.,
... Yano, J. (2017). Drop-on-demand sample delivery for
studying biocatalysts in action at X-ray free-electron
lasers. Nature Methods,
14(4), 443-+. https://doi.org/10.1038/nmeth.4195
Haikal,
R. R., Soliman, A. B., Amin, M., Karakalos, S. G.,
Hassan, Y. S., Elmansi, A. M., Hafez, I. H., Berber, M. R.,
Hassanien, A., & Alkordi, M. H. (2017). Synergism of
carbon nanotubes and porous-organic polymers (POPs) in CO2
fixation: One-pot approach for bottom-up assembly of tunable
heterogeneous catalyst. Applied catalysis
b-Environmental, 207, 347-357. https://doi.org/10.1016/j.apcatb.2017.02.009
Amin,
M., Askerka, M., Batista, V. S., Brudvig, G. W., &
Gunner, M. R. (2017). X-ray Free Electron Laser Radiation
Damage through the S-State Cycle of the Oxygen-Evolving Complex of
Photosystem II. Journal of Physical Chemistry
B, 121(40), 9382-9388. https://doi.org/10.1021/acs.jpcb.7b08371
2016
Amin,
M., Pokhrel, R., Brudvig, G. W., Badawi, A., & Obayya,
S. S. A. (2016). Effect of Chloride Depletion on the Magnetic
Properties and the Redox Leveling of the Oxygen-Evolving Complex in
Photosystem II. The Journal of Physical Chemistry
B, 120(18), 4243-4248. https://doi.org/10.1021/acs.jpcb.6b03545
Amin,
M., Badawi, A., & Obayya, S. S. (2016). Radiation
Damage in XFEL: Case study from the oxygen-evolving complex of
Photosystem II. Scientific Reports,
6, Article 36492. https://doi.org/10.1038/srep36492
2015
Amin,
M., Vogt, L., Szejgis, W., Vassiliev, S., Brudvig, G. W.,
Bruce, D., & Gunner, M. R. (2015). Proton-Coupled
Electron Transfer During the S-State Transitions of the
Oxygen-Evolving Complex of Photosystem II. Journal
of Physical Chemistry B, 119(24), 7366-7377.
https://doi.org/10.1021/jp510948e
2014
Sauter,
N., Brewster, A., Hattne, J., Amin, M., Kern, J.,
Yano, J., & Yachandra, V. (2014). Improving the accuracy
for Photosystem II and other XFEL structures. Acta
crystallographica a-Foundation and advances,
70, C571-C571. https://doi.org/10.1107/S2053273314094285
2013
Amin,
M., Vogt, L., Vassiliev, S., Rivalta, I., Sultan, M. M.,
Bruce, D., Brudvig, G. W., Batista, V. S., & Gunner, M. R.
(2013). Electrostatic Effects on Proton Coupled Electron
Transfer in Oxomanganese Complexes Inspired by the Oxygen-Evolving
Complex of Photosystem II. Journal of Physical
Chemistry B, 117(20), 6217-6226. https://doi.org/10.1021/jp403321b
Gunner,
M. R., Amin, M., Zhu, X., & Lu, J. (2013).
Molecular mechanisms for generating transmembrane proton
gradients. Biochimica et Biophysica
Acta, 1827(8-9), 892-913. https://doi.org/10.1016/j.bbabio.2013.03.001
2011
Rivalta,
I., Amin, M., Luber, S., Vassiliev, S., Pokhrel, R.,
Umena, Y., Kawakami, K., Shen, J.-R., Kamiya, N., Bruce, D.,
Brudvig, G. W., Gunner, M. R., & Batista, V. S. (2011).
Structural-Functional Role of Chloride in Photosystem
II. Biochemistry, 50(29),
6312-6315. https://doi.org/10.1021/bi200685w
| Last modified: | 27 May 2024 3.40 p.m. |