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BERRYMAN Josh

University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Physics and Materials Science (DPHYMS)

ORCID
0000-0002-6959-4607
Main Referenced Co-authors
Mezzenga, Raffaele (7)
SCHILLING, Tanja  (7)
Reynolds, Nicholas (5)
Zhang, Afang (5)
Charnley, Mirren (3)
Main Referenced Keywords
simulation (4); amyloid (3); COVID-19 (2); DNA (2); Ab initio (1);
Main Referenced Unit & Research Centers
ULHPC - University of Luxembourg: High Performance Computing (16)
Main Referenced Disciplines
Physical, chemical, mathematical & earth Sciences: Multidisciplinary, general & others (12)
Physics (11)
Biochemistry, biophysics & molecular biology (8)
Computer science (1)
Materials science & engineering (1)

Publications (total 27)

The most downloaded
507 downloads
ANWAR, M., BERRYMAN, J., & SCHILLING, T. (2014). Crystal nucleation mechanism in melts of short polymer chains under quiescent conditions and under shear flow. Journal of Chemical Physics, (141), 124910. doi:10.1063/1.4896568 https://hdl.handle.net/10993/18182

The most cited

330 citations (OpenAlex)

Smith, D. P., Knapman, T. W., Campuzano, I., Malham, R. W., BERRYMAN, J., Radford, S. E., & Ashcroft, A. E. (2009). Deciphering drift time measurements from travelling wave ion mobility spectrometry-mass spectrometry studies. European Journal of Mass Spectrometry, 15 (2), 113-130. doi:10.1255/ejms.947 https://hdl.handle.net/10993/3873

HAN, K., BOZIKI, A., TKATCHENKO, A., & BERRYMAN, J. (06 December 2024). TIHI Toolkit: A Peak Finder and Analyzer for Spectroscopic Data. ACS Omega, 9 (50). doi:10.1021/acsomega.4c06830
Peer Reviewed verified by ORBi

BONHENRY, D., Charnley, M., GONCALVES, J., Hammarström, P., HENEKA, M., Itzhaki, R., Lambert, J.-C., Mannan, M., Baig, A. M., Middeldorp, J., Nyström, S., Reynolds, N. P., Stefanatou, M., & BERRYMAN, J. (June 2024). SARS-CoV-2 infection as a cause of neurodegeneration. The Lancet Neurology, 23 (6), 562 - 563. doi:10.1016/S1474-4422(24)00178-9
Peer Reviewed verified by ORBi

Unke, O. T., Stöhr, M., Ganscha, S., Unterthiner, T., Maennel, H., Kashubin, S., Ahlin, D., Gastegger, M., Medrano Sandonas, L., BERRYMAN, J., TKATCHENKO, A.* , & Müller, K.-R.*. (05 April 2024). Biomolecular dynamics with machine-learned quantum-mechanical force fields trained on diverse chemical fragments. Science Advances, 10 (14), 4397. doi:10.1126/sciadv.adn4397
Peer Reviewed verified by ORBi
* These authors have contributed equally to this work.

BERRYMAN, J., TAGHAVI, A., MAZUR, F., & TKATCHENKO, A. (09 August 2022). Quantum machine learning corrects classical forcefields: Stretching DNA base pairs in explicit solvent. Journal of Chemical Physics, 157 (6). doi:10.1063/5.0094727
Peer reviewed

Charnley, M., Islam, S., Bindra, G., Engwirda, J., Ratcliffe, J., Zhou, J., Mezzenga, R., Hulett, M. D., HAN, K., BERRYMAN, J., & Reynolds, N. P. (13 June 2022). Neurotoxic amyloidogenic peptides in the proteome of SARS-COV2: potential implications for neurological symptoms in COVID-19. Nature Communications, 13. doi:10.1038/s41467-022-30932-1
Peer Reviewed verified by ORBi

Case, D. A., Duke, R. E., Walker, R. C., Skrynnikov, N. R., Cheatham III, T. E., Mikhailovskii, O., Simmerling, C., Xue, Y., Roitberg, A., Izmailov, S. A., Merz, K. M., Kasavajhala, K., Luo, R., Belfon, K., Li, P., Shen, J., Darden, T., Harris, R., Sagui, C., ... ET, A. (2022). AMBER 22 Reference Manual. San Francisco, United States - California: University of California.

Islam, S., Charnley, M., Bindra, G., Ratcliffe, J., Zhou, J., Mezzenga, R., Hulett, M., Han, K., BERRYMAN, J., & Reynolds, N. (2021). Neurotoxic Amyloidogenic Peptides Identified in the Proteome of SARS-COV2: Potential Implications for Neurological Symptoms in COVID-19. (1). ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/49323. doi:10.1101/2021.11.24.469537

HAKAMI ZANJANI, A. A., Reynolds, N., Zhang, A., SCHILLING, T., Mezzenga, R., & BERRYMAN, J. (19 May 2020). Amyloid Evolution: Antiparallel Replaced by Parallel. Biophysical Journal, 118, 2526–2536. doi:10.1016/j.bpj.2020.03.023
Peer Reviewed verified by ORBi

Maldonado, A., Basdogan, Y., BERRYMAN, J., Rempe, S., & Keith, J. (01 April 2020). First-principles modeling of chemistry in mixed solvents: Where to go from here? Journal of Chemical Physics, 152. doi:10.1063/1.5143207
Peer Reviewed verified by ORBi

Adamcik, J., Ruggeri, F. S., BERRYMAN, J., Zhang, A., Knowles, T. P. J., & Mezzenga, R. (2020). Evolution of Conformation, Nanomechanics, and Infrared Nanospectroscopy of Single Amyloid Fibrils Converting into Microcrystals. Advanced Science, 2002182. doi:10.1002/advs.202002182
Peer reviewed

HAKAMI ZANJANI, A. A., Reynolds, N., Zhang, A., SCHILLING, T., Mezzenga, R., & BERRYMAN, J. (2019). Kinetic Control of Parallel versus Antiparallel Amyloid Aggregation via Shape of the Growing Aggregate. Nature Scientific Reports. doi:10.1038/s41598-019-52238-x
Peer reviewed

TAGHAVI, A., van der Schoot, P., & BERRYMAN, J. (November 2017). DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase. Quarterly Reviews of Biophysics, 50. doi:10.1017/S0033583517000130
Peer Reviewed verified by ORBi

Reynolds, N., Adamcik, J., BERRYMAN, J., Handschin, S., HAKAMI ZANJANI, A. A., Li, W., Liu, K., Zhang, A., & Mezzenga, R. (November 2017). Competition between crystal and fibril formation in molecular mutations of amyloidogenic peptides. Nature Communications, 8. doi:10.1038/s41467-017-01424-4
Peer Reviewed verified by ORBi

BERRYMAN, J., ANWAR, M., DOROSZ, S., & SCHILLING, T. (2016). The early crystal nucleation process in hard spheres shows synchronised ordering and densification. Journal of Chemical Physics, 145, 211901. doi:10.1063/1.4953550
Peer Reviewed verified by ORBi

Case, D. A., BERRYMAN, J., Betz, R. M., Cerutti, D. S., Cheatham III, T. E., Darden, T. A., Duke, R. E., Giese, T. J., Gohlke, H., Goetz, A. W., Homeyer, N., Izadi, S., Janowski, P., Kaus, J., Kovalenko, A., Lee, T. S., LeGrand, S., Li, P., Luchko, T., ... Kollman, P. A. (2015). AMBER 2015. San Francisco, United States - California: University of California.

BERRYMAN, J., & SCHILLING, T. (31 December 2014). Absolute Free Energies for Biomolecules in Implicit or Explicit Solvent. Physics Procedia, 57, 7-15. doi:10.1016/j.phpro.2014.08.123
Peer reviewed

Lara, C., Reynolds, N., BERRYMAN, J., Xu, A., Zhang, A., & Mezzenga, R. (26 March 2014). ILQINS hexapeptide, identified in lysozyme left-handed helical ribbons and nanotubes, forms right-handed helical ribbons and crystals. Journal of the American Chemical Society, 136 (12), 4732-4739. doi:10.1021/ja500445z
Peer Reviewed verified by ORBi

ANWAR, M., BERRYMAN, J., & SCHILLING, T. (2014). Crystal nucleation mechanism in melts of short polymer chains under quiescent conditions and under shear flow. Journal of Chemical Physics, (141), 124910. doi:10.1063/1.4896568
Peer Reviewed verified by ORBi

Case, D. A., Babin, V., BERRYMAN, J., Betz, R. M., Cai, Q., Cerutti, D. S., Cheatham III, T. E., Darden, T. A., Duke, R. E., Gohlke, H., Goetz, A. W., Gusarov, S., Homeyer, N., Janowski, P., Kaus, J., Kolossváry, I., Kovalenko, A., Lee, T. S., LeGrand, S., ... Kollman, P. A. (2014). Amber 14. San Francisco, Unknown/unspecified: University of California.

Kratzer, K., BERRYMAN, J., Taudt, A., Zeman, J., & Arnold, A. (2014). The Flexible Rare Event Sampling Harness System (FRESHS). Computer Physics Communications. doi:10.1016/j.cpc.2014.03.013
Peer Reviewed verified by ORBi

BERRYMAN, J., & SCHILLING, T. (2012). Free Energies by Thermodynamic Integration Relative to an Exact Solution, Used to Find the Handedness-Switching Salt Concentration for DNA. Journal of Chemical Theory and Computation. doi:10.1021/ct3005968
Peer Reviewed verified by ORBi

BERRYMAN, J., Radford, S. E., & Harris, S. A. (2011). Systematic examination of polymorphism in amyloid fibrils by molecular-dynamics simulation. Biophysical Journal, 100 (9), 2234-2242. doi:10.1016/j.bpj.2011.02.060
Peer Reviewed verified by ORBi

BERRYMAN, J., & SCHILLING, T. (2010). A general algorithm for sampling rare events in non-equilibrium and non-stationary systems. Journal of Chemical Physics, 133, 244101-244101. doi:10.1063/1.3525099
Peer Reviewed verified by ORBi

Knapman, T. W., BERRYMAN, J., Campuzano, I., Harris, S. A., & Ashcroft, A. E. (2010). Considerations in experimental and theoretical collision cross-section measurements of small molecules using travelling wave ion mobility spectrometry-mass spectrometry. International Journal of Mass Spectrometry, 298 (1-3), 17-23. doi:10.1016/j.ijms.2009.09.011
Peer Reviewed verified by ORBi

BERRYMAN, J., Radford, S. E., & Harris, S. A. (2009). Thermodynamic Description of Polymorphism in Q- and N-Rich Peptide Aggregates Revealed by Atomistic Simulation. Biophysical Journal, 97 (1), 1-11. doi:10.1016/j.bpj.2009.03.062
Peer Reviewed verified by ORBi

Smith, D. P., Knapman, T. W., Campuzano, I., Malham, R. W., BERRYMAN, J., Radford, S. E., & Ashcroft, A. E. (2009). Deciphering drift time measurements from travelling wave ion mobility spectrometry-mass spectrometry studies. European Journal of Mass Spectrometry, 15 (2), 113-130. doi:10.1255/ejms.947
Peer Reviewed verified by ORBi

BERRYMAN, J., Radford, S., & Harris, S. (2008). Prediction of Twist of Amyloid Fibrils Using Molecular Dynamics. In Proceedings of the NIC Workshop 2008 (pp. 169-171).

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