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 |
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 |
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. |
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 |
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., & 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 |
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). |