|
2024 Journal Article On the Validation of Protein Force Fields Based on Structural CriteriaStroet, Martin, Setz, Martina, Lee, Thomas, Malde, Alpeshkumar K., van den Bergen, Glen, Sykacek, Peter, Oostenbrink, Chris and Mark, Alan E. (2024). On the Validation of Protein Force Fields Based on Structural Criteria. The Journal of Physical Chemistry B, 128 (19), 4602-4620. doi: 10.1021/acs.jpcb.3c08469 |
|
2024 Journal Article Molecular Insights into the dynamics of amyloid fibril growth: elongation and lateral assembly of GNNQQNY protofibrilsJohn, Torsten, Rampioni, Aldo, Poger, David and Mark, Alan E. (2024). Molecular Insights into the dynamics of amyloid fibril growth: elongation and lateral assembly of GNNQQNY protofibrils. ACS Chemical Neuroscience, 15 (4), 716-723. doi: 10.1021/acschemneuro.3c00754 |
|
2023 Journal Article Engineering transferable atomic force fields: empirical optimization of hydrocarbon Lennard–Jones interactions by direct mapping of parameter spaceZhou, Zihan, Mark, Alan E. and Stroet, Martin (2023). Engineering transferable atomic force fields: empirical optimization of hydrocarbon Lennard–Jones interactions by direct mapping of parameter space. Journal of Chemical Theory and Computation, 19 (13), 4074-4087. doi: 10.1021/acs.jctc.3c00427 |
|
2023 Journal Article OFraMP: a fragment-based tool to facilitate the parametrization of large moleculesStroet, Martin, Caron, Bertrand, Engler, Martin S., van der Woning, Jimi, Kauffmann, Aude, van Dijk, Marc, El-Kebir, Mohammed, Visscher, Koen M., Holownia, Josef, Macfarlane, Callum, Bennion, Brian J., Gelpi-Dominguez, Svetlana, Lightstone, Felice C., van der Storm, Tijs, Geerke, Daan P., Mark, Alan E. and Klau, Gunnar W. (2023). OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. Journal of Computer-Aided Molecular Design, 37 (8), 357-371. doi: 10.1007/s10822-023-00511-7 |
|
2023 Journal Article Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMRKuschert, Sarah, Stroet, Martin, Chin, Yanni Ka-Yan, Conibear, Anne Claire, Jia, Xinying, Lee, Thomas, Bartling, Christian Reinhard Otto, Strømgaard, Kristian, Güntert, Peter, Rosengren, Karl Johan, Mark, Alan Edward and Mobli, Mehdi (2023). Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR. Magnetic Resonance, 4 (1), 57-72. doi: 10.5194/mr-4-57-2023 |
|
2022 Journal Article PyThinFilm: Automated molecular dynamics simulation protocols for the generation of thin film morphologiesStroet, Martin, Sanderson, Stephen, Sanzogni, Audrey V., Nada, Sharif, Lee, Thomas, Caron, Bertrand, Mark, Alan E. and Burn, Paul L. (2022). PyThinFilm: Automated molecular dynamics simulation protocols for the generation of thin film morphologies. Journal of Chemical Information and Modeling, 63 (1), 2-8. doi: 10.1021/acs.jcim.2c01334 |
|
2022 Journal Article Understanding the performance differences between solution and vacuum deposited OLEDs: A computational approachSanderson, Stephen, Vamvounis, George, Mark, Alan E., Burn, Paul L., White, Ronald D. and Philippa, Bronson W. (2022). Understanding the performance differences between solution and vacuum deposited OLEDs: A computational approach. The Journal of Chemical Physics, 156 (21) 214703, 214703. doi: 10.1063/5.0091142 |
|
2022 Journal Article Modelling of the dynamic polarizability of macromolecules for single-molecule optical biosensingBooth, Larnii S., Browne, Eloise V., Mauranyapin, Nicolas P., Madsen, Lars S., Barfoot, Shelley, Mark, Alan and Bowen, Warwick P. (2022). Modelling of the dynamic polarizability of macromolecules for single-molecule optical biosensing. Scientific Reports, 12 (1) 1995. doi: 10.1038/s41598-022-05586-0 |
|
2022 Journal Article Understanding the effect of pH on the solubility and aggregation extent of humic acid in solution by combining simulation and the experimentLan, Tu, Wu, Peng, Liu, Ziyi, Stroet, Martin, Liao, Jiali, Chai, Zhifang, Mark, Alan E., Liu, Ning and Wang, Dongqi (2022). Understanding the effect of pH on the solubility and aggregation extent of humic acid in solution by combining simulation and the experiment. Environmental Science and Technology, 56 (2) acs.est.1c05938, 917-927. doi: 10.1021/acs.est.1c05938 |
|
2021 Journal Article Unraveling exciton processes in Ir(ppy)3:CBP OLED films upon photoexcitationSanderson, Stephen, Vamvounis, George, Mark, Alan E., Burn, Paul L., White, Ronald D. and Philippa, Bronson W. (2021). Unraveling exciton processes in Ir(ppy)3:CBP OLED films upon photoexcitation. The Journal of Chemical Physics, 154 (16) 164101, 164101. doi: 10.1063/5.0044177 |
|
2021 Journal Article On the effect of the various assumptions and approximations used in molecular simulations on the properties of bio-molecular systems: overview and perspective on issuesvan Gunsteren, Wilfred F., Daura, Xavier, Fuchs, Patrick F. J., Hansen, Niels, Horta, Bruno A. C., Hünenberger, Philippe H., Mark, Alan E., Pechlaner, Maria, Riniker, Sereina and Oostenbrink, Chris (2021). On the effect of the various assumptions and approximations used in molecular simulations on the properties of bio-molecular systems: overview and perspective on issues. ChemPhysChem, 22 (3), 264-282. doi: 10.1002/cphc.202000968 |
|
2020 Journal Article Understanding the activated form of a class-I fusion protein: modeling the interaction of the Ebola virus glycoprotein 2 with a lipid bilayerBarfoot, Shelley, Poger, David and Mark, Alan E. (2020). Understanding the activated form of a class-I fusion protein: modeling the interaction of the Ebola virus glycoprotein 2 with a lipid bilayer. Biochemistry, 59 (41) acs.biochem.0c00527, 4051-4058. doi: 10.1021/acs.biochem.0c00527 |
|
2020 Journal Article Evolution and morphology of thin films formed by solvent evaporation: an organic semiconductor case studyLee, Thomas, Sanzogni, Audrey V., Burn, Paul L. and Mark, Alan E. (2020). Evolution and morphology of thin films formed by solvent evaporation: an organic semiconductor case study. ACS Applied Materials and Interfaces, 12 (36) acsami.0c08454, 40548-40557. doi: 10.1021/acsami.0c08454 |
|
2020 Journal Article Editorial overview: Theory and simulation: Progress, yes; revolutions, noMark, Alan Edward and Peter, Christine (2020). Editorial overview: Theory and simulation: Progress, yes; revolutions, no. Current Opinion in Structural Biology, 61, iii-v. doi: 10.1016/j.sbi.2020.02.001 |
|
2019 Journal Article Revealing the interplay between charge transport, luminescence efficiency, and morphology in organic light‐emitting diode blendsGao, Mile, Lee, Thomas, Burn, Paul L., Mark, Alan E., Pivrikas, Almantas and Shaw, Paul E. (2019). Revealing the interplay between charge transport, luminescence efficiency, and morphology in organic light‐emitting diode blends. Advanced Functional Materials, 30 (9) 1907942, 1907942. doi: 10.1002/adfm.201907942 |
|
2019 Journal Article Curved or linear? Predicting the 3‐dimensional structure of α‐helical antimicrobial peptides in an amphipathic environmentvan den Bergen, Glen, Stroet, Martin, Caron, Bertrand, Poger, David and Mark, Alan E. (2019). Curved or linear? Predicting the 3‐dimensional structure of α‐helical antimicrobial peptides in an amphipathic environment. FEBS Letters, 594 (6) 1873-3468.13705, 1062-1080. doi: 10.1002/1873-3468.13705 |
|
2019 Journal Article Effect of surface roughness on light-absorber orientation in an organic photovoltaic filmLee, Thomas, Burn, Paul L. and Mark, Alan E. (2019). Effect of surface roughness on light-absorber orientation in an organic photovoltaic film. Chemistry of Materials, 31 (17) acs.chemmater.9b01337, 6918-6924. doi: 10.1021/acs.chemmater.9b01337 |
|
2019 Journal Article Response of microbial membranes to butanol: interdigitation vs. disorderGuo, Jingjing, Ho, James C.S., Chin, Hokyun, Mark, Alan E., Zhou, Cheng, Kjelleberg, Staffan, Liedberg, Bo, Parikh, Atul N., Cho, Nam-Joon, Hinks, Jamie, Mu, Yuguang and Seviour, Thomas (2019). Response of microbial membranes to butanol: interdigitation vs. disorder. Physical Chemistry Chemical Physics, 21 (22), 11903-11915. doi: 10.1039/c9cp01469a |
|
2019 Journal Article Effect of triclosan and chloroxylenol on bacterial membranesPoger, David and Mark, Alan E. (2019). Effect of triclosan and chloroxylenol on bacterial membranes. The Journal of Physical Chemistry B, 123 (25) acs.jpcb.9b02588, 5291-5301. doi: 10.1021/acs.jpcb.9b02588 |
|
2019 Journal Article Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approachEngler, Martin S., Caron, Bertrand, Veen, Lourens, Geerke, Daan P., Mark, Alan E. and Klau, Gunnar W. (2019). Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach. Algorithms for Molecular Biology, 14 (1) 1, 1. doi: 10.1186/s13015-019-0138-7 |
