2017

Xu, Yuanwei and Rodger, P. Mark (2017) MBAR-enhanced lattice Monte Carlo simulation of the effect of helices on membrane protein aggregation. Journal of Computational Physics, 333 . pp. 128-141. doi:10.1016/j.jcp.2016.12.016

Guardiani, Carlo, Rodger, P. Mark, Fedorenko, Olena A., Roberts, Stephen K. and Khovanov, Igor A. (2017) Data for Sodium binding sites and permeation mechanism in the NaChBac channel: a Molecular Dynamics study. [Dataset]

2016

Guardiani, Carlo, Rodger, P. Mark, Fedorenko, Olena A., Roberts, Stephen K. and Khovanov, Igor A. (2016) Sodium binding sites and permeation mechanism in the NaChBac channel : a molecular dynamics study. Journal of Chemical Theory and Computation, 13 (3). pp. 1389-1400. doi:10.1021/acs.jctc.6b01035

Rodger, P. Mark, Cox, S. J., Dove, M. T., Hogg, D. C., Kenny, S. D., Martin, R., Mulheran, P. A., Richards, A, Taylor, C., Metcalf, T., Sinclair , G., Real, A. N., Groenewald, W. and Fakhrkonandeh, A. (2016) The importance of regional e-­infrastructure within the national landscape. Regional e-Infrastructure Centres Network (ReICN)..

2015

Xu, Yuanwei and Rodger, P. Mark (2015) Improved estimation of density of states for Monte Carlo sampling via MBAR. Journal of chemical theory and computation . doi:10.1021/acs.jctc.5b00189 (In Press)

2014

Bano , Anthony M., Rodger , P. Mark and Quigley, David (2014) New insight into the stability of CaCO3 surfaces and nanoparticles via molecular simulation. Langmuir, Volume 30 (Number 25). pp. 7513-7521. doi:10.1021/la501409j

2013

Cosseddu, Salvatore M., Khovanov, I. A., Allen, M. P., Rodger, P. Mark, Luchinsky, Dmitri G. and McClintock, P. V. E. (2013) Dynamics of ions in the selectivity filter of the KcsA channel. European Physical Journal - Special Topics, Volume 222 (Number 10). pp. 2595-2605. doi:10.1140/epjst/e2013-02040-9

Desmond, Jasmine L., Rodger, P. Mark and Walsh, Tiffany R. (2013) Testing the inter-operability of the CHARMM and SPC/Fw force fields for conformational sampling. Molecular Simulation, Volume 40 (Number 12). pp. 912-921. doi:10.1080/08927022.2013.824574

Wright, Louise B., Rodger, P. Mark, Corni, Stefano and Walsh, Tiffany R. (2013) GolP-CHARMM : first-principles based force fields for the interaction of proteins with Au(111) and Au(100). Journal of Chemical Theory and Computation, Volume 9 (Number 3). pp. 1616-1630. doi:10.1021/ct301018m

Wright, Louise B., Rodger, P. Mark, Walsh, Tiffany R. and Corni, Stefano (2013) First-principles-based force field for the interaction of proteins with Au(100)(5 × 1) : an extension of GolP-CHARMM. The Journal of Physical Chemistry Part C: Nanomaterials, Interfaces and Hard Matter, Volume 117 (Number 46). pp. 24292-24306. doi:10.1021/jp4061329

Guo, Guang-Jun and Rodger, P. Mark (2013) Solubility of aqueous methane under metastable conditions : implications for gas hydrate nucleation. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, Volume 117 (Number 21). pp. 6498-6504. doi:10.1021/jp3117215

2012

Freeman, Colin L., Harding, John H., Quigley, David and Rodger, P. Mark (2012) Protein binding on stepped calcite surfaces : simulations of ovocleidin-17 on calcite {31.16} and {31.8}. Physical Chemistry Chemical Physics, Vol.14 (No.20). pp. 7287-7295. doi:10.1039/c2cp23987f

Finney, Aaron R. and Rodger, P. Mark (2012) Probing the structure and stability of calcium carbonate pre-nucleation clusters. Faraday Discussions, Vol.159 . pp. 47-60. doi:10.1039/c2fd20054f

2011

Finney, Aaron R. and Rodger, P. Mark (2011) Applying the Z method to estimate temperatures of melting in structure II clathrate hydrates. Physical Chemistry Chemical Physics, Vol.13 (No.44). pp. 19979-19987. doi:10.1039/c1cp21919g

Freeman, C. L., Harding, J. H., Quigley, David and Rodger, P. Mark (2011) Simulations of ovocleidin-17 binding to calcite surfaces and its implications for eggshell formation. The Journal of Physical Chemistry Part C: Nanomaterials, Interfaces and Hard Matter, Vol.115 (No.16). pp. 8175-8183. doi:10.1021/jp200145m

Quigley, David, Freeman, C. L., Harding, J. H. and Rodger, P. Mark (2011) Sampling the structure of calcium carbonate nanoparticles with metadynamics. The Journal of Chemical Physics, Vol.134 (No.4). 044703. doi:10.1063/1.3530288

2010

Rodger, P. Mark, Quigley, David, Harding, J. H. and Freeman, C. L. (2010) Simulating crystal nucleation : seeing the infrequent with molecular dynamics. In: Conference on Goldschmidt 2010 - Earth, Energy, and the Environment, Knoxville, TN, 13-18 Jun 2010. Published in: Geochimica et Cosmochimica Acta, Vol.74 (No.12 Suppl. 1). A875-A875. ISSN 0016-7037. doi:10.1016/j.gca.2010.04.044

Raiteri, P., Gale, J. D., Quigley, David and Rodger, P. Mark (2010) Towards accurate modeling of the growth and nucleation of carbonates. In: Conference on Goldschmidt 2010 - Earth, Energy, and the Environment, Knoxville, TN, 13-18 Jun 2010. Published in: Geochimica et Cosmochimica Acta, Vol.74 (No.12 Suppl. 1). A844-A844. ISSN 0016-7037. doi:10.1016/j.gca.2010.04.044

Raiteri, P., Gale, Julian D., Quigley, David and Rodger, P. Mark (2010) Derivation of an accurate force-field for simulating the growth of calcium carbonate from aqueous solution : a new model for the calcite-water interface. Journal of Physical Chemistry C, Vol.114 (No.13). pp. 5997-6010. doi:10.1021/jp910977a

Freeman, C. L., Harding, J. H., Quigley, David and Rodger, P. Mark (2010) Structural control of crystal nuclei by an eggshell protein. Angewandte Chemie (International Edition), Vol.49 (No.30). pp. 5135-5137. doi:10.1002/anie.201000679

San-Miguel, Miguel A. and Rodger, P. Mark (2010) Templates for wax deposition? Physical Chemistry Chemical Physics, Vol.12 (No.15). pp. 3887-3894. doi:10.1039/b920945j

2009

Subbotin, Oleg S., Adamova, Tatiana P., Belosludov, Rodion V., Mizuseki, Hiroshi, Kawazoe, Yoshiyuki, Kudoh, Jun-ichi, Rodger, P. Mark and Belosludov, Vladimir R. (2009) Theoretical study of phase transitions in Kr and Ar clathrate hydrates from structure II to structure I under pressure. Journal of Chemical Physics, Vol.131 (No.11). Article: 114507. doi:10.1063/1.3212965

Quigley, David, Rodger, P. Mark, Freeman, C. L., Harding, J. H. and Duffy, D. M. (2009) Metadynamics simulations of calcite crystallization on self-assembled monolayers. Journal of Chemical Physics, Vol.131 (No.9). article no. 094703 . doi:10.1063/1.3212092

Williams, Jonathan P., Bugarcic, Tijana, Habtemariam, Abraha, Giles, K. (Kevin), Campuzano, Iain, Rodger, P. Mark and Sadler, P. J. (2009) Isomer separation and gas-phase configurations of organoruthenium anticancer complexes : ion mobility mass spectrometry and modeling. Journal of The American Society for Mass Spectrometry, Vol.20 (No.6). pp. 1119-1122. doi:10.1016/j.jasms.2009.02.016

Duffy, D. M., Freeman, C. L., Harding, J. H., Quigley, David and Rodger, P. Mark (2009) Modelling biomineralization processes. In: 19th Annual VM Goldschmidt Conference, Davos, Switzerland, June 21, 2009. Published in: Geochimica et Cosmochimica Acta, Vol.73 (13 Suppl. S). A311-A311. ISSN 0016-7037. doi:10.1016/j.gca.2009.05.003

Yang, Mingjun, Rodger, P. Mark, Harding, John H. and Stipp, S. L. S. (2009) Molecular dynamics simulations of peptides on calcite surface. In: CCP5 Annual Conference on Surfaces and Interfaces, London Sch Econom, London, England, 2008. Published in: Molecular Simulation, Vol.35 (No.7). pp. 547-553. ISSN 0892-7022. doi:10.1080/08927020802627399

San-Miguel, Miguel A., Robinson, Colin and Rodger, P. Mark (2009) Secondary structure simulations of twin-arginine signal peptides in different environments. Molecular Simulation, Vol.35 (No.12-13). pp. 1033-1042. doi:10.1080/08927020902974063

Quigley, David and Rodger, P. Mark (2009) A metadynamics-based approach to sampling crystallisation events. Molecular Simulation, Vol.35 (No.7). pp. 613-623. doi:10.1080/08927020802647280

2008

Harding, J. H., Duffy, D. M., Sushko, Maria L., Rodger, P. Mark, Quigley, David and Elliott, J. A. (James A.) (2008) Computational techniques at the organic-inorganic interface in biomineralization. Chemical Reviews, 108 (11). pp. 4823-4854. doi:10.1021/cr078278y

Belosludov, R. V., Subbotin, O. S., Mizuseki, Hiroshi, Rodger, P. Mark, Kawazoe, Y. and Belosludov, V. R. (2008) Crystal-like low frequency phonons in the low-density amorphous and high-density amorphous ices. Journal of Chemical Physics, Vol.129 (No.11). Article: 114507. doi:10.1063/1.2977975

Zhang, Junfang, Hawtin, R. W., Yang, Ye, Nakagava, Edson, Rivero, M., Choi, S. K. and Rodger, P. Mark (2008) Molecular dynamics study of methane hydrate formation at a water/methane interface. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, Vol.112 (No.34). pp. 10608-10618. doi:10.1021/jp06904p

Rodger, P. Mark, Hawtin, R. W. and Quigley, David (2008) FUEL 20-Nucleation, growth and inhibition of methane hydrate. In: 236th National Meeting of the American Chemical Society, Philadelphia, PA, Aug 17-21, 2008. Published in: Abstracts of papers of the American Chemical Society, 236 ISSN 0065-7727.

Quigley, David and Rodger, P. Mark (2008) Free energy and structure of calcium carbonate nanoparticles during early stages of crystallization. Journal of Chemical Physics, Vol.128 (No.22). article no. 221101 . doi:10.1063/1.2940322

Quigley, David and Rodger, P. Mark (2008) Metadynamics simulations of ice nucleation and growth. Journal of Chemical Physics, Vol.128 (No.15). article no. 154518 . doi:10.1063/1.2888999

Hawtin, R. W., Quigley, David and Rodger, P. Mark (2008) Gas hydrate nucleation and cage formation at a water/methane interface. Physical Chemistry Chemical Physics, Vol.10 (No.32). pp. 4853-4864. doi:10.1039/b807455k

2007

Khalid, Syma, Hannon, M. J. (Michael J.), Rodger, Alison and Rodger, P. Mark (2007) Shape effects on the activity of synthetic major-groove binding ligands. Journal of Molecular Graphics and Modelling, Vol.25 (No.6). pp. 794-800. doi:10.1016/j.jmgm.2006.07.004

Moon, C., Hawtin, R. W. and Rodger, P. Mark (2007) Nucleation and control of clathrate hydrates : insights from simulation. Faraday Discussions, Volume 136 . pp. 367-382. doi:10.1039/b618194p

2006

Rajendra, Jascindra, Damianoglou, Angeliki, Hicks, Matthew R., Booth, Paula, Rodger, P. Mark and Rodger, Alison (2006) Quantitation of protein orientation in flow-oriented unilamellar liposomes by linear dichroism. Chemical Physics , Volume 326 (Number 1). pp. 210-220. doi:10.1016/j.chemphys.2006.02.036

Childs, Laura J., Malina, J., Rolfsnes, B. E., Pascu, Mirela, Prieto, M. J., Broome, Mark John, Rodger, P. Mark, Sletten, Einar, Moreno, Virtudes, Rodger, Alison and Hannon, M. J. (2006) A DNA-binding copper(I) metallosupramolecular cylinder that acts as an artificial nuclease. Chemistry : a European journal, Vol.12 (No.18). pp. 4919-4927. doi:10.1002/chem.200600060

Wilson, Michael P, Alcock, Nathaniel W. and Rodger, P. Mark (2006) Structure of anhydrous alkali-metal formates. Inorganic Chemistry, Volume 45 (Number 11). pp. 4359-4363. doi:10.1021/ic051910q

Khalid, Syma, Hannon, M. J. (Michael J.), Rodger, Alison and Rodger, P. Mark (2006) Simulations of DNA coiling around a synthetic supramolecular cylinder that binds in the DNA major groove. Chemistry: A European Journal, Vol.12 (No.13). pp. 3493-3506. doi:10.1002/chem.200501168

2002

Pinheiro, Philip, Scarlett, Garry, Rodger, Alison, Rodger, P. Mark, Murray, Anna, Brown, Tom, Newbury, Sarah F. and McCellan, James A. (2002) Structures of CUG repeats in RNA - Potential implications for human genetic diseases. Journal of Biological Chemistry, 277 (38). pp. 35183-35190. doi:10.1074/jbc.M202235200

Rodger, Alison, Nordén, Bengt, Rodger, P. Mark and Bates, Paula J. (2002) DNA as a catalyst and catalytic template for the racemisation of metal tris-phenanthroline complexes. European Journal of Inorganic Chemistry, Vol.2002 (No.1). pp. 49-53. doi:10.1002/1099-0682(20021)2002:1<49::AID-EJIC49>3.0.CO;2-8