Publications

Sutthibutpong T., Harris S. A., & A. Noy Comparison of Molecular Contours for Measuring Writhe in Atomistic Supercoiled DNA J. Chem. Theor. Comp. (2015) 11, 2768-2775.

Hanson B., Richardson R., Oliver R., Read D. J., Harlen O. & Harris S. Modelling biomacromolecular assemblies with continuum mechanics Biochem. Soc. Trans. (2015), 43, 186-192.

Gray A., Harlen O. G., Harris S. A., Khalid S., Leung Y. M., Lonsdale R., Mulholland A. J., Pearson A. R., Read D. J. & Richardson R. A. In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation Acta Cryst. (2015) D71, 162-172.

Richardson R., Papachristos K., Read D. J., Harlen O. G., Harrison M. A., Paci E., Muench S. P. & Harris S. A Understanding the apparent stator-rotor connections in the rotary ATPase family using coarse-grained computer modelling, Proteins: Structure, Function, Bioinformatics (2014), 82, 3298-3311.

Kato Y. S., Yagi T. , Harris S. A., Ohki S., Yura K. , Shimizu Y., Honda S., Kamiya R., Burgess S. A. & Tanokura M., Structure of the microtubule-binding domain of flagellar dynein Structure (2014), 22, 1628-1638.

Toroz D., Hammond R. B., Roberts K. J., Harris S. & Ridley T. Molecular dynamics simulations of organic crystal dissolution: The lifetime and stability of the polymorphic forms of para-amino benzoic acid in aqueous environment Journal of Crystal Growth (2014) 401, 38-43.

D’Annessa I., Coletta A., Sutthibutpong T., Mitchell J., Chillemi G., Harris S. & Desideri A. Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein-DNA binding site Nucleic Acids Res. (2014)

42, 9304-9312.

Shoura M. J., Ranatunga R. J. K. U., Harris S. A., Nielsen S. O. & Levene S. D. Contribution of fluorophore dynamics and solvation to resonant energy transfer in protein-DNA complexes: A molecular dynamics study. Biophys J. (2014) 104, 700-710.

Elsheshiny A. A. A., Ashcroft A. E. & Harris S. A. A comparison of the electromechanical properties of structurally diverse proteins by molecular dynamics simulation J. Biomol. Struct. Dyn. (2013), 32, 1734-1741.

Ndlovu H., Ashcroft A. E., Radford S. E., Harris S. A. (2013). Molecular dynamics simulations of mechanical failure in polymorphic arrangements of amyloid fibrils containing structural defects. Beilstein J. Nanotechnol. 4, 429-440.

Mitchell J. & Harris S. A. (2013) The thermodynamics of DNA writhe from atomistic molecular dynamics simulations. Phys. Rev Letts 110, 148105.

Young L., Ndlovu H., Knapman T. W., Harris S. A., Radford S. E. & Ashcroft A. E. (2013) Monitoring oligomer formation from self-aggregating amylin peptides using ESI-IMS-MS. Int J Ion Mobil Spec 1-11.

Oliver R., Read D. J., Harlen O. G. & Harris S (2013) A stochastic finite element model for the dynamics of globular macromolecules. J Comp Phys 239, 147-165.

Bates A. D., Noy A., Piperakis M. M., Harris S. A. & Maxwell A (2013) Small DNA circles as probes of DNA topology. Biochem Soc Trans 41, 565-570.

Fogg J. M., Randell G. L., Pettitt B. M., Sumners D. L., Harris S. A. & Zechiedrich L (2012) Bullied no more: When and how DNA shoves proteins around. Quart Rev Biophys 45, 257-299.

Ndlovu, H; Ashcroft, AE; Radford, SE; Harris, SA (2012) Effect of Sequence Variation on the Mechanical Response of Amyloid Fibrils Probed by Steered Molecular Dynamics Simulation. Biophys J 102, 587 – 596.

Valette, NM; Radford, SE; Harris, SA; Warriner, SL (2012) Phosphorylation as a tool to modulate aggregation propensity and to predict fibril architecture. ChemBioChem 13, 271-281.

Maude S, Tai LR, Davies RP, Liu B, Harris SA, Kocienski PJ, Aggeli A (2012) Peptide synthesis and self-assembly. Top Curr Chem. 310, 27-69.

Mitchell, JS; Laughton, CA; Harris, SA (2011) Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA. Nucleic Acids Res 39, 3928-3938.

Berryman, JT; Radford, SE; Harris, SA (2011) Systematic Examination of Polymorphism in Amyloid Fibrils by Molecular-Dynamics Simulation. Biophys J 100 2234-2242.

Patargias, GN; Harris, SA; Harding, JH (2010) A demonstration of the inhomogeneity of the local dielectric response of proteins by molecular dynamics simulations. J Chem Phys 132, 235103.

Rezac, J; Hobza, P; Harris, SA (2010) Stretched DNA Investigated Using Molecular-Dynamics and Quantum-Mechanical Calculations. Biophys J 98,101-110.

Harris, SA; Kendon, VM (2010) Quantum-assisted biomolecular modelling. Phil Trans R Soc 368, 3581-3592.

Reha, D; Voityuk, AA; Harris, SA (2010) An in Silico Design for a DNA Nanomechanical Switch. ACS Nano 4, 5737-5742.

Knapman, TW; Berryman, JT; Campuzano, I; Harris, SA; Ashcroft, AE (2010) Considerations in experimental and theoretical collision cross-section measurements of small molecules using travelling wave ion mobility spectrometry-mass spectrometry. Int J of Mass Spectrom 298 17-23.

Ndlovu, H; Laughton, CA; Harris, SA (2010) Testing the performance of the Cray XT6 for use in massively parallel atomistic molecular dynamics simulations.

Berryman, JT; Radford, SE; Harris, SA (2009) Thermodynamic description of polymorphism in Q- and N-rich peptide aggregates revealed by atomistic simulation. Biophys J 97(1), 1-11.

Duchesne, L; Wells, G; Fernig, DG; Harris, SA; Levy, R (2008) Supramolecular domains in mixed peptide self-assembled monolayers on gold nanoparticles. ChemBioChem 9 2127-2134.

Reha, D; Barford, W; Harris, S (2008) A multi-scale method for the calculation of charge transfer rates through the Pi-stack of DNA: application to DNA dynamics. Phys Chem Chem Phys 10, 5436-5444.

Gell, C; Sabir, T; Westwood, J, et al. (2008) Single-Molecule Fluorescence Resonance Energy Transfer Assays Reveal Heterogeneous Folding Ensembles in a Simple RNA Stem-Loop. J Mol Biol 384, 264-278.

Liverpool, TB; Harris, SA; Laughton, CA (2008) Supercoiling and denaturation of DNA loops. Phys Rev Lett 100, 238103.

Harris, SA; Laughton, CA; Liverpool, TB (2008) Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations. Nucleic Acids Res 36, 21-29.

Harris, SA; Laughton, CA (2007) A simple physical description of DNA dynamics: quasi-harmonic analysis as a route to the configurational entropy. J Phys Condens Matter 19, 0953-8984.

Harris, SA (2006) Modelling the biomechanical properties of DNA using computer simulation.Phil Trans R Soc A 364, 3319-3334

Harris, SA; Sands, ZA; Laughton, CA (2005) Molecular Dynamics Simulations of Duplex Stretching Reveal the Importance of Entropy in Determining the Biomechanical Properties of DNA. Biophys J 88, 1684-1691.

Grindon, C; Harris, S; Evans, T; Novik, K; Coveney, P; Laughton, C (2004) Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS. Philos Transact A Math Phys Eng Sci 362, 1373-1386.

Bostock-Smith, CE; Harris, SA; Laughton, CA; Searle, MS (2001)Induced fit DNA recognition by a minor groove binding analogue of Hoechst 33258: fluctuations in DNA A tract structure investigated by NMR and molecular dynamics simulations Nucleic Acids Res 29, 693-702.

Wattis, JA; Harris, SA; Grindon, CR; Laughton, CA (2001) Dynamic model of base pair breathing in a DNA chain with a defect. Phys Rev E 63, 061903.

Harris, SA; Gavathiotis, E; Searle, MS; Orozco, M; Laughton, CA (2001) Cooperativity in Drug-DNA Recognition: A Molecular Dynamics Study. J Am Chem Soc 123, 12658-12663.