School of Physics and Astronomy

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Dr Sarah A Harris

Theoretical Physics Group

Contact details

Room: 9.61
Tel: +44 (0)113 3433816
Email: s.a.harris @ leeds.ac.uk

Publications

Shah NR, Wilkinson C, Harborne SPD, Turku A, Li KM, Sun YJ, Harris S, Goldman A Insights into the mechanism of membrane pyrophosphatases by combining experiment and computer simulation Structural Dynamics 4 -, 2017
DOI:10.1063/1.4978038
View abstract

Noy A, Maxwell A, Harris SA Interference between Triplex and Protein Binding to Distal Sites on Supercoiled DNA Biophysical Journal 112 523-531, 2017
DOI:10.1016/j.bpj.2016.12.034
View abstract

Sutthibutpong T, Matek C, Benham C, Slade GG, Noy A, Laughton C, K Doye JP, Louis AA, Harris SA Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation. Nucleic acids research 44 9121-9130, 2016
DOI:10.1093/nar/gkw815
View abstract

Noy A, Sutthibutpong T, A Harris S Protein/DNA interactions in complex DNA topologies: expect the unexpected Biophysical Reviews 8 145-155, 2016
DOI:10.1007/s12551-016-0241-7

Schiffrin B, Calabrese AN, Devine PWA, Harris SA, Ashcroft AE, Brockwell DJ, Radford SE Skp is a multivalent chaperone of outer-membrane proteins Nature Structural and Molecular Biology 23 786-793, 2016
DOI:10.1038/nsmb.3266

Noy A, Sutthibutpong T, Harris SA Protein/DNA interactions in complex DNA topologies: expect the unexpected Biophysical Reviews 8 233-243, 2016
DOI:10.1007/s12551-016-0208-8
View abstract

Rajasekar KV, Lovering AL, Dancea F, Scott DJ, Harris SA, Bingle LEH, Roessle M, Thomas CM, Hyde EI, White SA Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator Nucleic Acids Research 44 4947-4956, 2016
DOI:10.1093/nar/gkw191
View abstract

Hanson B, Harris S, Read D, Harlen O Fluctuating Finite Element Analysis: Development and Applications to Cytoplasmic Dynein, 2016

Sutthibutpong T, Noy A, Harris S Atomistic molecular dynamics simulations of DNA minicircle topoisomers: A practical guide to setup, performance, and analysis In Chromosome Architecture: Methods and Protocols , 2016
DOI:10.1007/978-1-4939-3631-1_15
View abstract

Ivani I, Dans PD, Noy A, Perez A, Faustino I, Hospital A, Walther J, Andrio P, Goni R, Balaceanu A, Portella G, Battistini F, Lluis Gelpi J, Gonzalez C, Vendruscolo M, Laughton CA, Harris SA, Case DA, Orozco M Parmbsc1: a refined force field for DNA simulations Nature Methods 13 55-58, 2016
DOI:10.1038/NMETH.3658
View abstract

Irobalieva RN, Fogg JM, Catanese CDJ, Sutthibutpong T, Chen M, Barker AK, Ludtke SJ, Harris SA, Schmid MF, Chiu W, Zechiedrich L Structural diversity of supercoiled DNA Nature Communications 6 -, 2015
DOI:10.1038/ncomms9440
View abstract

Solernou A, Harris SA, Harlen OG, Read DJ, Smith KA, Muench SP Understanding fibrin protofibrils at the molecular level: formation and flexibility through a new coarse-grained protein modelling approach, 2015

Sutthibutpong T, Harris SA, Noy A Comparison of Molecular Contours for Measuring Writhe in Atomistic Supercoiled DNA Journal of Chemical Theory and Computation 11 2768-2775, 2015
DOI:10.1021/acs.jctc.5b00035
View abstract

Harris S Polymorphism within complex DNA topologies JOURNAL OF BIOMOLECULAR STRUCTURE&DYNAMICS 33 85-85, 2015
DOI:10.1080/07391102.2015.1032760

Hanson B, Richardson R, Oliver R, Read DJ, Harlen O, Harris S Modelling biomacromolecular assemblies with continuum mechanics Biochemical Society Transactions 43 186-192, 2015
DOI:10.1042/BST20140294
View abstract

Harris SA, Hanson B, Richardson R, Read DJ, Harlen OG Mesoscale Modelling of Biomolecules using Continuum Mechanics BIOPHYSICAL JOURNAL 108 183A-183A, 2015

Gray A, Harlen OG, Harris SA, Khalid S, Leung YM, Lonsdale R, Mulholland AJ, Pearson AR, Read DJ, Richardson RA In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: A perspective on computer simulation Acta Crystallographica Section D: Biological Crystallography 71 162-172, 2015
DOI:10.1107/S1399004714026777
View abstract

Harris S 131 Polymorphism within complex DNA topologies. Journal of biomolecular structure&dynamics 33 Suppl 1 85-, 2015
DOI:10.1080/07391102.2015.1032764

Richardson RA, Papachristos K, Read DJ, Harlen OG, Harrison M, Paci E, Muench SP, Harris SA Understanding the apparent stator-rotor connections in the rotary ATPase family using coarse-grained computer modeling. Proteins 82 3298-3311, 2014
DOI:10.1002/prot.24680
View abstract

Kato YS, Yagi T, Harris SA, Ohki SY, Yura K, Shimizu Y, Honda S, Kamiya R, Burgess SA, Tanokura M Structure of the Microtubule-Binding Domain of Flagellar Dynein Structure 22 1628-1638, 2014
DOI:10.1016/j.str.2014.08.021
View abstract

Shoura MJ, Ranatunga RJKU, Harris SA, Nielsen SO, Levene SD Contribution of fluorophore dynamics and solvation to resonant energy transfer in protein-DNA complexes: a molecular-dynamics study. Biophys J 107 700-710, 2014
DOI:10.1016/j.bpj.2014.06.023
View abstract

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 42 9304-9312, 2014
DOI:10.1093/nar/gku654
View abstract

Oliver R, Richardson RA, Hanson B, Kendrick K, Read DJ, Harlen OG, Harris SA Modelling the dynamic architecture of biomaterials using continuum mechanics In Protein Modelling , 2014
DOI:10.1007/978-3-319-09976-7_8
View abstract

Toroz D, Hammond RB, Roberts KJ, 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
DOI:10.1016/j.jcrysgro.2014.01.064
View abstract

Elsheshiny AAA, Ashcroft AE, Harris SA A comparison of the electromechanical properties of structurally diverse proteins by molecular dynamics simulation. J Biomol Struct Dyn 32 1734-1741, 2014
DOI:10.1080/07391102.2013.833864
View abstract

Ndlovu H, Ashcroft AE, Radford SE, Harris SA Molecular dynamics simulations of mechanical failure in polymorphic arrangements of amyloid fibrils containing structural defects BEILSTEIN JOURNAL OF NANOTECHNOLOGY 4 429-440, 2013
DOI:10.3762/bjnano.4.50

Mitchell JS, Harris SA Thermodynamics of writhe in DNA minicircles from molecular dynamics simulations Physical Review Letters 110 -, 2013
DOI:10.1103/PhysRevLett.110.148105
View abstract

Bates AD, Noy A, Piperakis MM, Harris SA, Maxwell A Small DNA circles as probes of DNA topology Biochemical Society Transactions 41 565-570, 2013
DOI:10.1042/BST20120320
View abstract

Stasiak A, Bates AD, Buck DE, Harris SA, Witt S Topological aspects of DNA function and protein folding Biochemical Society Transactions 41 491-493, 2013
DOI:10.1042/BST20130006
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Oliver R, Read DJ, Harlen OG, Harris SA A Stochastic Finite Element Model for the Dynamics of Globular Macromolecules Journal of Computational Physics 239 147-165, 2013
DOI:10.1016/j.jcp.2012.12.027
View abstract

Young L, Ndlovu H, Knapman TW, Harris SA, Radford SE, Ashcroft AE Monitoring oligomer formation from self-aggregating amylin peptides using ESI-IMS-MS International Journal for Ion Mobility Spectrometry 16 29-39, 2013
DOI:10.1007/s12127-012-0115-z
View abstract

Young L, Ndlovu H, Knapman TW, Harris SA, Radford SE, Ashcroft AE Monitoring oligomer formation from self-aggregating amylin peptides using ESI-IMS-MS International Journal for Ion Mobility Spectrometry 1-11, 2013
DOI:10.1007/s12127-012-0115-z
View abstract

Fogg JM, Randall GL, Pettitt BM, Sumners DWL, Harris SA, Zechiedrich L Bullied no more: When and how DNA shoves proteins around Quarterly Reviews of Biophysics 45 257-299, 2012
DOI:10.1017/S0033583512000054
View abstract

Ndlovu H, Ashcroft AE, Radford SE, Harris SA Effect of sequence variation on the mechanical response of amyloid fibrils probed by steered molecular dynamics simulation. Biophys J 102 587-596, 2012
DOI:10.1016/j.bpj.2011.12.047
View abstract

Maude S, Tai LR, Davies RPW, Liu B, Harris SA, Kocienski PJ, Aggeli A Peptide synthesis and self-assembly Topics in Current Chemistry 310 27-69, 2012
DOI:10.1007/128_2011_234
View abstract

Valette NM, Radford SE, Harris SA, Warriner SL Phosphorylation as a tool to modulate aggregation propensity and to predict fibril architecture. Chembiochem 13 271-281, 2012
DOI:10.1002/cbic.201100607
View abstract

Maude S, Tai LR, Davies RPW, Liu B, Harris SA, Kocienski PJ, Aggeli A Peptide synthesis and self-assembly. Top Curr Chem 310 27-69, 2012
DOI:10.1007/128_2011_234
View abstract

Laughton CA, Harris SA The atomistic simulation of DNA WIRES COMPUT MOL SCI 1 590-600, 2011
DOI:10.1002/wcms.46

Berryman JT, Radford SE, Harris SA Systematic Examination of Polymorphism in Amyloid Fibrils by Molecular-Dynamics Simulation BIOPHYS J 100 2234-2242, 2011
DOI:10.1016/j.bpj.2011.02.060

Mitchell JS, Laughton CA, Harris SA Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA. Nucleic Acids Res 39 3928-3938, 2011
DOI:10.1093/nar/gkq1312
View abstract

Mitchell J, Harris S Testing the Use of Implicit Solvent in the Molecular Dynamics Modelling of DNA Flexibility, 2011

Reha D, Voityuk AA, Harris SA An in Silico Design for a DNA Nanomechanical Switch ACS NANO 4 5737-5742, 2010
DOI:10.1021/nn1014038

Valette NM, Radford SE, Harris SA, Warriner SL Studying peptide aggregation with a series of phosphopeptide variants ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 240 -, 2010

Harris SA, Kendon VM Quantum-assisted biomolecular modelling PHILOS T R SOC A 368 3581-3592, 2010
DOI:10.1098/rsta.2010.0087

Patargias GN, Harris SA, Harding JH A demonstration of the inhomogeneity of the local dielectric response of proteins by molecular dynamics simulations. J Chem Phys 132 235103-, 2010
DOI:10.1063/1.3430628
View abstract

Rezac J, Hobza P, Harris SA Stretched DNA Investigated Using Molecular-Dynamics and Quantum-Mechanical Calculations BIOPHYS J 98 101-110, 2010
DOI:10.1016/j.bpj.2009.08.062

Knapman TW, Berryman JT, Campuzano I, Harris SA, Ashcroft AE 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 17-23, 2010
DOI:10.1016/j.ijms.2009.09.011

Berryman JT, Radford SE, Harris SA Thermodynamic description of polymorphism in Q- and N-rich peptide aggregates revealed by atomistic simulation. Biophys J 97 1-11, 2009
DOI:10.1016/j.bpj.2009.03.062
View abstract

Gell C, Sabir T, Westwood J, Rashid A, Smith DAM, Harris SA, Stockley PG Single-Molecule Fluorescence Resonance Energy Transfer Assays Reveal Heterogeneous Folding Ensembles in a Simple RNA Stem-Loop J MOL BIOL 384 264-278, 2008
DOI:10.1016/j.jmb.2008.08.088

Reha D, Barford W, Harris S 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, 2008
DOI:10.1039/b719619a
View abstract

Duchesne L, Wells G, Fernig DG, Harris SA, Levy R Supramolecular domains in mixed peptide self-assembled monolayers on gold nanoparticles CHEMBIOCHEM 9 2127-2134, 2008
DOI:10.1002/cbic.200800326

Liverpool TB, Harris SA, Laughton CA Supercoiling and denaturation of DNA loops PHYS REV LETT 100 -, 2008
DOI:10.1103/PhysRevLett.100.238103

Harris SA, Laughton CA, Liverpool TB Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations. Nucleic Acids Res 36 21-29, 2008
DOI:10.1093/nar/gkm891
View abstract

Harris SA, Laughton CA A simple physical description of DNA dynamics: quasi-harmonic analysis as a route to the configurational entropy J PHYS-CONDENS MAT 19 -, 2007
DOI:10.1088/0953-8984/19/7/076103

Harris SA Modelling the biomechanical properties of DNA using computer simulation. Philos Trans A Math Phys Eng Sci 364 3319-3334, 2006
DOI:10.1098/rsta.2006.1906
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Harris SA, Laughton CA The importance of entropic factors in DNA behaviour: Insights from simulations In Computational Studies of RNA and DNA , 2006
DOI:10.1007/978-1-4020-4851-3_21
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Natarajan S, Harris SA, Ford IJ Kinetic stability of complex molecular clusters J CHEM PHYS 124 -, 2006
DOI:10.1063/1.2160511

Harris SA, Sands ZA, Laughton CA Molecular Dynamics Simulations of Duplex Stretching Reveal the Importance of Entropy in Determining the Biomechanical Properties of DNA Biophysical Journal 88 1684-1691, 2005
DOI:10.1529/biophysj.104.046912

Grindon C, Harris S, Evans T, Novik K, Coveney P, Laughton C Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS. Philos Trans A Math Phys Eng Sci 362 1373-1386, 2004
DOI:10.1098/rsta.2004.1381
View abstract

Ford IJ, Harris SA Molecular cluster decay viewed as escape from a potential of mean force Journal of Chemical Physics 120 4428-4440, 2004
DOI:10.1063/1.1644533

Harris SA The physics of DNA stretching Contemporary Physics 45 11-30, 2004
DOI:10.1080/00107510310001624478
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Harris SA, Ford IJ A dynamical definition of quasibound molecular clusters Journal of Chemical Physics 118 9216-9223, 2003
DOI:10.1063/1.1568336
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Harris SA, Gavathiotis E, Searle MS, Orozco M, Laughton CA Cooperativity in Drug-DNA Recognition: A Molecular Dynamics Study Journal of the American Chemical Society 123 12658-12663, 2001
DOI:10.1021/ja016233n

Wattis JAD, Harris SA, Grindon CR, Laughton CA Dynamic model of base pair breathing in a DNA chain with a defect PHYS REV E 63 art. no.-061903, 2001

Wattis JA, Harris SA, Grindon CR, Laughton CA Dynamic model of base pair breathing in a DNA chain with a defect. Phys Rev E Stat Nonlin Soft Matter Phys 63 061903-, 2001
DOI:10.1103/PhysRevE.63.061903
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Bostock-Smith CE, Harris SA, Laughton CA, Searle MS 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 Research 29 693-702, 2001
DOI:10.1093/nar/29.3.693