Cole, Daniel - Newcastle University

个人简介

M.Sci. and B.A. in Natural Sciences, University of Cambridge, 2004. Ph.D. in Physics, Theory of Condensed Matter group, University of Cambridge, 2008.

近期论文

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Cole DJ, Hine NDM. Applications of Large-Scale Density Functional Theory in Biology. Journal of Physics: Condensed Matter 2016, 28(39), 393001. Cole DJ, Vilseck JZ, Tirado-Rives J, Payne MC, Jorgensen WL. Biomolecular Force Field Parameterization via Atoms-in-Molecular Electron Density Partitioning. Journal of Chemical Theory and Computation 2016, 12(5), 2312-2323. Morgan SE, Cole DJ, Chin AW. Nonlinear network model analysis of vibrational energy transfer and localisation in the Fenna-Matthews-Olson complex. Scientific Reports 2016, 6, 36703. Fokas AS, Cole DJ, Ahnert SE, Chin AW. Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis. Scientific Reports 2016, 6, 33213. Cole DJ, Tirado-Rives J, Jorgensen WL. Molecular Dynamics and Monte Carlo Simulations for Protein-Ligand Binding and Inhibitor Design. Biochimica et Biophysica Acta (BBA) General Subjects 2015, 1850(5), 966-971. Fokas AS, Cole DJ, Chin AW. Constrained geometric dynamics of the Fenna–Matthews–Olson complex: the role of correlated motion in reducing uncertainty in excitation energy transfer. Photosynthesis Research 2014, 122(3), 275-292. Belfield WJ, Cole DJ, Martin IL, Payne MC, Chau P-L. Constrained geometric simulation of the nicotinic acetylcholine receptor. Journal of Molecular Graphics and Modelling 2014, 52, 1-10. Cole DJ, Tirado-Rives J, Jorgensen WL. Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering. Journal of Chemical Theory and Computation 2014, 10(2), 565-571. Lee LP, Gabaldon Limas N, Cole DJ, Payne MC, Skylaris C-K, Manz TA. Expanding the Scope of Density Derived Electrostatic and Chemical Charge Partitioning to Thousands of Atoms. Journal of Chemical Theory and Computation 2014, 10(12), 5377-5390. Kozuska JL, Paulsen IM, Belfield WJ, Martin IL, Cole DJ, Holt A, Dunn SMJ. Impact of Intracellular Domain Flexibility upon Properties of Activated Human 5-HT3 Receptors. British Journal of Pharmacology 2014, 171(7), 1617-1628. Lever G, Cole DJ, Lonsdale R, Ranaghan KE, Wales DJ, Mulholland AJ, Skylaris C-K, Payne MC. Large-Scale Density Functional Theory Transition State Searching in Enzymes. Journal of Physical Chemistry Letters 2014, 5(21), 3614-3619. Weber C, Cole DJ, O'Regan DD, Payne MC. Renormalization of Myoglobin-ligand Binding Energetics by Quantum Many-body Effects. Proceedings of the National Academy of Sciences of the United States of America 2014, 111(16), 5790-5795. Lever G, Cole DJ, Hine NDM, Haynes PD, Payne MC. Electrostatic Considerations Affecting the Calculated HOMO-LUMO Gap in Protein Molecules. Journal of Physics: Condensed Matter 2013, 25(15). Lee LP, Cole DJ, Payne MC, Skylaris C-K. Natural Bond Orbital Analysis in the ONETEP Code: Applications to Large Protein Systems. Journal of Computational Chemistry 2013, 34(6), 429-444. Lee LP, Cole DJ, Skylaris C-K, Jorgensen WL, Payne MC. Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning. Journal of Chemical Theory and Computation 2013, 9(7), 2981-2991. Cole DJ, Chin AW, Hine NDM, Haynes PD, Payne MC. Toward Ab Initio Optical Spectroscopy of the Fenna-Matthews-Olson Complex. Journal of Physical Chemistry Letters 2013, 4(24), 4206-4212. Cole DJ, O'Regan DD, Payne MC. Ligand Discrimination in Myoglobin from Linear-Scaling DFT+U. Journal of Physical Chemistry Letters 2012, 3(11), 1448-1452. Cole DJ, Rajendra E, Roberts-Thomson M, Hardwick B, McKenzie GJ, Payne MC, Venkitaraman AR, Skylaris C-K. Interrogation of the Protein-Protein Interactions between Human. PLOS Computationsl Biology 2011, 7. Cole DJ, Ang PK, Loh KP. Ion Adsorption at the Graphene/Electrolyte Interface. Journal of Physical Chemistry Letters 2011, 2(14), 1799-1803. Cole DJ, Skylaris C-K, Rajendra E, Venkitaraman AR, Payne MC. Protein-protein Interactions form Linear-scaling First-principles Quantum-mechanical Calculations. Europhysics Letters Association 2010, 91(3). Kubair DV, Cole DJ, Colombi-Ciacchi L, Spearing SM. Multiscale Mechanics Modeling of Direct Silicon Wafer Bonding. Scripta Materialia 2009, 60(12), 1125-1128. Cole DJ, Payne MC, Ciacchi LC. Water Structuring and Collagen Adsorption at Hydrophilic and Hydrophobic Silicon Surfaces. Physical Chemistry Chemical Physics 2009, 11, 11395-11399. Colombi-Ciacchi L, Cole DJ, Payne MC, Gumbsch P. Stress-Driven Oxidation Chemistry of Wet Silicon Surfaces. Journal of Physical Chemistry 2008, 112(32), 12077-12080. Cole DJ, Payne MC, Csanyi G, Spearing SM, Colombi-Ciacchi L. Development of a classical force field for the oxidized Si surface: Application to Hydrophilic Wafer Bonding. Journal of Chemical Physics 2007, 127(20), 204704. Cole DJ, Payne MC, Colombi-Ciacchi L. Stress Development and Impurtity Segregation During Oxidation of the Si(1 0 0) Surface. Surface Science 2007, 601(21), 4888-4898.