Daniel Cole
I am a Research Associate in the Jorgensen Lab at the Chemistry Department of Yale University. I have previously worked as a Research Associate at the Theory of Condensed Matter Group of the University of Cambridge and at the Chemistry department of the National University of Singapore and the Institute of High Performance Computing, Singapore.
I completed my Ph.D. in the Theory of Condensed Matter group at the University of Cambridge, working with Prof. Mike Payne and Prof. Lucio Colombi Ciacchi.
Email: daniel.cole (append @yale.edu)
Research Interests
For an overview, please see pages 4-5 of a recent CavMag article (The Quantum Mechanics of Biological Molecules).
I am interested in the application of electronic structure theory to problems in the life sciences. In particular, by combining large-scale density functional theory calculations on systems comprising thousands of atoms with long time scale classical molecular dynamics or constrained geometric simulations, we hope to gain insight into the structure, energetics and electronic properties of molecules of genuine biological interest. These include, for example, a protein-protein interaction implicated in the maintenance of genome stability and ultimately the prevention of cancer, the oxygen binding site of haem proteins and the active site of the enzyme chorismate mutase. These methods may be extended to study optical absorption spectra of bacterial light-harvesting proteins, or to provide greater chemical insight into large-scale electronic structure calculations through natural bond orbital theory.
Update: Our recent paper on NBO theory in ONETEP features on the front cover of J. Comp. Chem. (Volume 34, Issue 6)
My Ph.D. was based on the use of molecular dynamics techniques to study the atomic-level processes that occur at interfaces between silicon-based devices and their external environment. The adhesive properties of such devices are determined by the ultrathin native oxide layer that spontaneously forms on the silicon surface under normal conditions and so precise characterisation of its structure is important for a range of technological applications. I have used Density Functional Theory to monitor the structure, charge distribution and stress development during oxidation of the silicon surface and investigated the behaviour of phosphorous and boron dopants in the oxide layer through quantum mechanical static and dynamic approaches. These techniques are limited by the small system size and the short simulation time addressable, but combined they provide us with detailed information on the thermodynamically stable dopant positions and reveal reaction mechanisms that would be difficult to access experimentally.
The industrial preparation of silicon-on-insulator devices takes advantage of the strong adhesion between hydrophilic silicon surfaces to bond together crystalline wafers at room temperature. I have used information from first principles simulations of the natively oxidised silicon surface to develop a new classical potential for oxidised silicon systems. By parameterising the interactions of the surface with individual water molecules, I am able to study the atomic-level processes that determine the strength of adhesion between silicon wafers in a wet environment.
Meanwhile, the implantation of silicon-based medical devices into tissues or into the bloodstream results in immediate protein and cell adsorption onto the material surface. The key to successful device implantation is the ability of the surface to control protein adsorption and, hence, guide cell assembly and promote compatibility with the surrounding tissue. By further extending the classical potential to include interactions between biomolecules and the natively oxidised silicon surface, I have performed large-scale computer simulations of the adsorption of proteins, such as collagen (left) and human serum albumin (right), onto realistic models of device surfaces in the presence of water.
The high carrier mobilities and 2D nature of graphene make it a promising candidate for applications in carbon-based nanoelectronics. In the solution-gate field effect transistor, modulation of the channel conductance is achieved by applying a gate potential from a reference electrode across an electrolyte, which acts as the dielectric. We have used classical molecular dynamics simulations, employing polarisable force fields, to rationalise the response of such devices to changes in solution pH at varying gate voltages.
Publications
L. P. Lee, D. J. Cole, C.-K. Skylaris, W. L. Jorgensen, M. C. Payne
Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning
Submitted (2013).
G. Lever, D. J. Cole, N. D. M. Hine, P. D. Haynes, M. C. Payne
Electrostatic Considerations Affecting the Calculated HOMO-LUMO Gap in Protein Molecules
Journal of Physics: Condensed Matter (Fast Track Communications) 25, 152101 (2013) Abstract Full text
L. P. Lee, D. J. Cole, M. C. Payne, C.-K. Skylaris
Natural Bond Orbital Analysis in the ONETEP Code: Applications to Large Protein Systems
Journal of Computational Chemistry, 34, 429 (2013) Abstract Full text
D. J. Cole, D. D. O'Regan, M. C. Payne
Ligand Discrimination in Myoglobin from Linear-Scaling DFT+U
Journal of Physical Chemistry Letters, 3, 1448 (2012) Abstract Full text
D. J. Cole, P. K. Ang, K. P. Loh
Ion Adsorption at the Graphene/Electrolyte Interface
Journal of Physical Chemistry Letters, 2, 1799 (2011) Abstract Full text
D. J. Cole, E. Rajendra, M. Roberts-Thomson, B. Hardwick, G. J. McKenzie, M. C. Payne, A. R. Venkitaraman, C. -K. Skylaris
Interrogation of the Protein-Protein Interactions between Human BRCA2 BRC Repeats and RAD51 Reveals Atomistic Determinants of Affinity
PLoS Computational Biology, 7, e1002096 (2011) Abstract Full text
D. J. Cole, C. -K. Skylaris, E. Rajendra, A. R. Venkitaraman, M. C. Payne
Protein-Protein Interactions from Linear-Scaling First-Principles Quantum-Mechanical Calculations
Europhysics Letters, 91, 37004 (2010) Abstract Full text
D. J. Cole, M. C. Payne, L. Colombi Ciacchi
Water Structuring and Collagen Adsorption at Hydrophilic and Hydrophobic Silicon Surfaces
Phys. Chem. Chem. Phys., 11, 11395 (2009) Abstract Full text
D. V. Kubair, D. J. Cole, L. Colombi Ciacchi, S. M. Spearing
Multiscale Mechanics Modeling of Direct Silicon Wafer Bonding
Scripta Materialia 60, 1125 (2009) Abstract Full text
L. Colombi Ciacchi, D. J. Cole, M. C. Payne, P. Gumbsch
Stress-driven oxidation chemistry of wet silicon surfaces
Journal of Physical Chemistry C 112, 12077 (2008) Abstract Full text
D. J. Cole, G. Csányi, M. C. Payne, S. M. Spearing, L. Colombi Ciacchi
Development of a classical force field for the oxidised Si surface: Application to hydrophilic wafer bonding
Journal of Chemical Physics 127, 204704 (2007) Abstract Full text
D. J. Cole, M. C. Payne, L. Colombi Ciacchi
Stress development and impurity segregation during oxidation of the Si(100) surface
Surface Science 601, 4888 (2007) Abstract Full text
My Ph.D. thesis is available here
Selected Talks
"Ligand Discrimination in Myoglobin from Linear-Scaling DFT+U",
American Chemical Society March Meeting, San Diego, U.S.A. (2012).
"Biomolecular Simulation with ONETEP",
India-UK workshop on "Trends in protein biophysics: from in silico molecules to in vivo and vitro proteins" (2011).
"Protein-Protein Interactions from Linear Scaling First Principles Quantum Mechanical Calculations",
American Physical Society March Meeting, Portland, U.S.A. (2010).
"pH Sensitivity of Solution-Gated Graphene",
International Conference on Materials for Advanced Technologies, Singapore (2009).
"ONETEP and Protein Adsorption Simulations on the Darwin Cluster",
SciComp@Cam, Centre for Mathematical Sciences, Cambridge (2008).
"Molecular Dynamics Simulations of Protein-Surface Interactions",
Physics of Medicine Roadshow, Cambridge Institute for Medical Research (2008).
"Development of a Classical Force Field for the Simulation of Solvated Proteins on Oxidised Si Surfaces",
International Conference on Materials for Advanced Technologies, Singapore (2007).
Links
- DFT Research in TCM
- The TCM Home Page
- The ONETEP Home Page
- Cambridge Molecular Therapeutics Programme
- The AMBER Home Page
- FIRST/FRODA constrained geometric simulation
- Natural Bond Orbitals
- National University of Singapore
- A-Star Institute of High Performance Computing
- Queens' College
- Strange Blue Ultimate Frisbee
Last modified: March 2013