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Daniel Cole

I am a Research Associate in the Theory of Condensed Matter group at the University of Cambridge. I have previously worked as a Research Fellow 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: djc56 (append @cam.ac.uk)


Research Interests

For an overview, please see pages 4-5 of a recent CavMag article (The Quantum Mechanics of Biological Molecules).

Protein-Protein Interface Electron Density on Stacked G-tetrads

Computational methods that are capable of elucidating features of molecular recognition, binding affinities and structural stability are likely to drive experimental approaches to studying macromolecules. I am using approaches that combine linear-scaling Density Functional Theory with long time scale classical molecular dynamics to investigate problems of genuine biological interest. These methods provide insight into the structure, energetics and electronic properties of, for example, protein-protein interfaces, the G-quadruplex structure of DNA and the oxygen binding site of myoglobin. I am working with Louis Lee on methods to provide greater chemical insight into accurate, large-scale DFT calculations and with Greg Lever on transition state searching in enzymes and measurement of activation energy barriers.

Despite their many successful applications, conventional molecular dynamics simulations are generally limited to submicrosecond time scales and to systems of a few hundred thousand atoms. This makes the exploration of conformational changes of large systems over high kinetic barriers infeasible. I am working with William Belfield to explore the use of "coarse-grained" simulations in the study of systems such as ligand-gated ion channels.




Oxidation of the B-doped Si surface

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.



Hydrophilic wafer bonding


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.




Collagen adsorption on the native oxide surface HSA adsorption on the native oxide surface
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.




Solution-gated Graphene



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

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

"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

  1. DFT Research in TCM
  2. TCM Journal Club Wiki
  3. The TCM Home Page
  4. The ONETEP Home Page
  5. The AMBER Home Page
  6. National University of Singapore
  7. A-Star Institute of High Performance Computing
  8. Queens' College
  9. Strange Blue Ultimate Frisbee
  10. Cambridge Intra-University Badminton League
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Last modified: Tue 30th August 2011