Atomistic computer simulations are virtual experiments that complement (but not replace) real experiments. In increasingly many situations they can give an atom-scale understanding, a microscopic explanation of condensed phase electronic and chemical processes that is often difficult to obtain from real experiments. Yet, major limitations are the approximations necessary to solve the underlying equations of many-particle systems (particularly the electronic Schrodinger equation), and the time and length scales that are accessible to computer simulations. Our group carries out research (i) to further advance the predictive power of atom-scale computer simulation techniques and (ii) to raise their significance by developing accurate multi-scale models that bridge the gap between the atomistic and the experimentally relevant time and length scales. While much of the research being carried out is fundamental in nature, we have a keen interest to apply the methodologies developed to relevant problems in the energy and health sector.
A major current research focus is the computer simulation of charge transport processes in soft condensed phase systems such as organic semiconductors and proteins as well as at solid/liquid interfaces relevant for (photo)electrochemical applications.
Charge transport in soft condensed matter is at the heart of many exciting and potentially revolutionising technologies ranging from organic photovoltaic cells to nanobioelectronic transistors. Tremendous progress has been made on these research frontiers over the last twenty years. Yet, our fundamental understanding of CT in organic and biological semiconductors that could rationalise experimental observations and guide further advances in the field is still very limited. These materials are characterised by strong, anharmonic thermal fluctuations and small energy barriers for CT, which renders standard theories such as band theory or activated electron hopping in many cases entirely inadequate (JPCL13). Thus, key features relating to the nature of the charge carrier, their localization length and transport mechanism remain unknown, especially in the relevant ambient and high temperature regimes. We have recently begun to develop an efficient mixed quantum-classical non-adiabatic simulation method that will open the door for ground-breaking new insight into this problem (JCTC14).
Electron Transfer in Proteins
Certain microbes like Shewanella oneidensis are equipped with a fascinating biomolecular machinery that allows them to transport electrons from the inside of the cell across the bacterial cell membrane to extracellular space over distances exceeding 100 Angstroms. This way the microbe can reduce extracellular minerals like iron-oxide when oxygen is a limited resource, literally “breathing rocks” instead of oxygen. The biomolecules mediating the electron transfer to extracellular space are multi-heme proteins (see our recent review, JRSI15). They contain a large array of densely spaced, redox-active heme cofactors, which is why they are often referred to as “nano-wires”. We have recently calculated the thermodynamics (JACS12) and kinetics (PNAS14) of ET in multi-heme proteins using quantum mechanical and classical molecular dynamics simulation methods. In future work, we would like to obtain further molecular-level insight into the transport mechanism and electron flux that these proteins support at in vivo conditions and when sandwiched between two electrodes in conductive AFM and field effect transistor experiments.
Interface Water Splitting Cells
Interfaces between transition metal oxides and liquid water have attracted research attention for quite a long time. In particular, the potential of photoelectrochemical (PEC) water splitting cells to provide carbon neutral H2 or fuels from CO2 (artificial photosynthesis) is in the focus of the research community. Our aim is to learn about the atomistic structure and the mechanism of charge transfer reactions at solid/liquid interfaces, such as e.g. the hematite/water system, using density-functional based molecular dynamics simulation. We are particularly interested in the microscopic structure (e.g. protonation states) of the interface, the nature and transport properties of excess charge carriers in photoelectrodes, and the thermodynamics and kinetics of charge transfer across the solid/liquid interface. This knowledge may lead to atom-scale modifications that could improve photoanodes for water splitting.
Small Molecule Transport
The diffusion of small ligands within enzymes and their binding to enzyme active sites are ubiquitous molecular processes in biology. But how does a small molecule like H2, O2 or CO2 find its way through a dense and heterogeneous protein medium to the active site? In collaboration with Robert Best at the National Institutes of Health, USA, we have recently developed a multiscale molecular simulation approach, where MD simulation and Markov state modelling are combined to shed light on the kinetics of ligand diffusion and binding (JACS11, PCCP11). For the proteins studied so far we have found that the ligands move within multiple hydrophobic cavities or `tunnels’ towards a central cavity from where the ligand makes the final transit to the catalytic site. The functional role of the protein can be compared to the one of a funnel guiding the small molecules towards the target. (PNAS12, JACS13) Very recently we have extended our method to calculate sensitivity maps of the protein that identify residues (`hot spots’) that are expected to show the greatest affect on ligand diffusion when mutated (JCTC15). Such in-silico predictions could help protein engineers to optimize or control the kinetics of ligand, substrate or inhibitor diffusion in proteins.