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Frontiers of computer simulation in chemistry and materials science

Event

Starts:

February
062014

09:00

Ends:

February
072014

17:00

Location

Kavli Royal Society Centre, Chicheley Hall, Newport Pagnell, Buckinghamshire, MK16 9JJ

Overview

The image shows a single hydrogen atom bonding to a single atomic layer of graphite (graphene). Courtesy of Erlend Davidson and Angelos Michaelides, Thomas Young Centre, UCL.

Theo Murphy international scientific meeting organised by Professor David Manolopoulos FRS, Professor David Logan, Dr Mark Wilson and Professor David Chandler ForMemRS

Event details


The last few years have seen spectacular advances in the application of computer simulation to complex systems that have shed light on phenomena across the breadth of chemistry – from biophysical chemistry to chemical physics and materials science. This meeting will bring together world leaders in computer simulation to celebrate these advances, identify new challenges, and discuss the methodology needed to solve them.

Biographies of the key contributors are available below and you can also download a programme (PDF). Recorded audio of the presentations will be available on this page shortly after the event.

Enquiries: Contact the events team

Schedule of talks

Organisers

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Professor David Chandler ForMemRS, University of California Berkeley, USA

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Professor David Logan, University of Oxford, UK

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Professor David Manolopoulos FRS, University of Oxford, UK

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Dr Mark Wilson, University of Oxford, UK

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Session 1

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Chair

Professor Michael Klein FRS, Temple University, USA

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Granular packing and the Gibbs Paradox

Professor Daan Frenkel ForMemRS, University of Cambridge, UK

Abstract

Some questions are easy to pose yet difficult to answer.

One such question is:

"How many distinct ways are there to pack N particles in a volume V?"

It has been argued by Edwards that the logarithm of this number is analogous to entropy and plays a key role in the theory of granular media. However, the number could not be computed.

In my talk I will show that the number can now be computed for non-trivial system sizes. And, no, its logarithm is not like an entropy.

Luckily, the problem can be fixed.

My main conclusions are that, once again, Gibbs was right and that Boltzmann gravestone may need editing.

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How biomolecules use hydrophobicity to function

Dr Gerhard Hummer, Max Planck Institute of Biophysics, Germany

Abstract

Biomolecular machines carry out a wide range of functions, from chemical sensing and signalling over highly selective molecular transport to the efficient interconversion of chemical, mechanical, electrical, and light energy.  We have used statistical mechanical theory and molecular dynamics simulations to characterize the molecular mechanisms underlying these biological processes. Remarkably, common physical principles emerge in the function of proteins serving as water and ion channels, proton pumps or molecular motors, despite large variations in their structure and biological role.  In particular, water and hydration effects occupy central roles in the operation of these molecular machines, and are key to achieving both high efficiency and high fidelity.

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New approaches to simulating biological and molecular catalysts

Professor Tom Miller, Caltech, USA

Abstract

A primary focus of the Miller group is the development of simulation methods to reveal the mechanistic features of quantum mechanical reactions that are central to biological and molecular catalysis.  The current talk will describe new path-integral methods for the direct simulation of condensed-phase electron transfer, proton transfer, and proton-coupled electron transfer (PCET) reactions.  Specific topics will include the investigation of PCET reaction mechanisms and rates in iron bi-imidazoline systems across multiple regimes, as well as recent progress in simulation of multi-electron processes.

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Quantum simulation of exciton dynamics in conjugated systems

Professor Peter Rossky, University of Texas at Austin, USA

Abstract

Exciton dynamics are important for energy transfer in both natural (photosynthetic) and man-made (organic photovoltaic) materials. The potential role of quantum coherence in influencing the transport of excitation has received a lot of attention, particularly in the biological arena, but experimental studies of conjugated polymers have reported signals that have also indicated evidence of coherence in these systems.  In this presentation, quantum dynamics simulations of exciton dynamics in a detailed model of the polymer MEH-PPV will be discussed†.  Comparison with experiment indicates reproduction of the data, allowing a detailed analysis of the origins of coherence and a description of exciton diffusion mechanism in this class of polymer.

† In collaboration with Dr Atsushi Yamada (Nagoya University), Professor Adam P Willard (M.I.T.)

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Session 2

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Adsorption, self assembly, and friction in oil-based lubricants

Dr Philip Camp, University of Edinburgh, UK

Abstract

The tribological properties of oil-based lubricants can be tuned by the addition of friction modifiers, which are normally surfactant-type molecules that adsorb on to the surfaces of moving metal parts. In experiments it is difficult to investigate directly the adsorption of surfactants on to surfaces and dispersed nanoparticles from oil, the detailed structures of the adsorbed films, and the consequent effects on friction under typical operating conditions. Computer simulations provide unique insights on these properties, and on the connections to molecular structure. Recent simulation results on the thermodynamics of surface adsorption [1], adsorbed-film structure [2], kinetic friction [2,3], and micelle formation, all in base oils, will be discussed.

[1]      M R Farrow, P J Camp, P J Dowding, and K Lewtas, Phys. Chem. Chem. Phys.15, 11653 (2013).
[2]      M Doig, C P Warrens, and P J Camp, Langmuir30, 186 (2014).
[3]      M R Farrow, A Chremos, P J Camp, S G Harris, and R F Watts, Tribol. Lett.42, 325 (2011).

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Assembly and packing on GPUs

Professor Sharon Glotzer, University of Michigan, USA

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Chair

Professor David Chandler ForMemRS, University of California Berkeley, USA

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Crystal nucleation

Professor Michele Parrinello ForMemRS, ETH Zurich, Switzerland

Abstract

Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables it can explore complex free energy surfaces characterized by several metastable states separated by large free energy barriers. Here we extend its scope by introducing a simple yet powerful method for calculating the rates of transition between different metastable states. The method does not rely on a previous knowledge of the transition states or reaction coordinates, as long as collective variables are known that can distinguish between the various stable minima in free energy space. A statistical analysis of the distribution of transition times allows us to verify a posteriori the accuracy of our calculations. We apply our method to a number of examples of increasing complexity. We find excellent agreement between our calculations and the results of long unbiosed molecular dynamics simulations whenever the latter are feasible.

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How liquids become rigid: stress fluctuations in supercooled liquids

Professor Peter Harrowell, University of Sydney, Australia

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Session3

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Collective behavior at the water platinum interface

Professor Adam Willard, MIT and Dr David Limmer, Princeton University, USA

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Chair

Professor Ruth Lynden-Bell FRS, University of Cambridge, UK

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First principles simulations of ice and water

Professor Roberto Car, Princeton University, USA

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Hydrogen bonding and proton transfer at water/solid interfaces

Professor Angelos Michaelides, University College London, UK

Abstract

Recent years have seen huge advances in the accuracy and realism of first principles simulations. It is now an exciting time that issues such the role of van der Waals dispersion forces, quantum nuclear effects, and thermal (dynamical) effects can all be explored with first principles approaches. In this talk some of our recent work in this area will be discussed, particularly focussing on the structure and dynamics of water at interfaces and proton transfer in interfacial hydogen bonds

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Network-forming materials in variable dimensions

Dr Mark Wilson, University of Oxford, UK

Abstract

The concept of amorphous structure being described as a network (constructed from relatively simple repeating units) goes back to the two-dimensional representation proposed by Zachariasen in 1932. In three-dimensions systems such as C, Si or Ge, or more complex systems like SiO2, GeO2 or GeSe2 can usefully considered as network materials. However, diffraction experiments which are most commonly used to probe the structures of these systems, highlight structure primarily at a pair-wise level often displaying ordering on multiple length-scales. Potentially more complex structure (bond angles, ring structure) must be inferred from the experimental data often augmented with parallel simulation studies.

Recent experimental developments have allowed for the generation of two- (or near two-) dimensional amorphous structures for C and SiO2. Electron microscopy allows the atomistic structure of these systems to be determined unequivocally and, as a result, complex structural correlations, such as those expressed in terms of the ring structure, are easily obtained. However, these experiments are in their infancy and the effect of the formation conditions on the underlying structure is unclear. As a result, a detailed understanding of the underlying interactions is required if materials are to be grown in a controlled fashion.

In this talk key target systems (C and SiO2) will be modelled in both three- and two-dimensions. The structure of both amorphous graphene (a-G) and bilayers of SiO2 will be rationalised in terms of the ring structure and growth conditions.

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Session 4

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At last: orbital-free DFT simulations of semiconductors and transition metals

Professor Emily Carter, Princeton University, USA

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Chair

Professor Paul Madden FRS, University of Oxford, UK

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First principles electrochemistry

Professor Michiel Sprik, University of Cambridge, UK

Abstract

The electrodes in electrochemical cells are interfaces between electronic and ionic conductors converting one type of charge transport into the other. Experimental electrochemistry has developed a range of current-voltage measurement techniques to probe this process. Atomistic modelling is not yet ready for this challenge, or at least we, using electronic structure based methods, are not. Electrochemical interfaces also act as capacitors, which can be charged (electrified). This can be studied under open circuit conditions (zero current). Here computational methods have more of a chance and considerable progress has been made in the calculation of open circuit electrode potentials. This talk is a brief overview of the efforts of our group focusing on the level alignment at transition metal oxide interfaces including the dependence on the pH of the electrolytic solution*.

* In collaboration with Jun Cheng, Marialore Sulpizi and Joost VandeVondele

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First principles simulations of metal oxide electrodes for water oxidation

Professor Annabella Selloni, Princeton University, USA

Abstract

Water splitting on metal oxide surfaces has attracted enormous interest for decades.  While a great deal of work has focused on titanium dioxide (TiO2), recently other oxides, e.g. cobalt and Ni/Fe mixed oxides, have emerged as promising candidates for use as anode materials in electrochemical water splitting.  In this talk I shall discuss various aspects of water oxidation on metal oxide surfaces, including the changes in composition and structure of the material under electrochemical environment and the mechanism of the first proton-coupled-electron transfer at  the oxide/water interface in the presence of a photoexcited hole. In particular, I shall provide evidence that the first proton and electron transfers at the water/TiO2 interface are not concerted but rather represent two separate processes.

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Modeling ion adsorption and dynamics in nanoporous carbon electrodes

Dr Mathieu Salanne, Paris (Université Pierre et Marie Curie), France

Abstract

The recent demonstration that in supercapacitors ions from the electrolyte could enter sub-nanometer pores increasing greatly the capacitance opened the way for valuable improvements of the devices performances. Despite the recent experimental and fundamental studies on that subject, the molecular mechanism at the origin of this capacitance enhancement is still not quite clear. We report here molecular dynamics simulations including two key features: the use of realistic electrode structures comparable with carbide-derived carbons and the polarization of the electrode atoms by the electrolyte. This original design of an electrochemical cell allows us to recover capacitance values in quantitative agreement with experiment and to gain knowledge about the local structure and dynamics of the ionic liquid inside the pores. Then, from the comparison between planar (graphite) and porous electrodes, we propose a new mechanism explaining the capacitance enhancement in nanoporous carbons. We also set up some simulations where, starting from 0V, an electric potential is applied between the electrodes. It is then possible to follow the dynamical aspects of the charging of supercapacitors.

References: 
- Merlet, Rotenberg, Madden, Taberna, Simon, Gogotsi and Salanne, Nat. Mater., 11, 306 (2012)
- Merlet, Pean, Rotenberg, Madden, Simon and Salanne, J. Phys. Chem. Lett., 4, 264 (2013)
- Merlet, Rotenberg, Madden and Salanne, Phys. Chem. Chem. Phys., 15, 15781 (2013)
- Merlet, Pean, Rotenberg, Madden, Daffos, Taberna, Simon and Salanne, Nat. Commun., doi : 10.1038/ncomms3701 (2013)

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Frontiers of computer simulation in chemistry and materials science Kavli Royal Society Centre, Chicheley Hall Newport Pagnell Buckinghamshire MK16 9JJ