Author Archives: fredmanby

Welcome new group members!

Five people have (fairly) recently joined the group: Callum Bungey and Rocco Meli as graduate students through the TMCS programme; Alex Buccheri as a PDRA working with my colleague Neil Allan and me on the CCP5 flagship project;  Thomas Dresselhaus as a PDRA working on the entos project; and Fidel Batista Romero as a Royal Society Newton International Fellow. Apologies for not recording these arrivals earlier!

 

Welcome to summer students

This year we have four summer students in the group, working on projects ranging from basic theory of quantum polarization models through to biological applications of projector-based embedding methods.

IMG_6100 copy

Left to right: Fred, Shubham, Dom, Aidan and Rebecca. (And yes, Dom’s eyes were closed in all of the shots.)

Shubham joins us from IIT Kharagpur, India, where he is studying Chemistry. Dom and Aidan are Bristol chemistry undergraduates, and are both funded by RSC Undergraduate Bursaries. Rebecca is studying on a combined Chemistry with Maths degree at the University of Southampton.

Welcome to the group!

How Markovian is exciton dynamics in purple bacteria?

Felix’s work on Markovianity in photosynthetic energy transport has been published: Felix Vaughan, N Linden and F R Manby, J. Chem. Phys. 146, 124113 (2017); http://dx.doi.org/10.1063/1.4978568.

Modelling the interaction between excitons and the surrounding environment is a non-trivial problem. Many interesting insights about excitonic energy transfer have made use of a Markovian or “memoryless” approximation to this interaction. In this paper we assess the applicability of this approximation by employing a new metric of non-Markovianity.

We find that for smooth spectral densities the Markovian approximation works well provided that a precise change to the system Hamiltonian is made, which for the dimer system studied corresponds to an increase in the coupling strength between chromophores. We also find that discrete vibrational modes resonant with the eigenstates of the Hamiltonian induce the greatest degree of non-markovianity. Ultimately we conclude that to model exciton dynamics coupled to realistic spectral densities a Markovian approximation is not suitable.

Delocalization errors in WF-in-DFT embedding are large, but fixable

Delocalization error in approximate DFT clearly manifests itself in homodimer cation systems (like H2+ or (H2O)2+), with GGA functionals typically leading to large energy errors and qualitatively incorrect structures. It also causes problems in a variety of other chemically important contexts.

water-deloc.jpg

Spurious delocalization of spin density in a small radical-cation water cluster.

We have found that the delocalization error in densities can cause major errors in WF-in-DFT embedding – these errors are not particular to the projector-based scheme we use,but simple expose a limitation of partitioning systems based on the electron density when that electron density is qualitatively flawed.

Following work from Kieron Burke, we have found the simple expedient of using Hartree-Fock densities in WF-in-DFT calculations really improves reliability in cases where there is a serious delocalization error, and doesn’t cause major problems (in the examples we have studied) when there is not a big delocalization error.

You can read about this work in a paper that has just appeared online: Pennifold et al., ‘Correcting density-driven errors in projection-based embedding’, J. Chem. Phys. 146, 084113 (2017); DOI: 10.1063/1.4974929.

Pump-probe experiments on photosynthetic light-harvesting complexes are not easy to interpret

Clem’s paper on the interpretation of pump-probe experiments on the purple-bacteria light-harvesting complex LHII is now in print in J Phys Chem B.

jp-2016-09916z_0008Through careful and extensive calculations involving molecular dynamics, time-dependent density functional theory, and quantum dynamics we have shown that the interpretation of anisotropy decay rates in terms of strength of coupling to a dissipative bath is not so easily justified. The reason is that static (or inhomogeneous) disorder itself produces anisotropy decay at about the experimentally observed rate.

The paper also contains an epic, paper-length appendix on how to compute such quantities for the circularly degenerate oscillator model.

Congratulations Clem!

C. Stross, M. W. Van der Kamp, T. A. A. Oliver, J. N. Harvey, N. Linden and F. R. Manby, “How Static Disorder Mimics Decoherence in Anisotropy Pump–Probe Experiments on Purple-Bacteria Light Harvesting Complexes”, J. Phys. Chem. B, 120, 11449-11463 (2016), DOI: 10.1021/acs.jpcb.6b09916

New opportunities for joining the group

University of Bristol EPSRC Doctoral Prize Fellowships

There is a great opportunity to join the Manby group if you have recently finished (or are just about to finish) an EPSRC-funded PhD project in the UK. The University of Bristol is advertising prestigious one- to two-year Doctoral Prize Fellowships for outstanding applicants.

The application deadline is 31st October, and if this opportunity interests you, please email Fred to discuss potential projects.

TMCS Centre for Doctoral Traininglogo_screen

We are now seeking applications to join our fourth cohort of students in the Theory and Modelling in Chemical Sciences CDT.  Our students study theory, modelling and software development together in year one, based in Oxford. Years two-four are devoted to the main PhD project in one of the many research groups associated with the Centre.