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.

Quantum Drude oscillators without the dipole approximation

Interactions between Drude oscillators (two opposite charges, one fixed, one mobile, interacting by a spring) are almost always modelled in the dipole approximation. This is because the Hamiltonian for describing Drude oscillators in this way is quadratic in the creation/annihilation operators (or equivalently, is quadratic in position and momentum) and can therefore be diagonalized exactly through a normal-mode transformation.


Second-order perturbation theory for the interaction of two such oscillators produces the expected –C6 R–6 dispersion interaction. At short distances this diverges, and the exact interaction energy ceases to be defined at all.

Therefore people use screening functions to fix up the short range. How much are the screening functions fixing up the divergence, and how much are they just compensating for the use of the dipole interaction Hamiltonian? Now we can find out, because Mainak has calculated the (almost) exact binding energy between Drude oscillators with the full Coulomb interaction.

Quantum mechanics of Drude oscillators with full Coulomb interaction
M. Sadhukhan and F. R. Manby, Phys. Rev. B 94, 115106 (2016) 10.1103/PhysRevB.94.115106

Jenna and Ed join us for summer projects

Bristol Chemistry undergrads Jenna Ram and Ed Smith have joined the group for summer projects. Jenna is working on mean-field and perturbative approaches for model Hamiltonians describing systems that contain both fermions and bosons. Ed is working on optimization of density-functional quadrature grids in our in new code.

CCSD(T)-in-DFT for enzymology

Our paper A Projector-Embedding Approach for Multiscale Coupled-Cluster Calculations Applied to Citrate Synthase has appeared online in JCTC, and was one of the most highly downloaded papers soon after publication.


Citrate synthase active site and QM/MM reaction profiles computed with DFT and with CCSD(T)-in-DFT for various approximate exchange-correlation functionals.

The great thing about this is that by tuning in CCSD(T) for just a handful of reacting atoms, almost all of the dependence on the approximate exchange-correlation functional is eliminated.


Welcome to the TMCS students!

logo_screenWe’re excited to be welcoming around half of our current TMCS cohort of students to the CCC in Bristol on Monday, and the other half the following week.

The first batch of students will be with us for the week, talking science with academics and group members, and trying to decide what they’re going to work on for their PhD project.


TMCS 2015 cohort

The second group of students will be working on 5-week short projects with all of the groups in the CCC.

Molpro 2015

The latest release of Molpro provides a range of new functionality, including methods developed in the Manby group

Wavefunction-in-DFT embedding

A key new addition is wavefunction-in-DFT embedding through the projector method with basis-set truncation. This enables straightforward embedding of practically any electronic structure method implemented in Molpro in a chembedemical environment modelled by DFT. Unlike many embedding methods of this kind
there are no issues with partitioning across covalent bonds.

We have performed many calculations using the combination CCSD(T)-in-DFT, with the expensive coupled-cluster calculation only on a few, chemically active atoms. The exciting opportunity here is that the method all but eliminates dependence on choice of exchange-correlation functional.

The research behind this functionality was carried out by Martina Stella, Simon Bennie and Rob Pennifold in the Manby group; and by Jason Goodpaster and Taylor Barnes in Tom Miller’s group at Caltech.

Distinguishable cluster theory

dcdDistinguishable cluster theory with singles and doubles (DCSD) is a simple modification of CCSD, but with remarkable properties, including the ability to dissociate molecules correctly even with a closed-shell reference state.

The method was developed by Daniel Kats while he was a DFG-funded postdoc in the Manby group. There is much discussion about what exactly this approximation means (but see Daniel’s interesting paper about a screened Coulomb derivation). Whatever it turns out to mean, DCSD is already a useful tool and a powerful addition to the set of available methods. Now in Molpro running it is as simple as replacing ccsd with dcsd in the input (and the computational cost is the same as CCSD). Gradients as well as F12, orbital-optimized and Brueckner variants are available.