Author Archives: fredmanby

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.

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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.

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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.

Postdoc vacancy in the group

We have just been awarded over £0.5m in a Software Infrastructure grant from EPSRC for a project on Beyond Classical Molecular Dynamics: Developing DL_POLY, led by my colleague in Bristol, Prof Neil Allan. This means we will be looking to recruit a talented postdoc in the near future, and informal inquiries – either to me or to Prof Allan – are welcome. This part of the project will focus on a top-quality MPI-parallel implementation of density-functional tight binding (DFTB) for use in DL_POLY and elsewhere. Initial aims will be DFTB (and self-consistent-charge extensions) energies, forces and extrapolation for dynamics, followed by preliminary investigations of DFTB response theory for excited states and excited-state properties.

See here for the advertisement and how to apply.

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.

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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.

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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