Applications of large-scale density functional theory in biology

Cole, D. J. A.; Hine, Nicholas D. M.

doi:10.1088/0953-8984/28/39/393001

Cited by 139 publications

(76 citation statements)

References 312 publications

(505 reference statements)

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“…First of all, the computational cost involved necessarily requires new numerical strategies in order to go beyond model systems and extremely short time-scales. In the last years, a large activity has been focused on improving the scaling of the QM calculations, 78,[130][131][132] also by introducing novel semiempirical methods 133 including Density Functional tight binding. 134 However, also the classical models have to be reconsidered in terms of their scaling as, when coupled to fast QM methods, they can become the real bottleneck of the calculation.…”

Section: Discussionmentioning

confidence: 99%

Multiscale modelling of photoinduced processes in composite systems

2019

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| In the last decades, the quantum mechanical modeling has moved from isolated molecules made of few atoms, to large supramolecular aggregates embedded in complex environments. This has been made possible by the important progress achieved by multiscale models based on the integration of QM methods with classical descriptions. One of the first example of this integration is represented by continuum solvation models that starting from the eighties of the last century have been largely and successfully applied to predict properties and processes of solvated molecules. Almost in the same years, another alternative classical description, based on Molecular Mechanics (MM) has been coupled to QM methods to give the hybrid QM/MM approach. Since their first formulations, these QM/classical models have seen an enormous development in terms of accuracy, robustness and generalizability. This progress has allowed their application to systems of increasing complexity and to processes never faced before within a QM framework. An important example of such an achievement is represented by the novel insights reached in the fundamental understanding and the possible exploitation of photoinduced processes in biomolecules, nanomaterials and, more in general, composite systems where different "objects" of molecular, nano and mesoscopic scale are coupled together. In this review, we highlight the potentials and the limitations of such modeling, thereby showing which developments are still needed to definitely make the QM-based multiscale strategy the gold-standard for explaining the outputs of novel advanced spectroscopic techniques and predicting the outcome of light-activated events in composite systems. The multiscale strategiesIn the years, two main strategies to combine QM descriptions of the target and classical models of the environment, have been proposed. Interestingly, their first formulations date back to the same years, namely the end of the seventies of the previous century. [8][9][10] The two strategies refer to continuum and discrete (or atomistic) descriptions of the environment, respectively. In the latter case, the atoms of the environment (or group of atoms in coarser grained versions of the model) are treated through a Molecular Mechanics (MM) force field (FF). [11][12][13][14][15] In the former case, instead, the atomic nature of the environment is lost and a continuum description in terms of macroscopic properties is introduced instead. 16-18 Despite this huge "modellistic" difference, the two formulations present important common elements when reconsidered from the point of view of the QM target. In any case, for simplicity's sake two separate presentations will be given. QM/continuum. If the environment loses its atomic nature, an effective description has to be introduced which is based on some macroscopic properties. This is exactly what is done in continuum models where the target sees the environment as an infinite dielectric medium characterized by a (generally) frequency and position dependent permittivit...

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Section: Discussionmentioning

confidence: 99%

Multiscale modelling of photoinduced processes in composite systems

2019

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“…The set of function Ω jβ is effectively defined by the density matrix range, and the need for jβ to overlap with atoms lν, which naturally control the number of functions entering in the sums of Eqs. (12) and (14). Note that the calculation time can be reduced by imposing a range condition (R X ) on the exchange matrix.…”

Section: E Exact Exchangementioning

confidence: 99%

Large scale and linear scaling DFT with the CONQUEST code

Nakata

Baker

Mujahed

et al. 2020

The Journal of Chemical Physics

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We survey the underlying theory behind the large-scale and linear scaling DFT code, Conquest, which shows excellent parallel scaling and can be applied to thousands of atoms with diagonalisation, and millions of atoms with linear scaling. We give details of the representation of the density matrix and the approach to finding the electronic ground state, and discuss the implementation of molecular dynamics with linear scaling. We give an overview of the performance of the code, focussing in particular on the parallel scaling, and provide examples of recent developments and applications.

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“…Formally, the excitation energies are determined by solving the electronic Schrödinger equation for each chromophore molecule in the protein, but in the absence of the other chromophore molecules [10,31,53,54,61]. Both the excitation energies and coupling elements can be calculated using ab initio electronic structure methods [10,53,61,72] although the large scale of such calculations for PPCs demands high-performance computing strategies, such as linear-scaling methods [72] or GPU-enabled approaches [61]. Instead, a more common route to determining the parameters of the electronic sub-system Hamiltonian is to use an approach such as the dipole-dipole approximation [35,54], derived by assuming that the transition densities can be treated within a point approximation.…”

Section: Theorymentioning

confidence: 99%

Photosynthetic pigment-protein complexes as highly connected networks: implications for robust energy transport

Baker¹,

Habershon²

2017

Proc. R. Soc. A.

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Photosynthetic pigment-protein complexes (PPCs) are a vital component of the light-harvesting machinery of all plants and photosynthesizing bacteria, enabling efficient transport of the energy of absorbed light towards the reaction centre, where chemical energy storage is initiated. PPCs comprise a set of chromophore molecules, typically bacteriochlorophyll species, held in a well-defined arrangement by a protein scaffold; this relatively rigid distribution leads to a viewpoint in which the chromophore subsystem is treated as a network, where chromophores represent vertices and inter-chromophore electronic couplings represent edges. This graph-based view can then be used as a framework within which to interrogate the role of structural and electronic organization in PPCs. Here, we use this network-based viewpoint to compare excitation energy transfer (EET) dynamics in the light-harvesting complex II (LHC-II) system commonly found in higher plants and the FennaMatthews-Olson (FMO) complex found in green sulfur bacteria. The results of our simple networkbased investigations clearly demonstrate the role of network connectivity and multiple EET pathways on the efficient and robust EET dynamics in these PPCs, and highlight a role for such considerations in the development of new artificial light-harvesting systems.

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Applications of large-scale density functional theory in biology

Cited by 139 publications

References 312 publications

Multiscale modelling of photoinduced processes in composite systems

Multiscale modelling of photoinduced processes in composite systems

Large scale and linear scaling DFT with the CONQUEST code

Photosynthetic pigment-protein complexes as highly connected networks: implications for robust energy transport

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