Abstract
Fast and efficient calculations of optical responses using electromagnetic models require computational acceleration and compression techniques. A hierarchical matrix approach is adopted for this purpose. In order to model large-scale molecular structures, these methods should be applied over wide frequency spectra. Here, we introduce a novel parametric hierarchical matrix method that allows one for a rapid construction of a wideband system representation and enables an efficient wideband solution. We apply the developed method to the modeling of the optical response of bacteriochlorophyll tubular aggregates as found in green photosynthetic bacteria. We show that the parametric method can provide one with the frequency and time-domain solutions for structures of the size of 100 000 molecules, which is comparable to the size of the whole antenna complex in a bacterium. The absorption spectrum is calculated and the significance of electrodynamic retardation effects for relatively large structures, i.e., with respect to the wavelength of light, is briefly studied.
Highlights
The prediction of optical properties is one of the main challenges for the theoretical characterization of molecular aggregates [1,2,3,4]
Besides the polynomial scaling of complexity, the approach opens the venue for the implementation of more efficient acceleration techniques such as the fast multipole method (FMM) [15], the integral equation fast Fourier transform (IE-FFT)[16] and the hierarchical matrix (H-matrix ) method [17, 18], all widely employed in computational electromagnetics (CEM)
All acceleration techniques introduced in computational electromagnetics, provide efficient means to reduce the complexity associated with the latter operation
Summary
Ansari-Oghol-Beig, Davood, Masoud Rostami, Ekaterina Chernobrovkina, Semion K. We introduce a characterization method – a parametric H-matrix method – to model the multi-frequency electromagnetic response of large scale molecular aggregates. We apply it to calculate stationary and time dependent optical responses of tubular aggregates (rolls) of bacteriochlorophylls (BChls) These are the building blocks of the light-absorbing antenna complex – the chlorosome – in green photosynthetic bacteria. If an iterative matrix solution method is utilized, the operation complexity is of order O(kN 2), where k is the number of required iterations and O(N 2) is due to the complexity of a single matrix-vector multiplication[21] In this respect, all acceleration techniques introduced in computational electromagnetics, provide efficient means to reduce the complexity associated with the latter operation.
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