@inproceedings {670,
	title = {Exploring quantum efficiency in cyanobacterial photosystem I: Influence of chlorophyll positioning and dissipation rates},
	booktitle = {Proceedings of the 42nd Samahang Pisika ng Pilipinas Physics Conference},
	year = {2024},
	month = {3{\textendash}6 Jul 2024},
	pages = {SPP-2024-PB-01},
	address = {Batangas City},
	abstract = {The efficiency of excitation energy transfer in photosystems can be quantified by the quantum efficiency q, defined as the fraction of incident excitation energy that initiates charge separation at the photosynthetic reaction-center. This efficiency can be calculated from a rate matrix that governs the stochastic migration of chlorophyll excitations within the photosystem. In this paper, we examined the resulting distributions of q in cyanobacterial photosystem I when chlorophylls are displaced randomly within the experimental spatial resolution of the photosystem structure and subjected to random rotational displacements. We also investigated how q varies with the internal dissipation rates of the chlorophylls. We found that q is largely unaffected by variations in the chlorophyll positions, which shows that photosynthesis in this photosystem is robust against structural perturbations. Meanwhile, the efficiency decreases sharply with increasing internal dissipation rate{\textemdash}photosynthesis is quickly suppressed even for small increases in dissipation rates, even if the dissipation rate is 10 times smaller than the rate of charge-separation at the P700.},
	url = {https://proceedings.spp-online.org/article/view/SPP-2024-PB-01},
	author = {Ron Michael V. Acda and Francis N. C. Paraan}
}
@inproceedings {631,
	title = {Excitation transfer rates in a cyanobacterial photosystem I in the dipolar coupling approximation},
	booktitle = {Proceedings of the 41st Samahang Pisika ng Pilipinas Physics Conference},
	year = {2023},
	month = {19{\textendash}21 July 2023},
	pages = {SPP-2023-PB-15},
	address = {Siargao},
	abstract = {Photosystems are light-harvesting units utilized by photosynthetic organisms. The arrangement of chlorophylls (Chl) in each photosystem varies from organism to organism and is fine-tuned by evolution. In this paper, we study the pathways of excitation transfer in a cyanobacterial photosystem I (<em>Synechococcus elongatus</em>) using an effective Hamiltonian based on F{\"o}rster theory of resonance energy transfer. The off-diagonal terms of the Hamiltonian matrix were calculated in the dipolar coupling approximation to obtain excitation transfer rates between Chl pairs in the network. From these rates, it was found that there is a four-fold preferential excitation flow from the peripheral antenna to the B39 Chl compared to A40. The transfer rate discrepancy can be attributed to the difference in the dipole moment orientations and the spatial locations of the central Mg atom of the Chls. Strongly coupled antenna Chls were identified based on a threshold on the maximum transfer rates.},
	url = {https://proceedings.spp-online.org/article/view/SPP-2023-PB-15},
	author = {Ron Michael V. Acda and Francis N. C. Paraan}
}
@conference {647,
	title = {Network modeling of chlorophyll excitation transfer rates in cyanobacterial photosystem I in the dipolar coupling approximation},
	year = {2023},
	month = {28{\textendash}29 Nov 2023},
	pages = {BCB-21},
	publisher = {50th Philippine Society of Biochemistry and Molecular Biology Annual Convention},
	address = {The Manila Hotel},
	abstract = {The flow of excitation energy in photosystems can be described by the energy funnel model, where excitations from the higher-energy antenna pigments are funneled toward the lower-energy reaction-center chlorophylls, eventually reaching the P700 where charge separation takes place. Thus, energy transfer flow between chlorophylls in a photosystem can be modeled as a network. In this study, a network of the energy flow between individual chlorophyll nodes in cyanobacterial photosystem I (from <em>Synechococcus elongatus</em>) is constructed. The nodes of the graph are the chlorophyll molecules, which are all the chlorophyll a type. The edge weights are the quantum-mechanical transfer rates constructed under the F{\"o}rster dipole-dipole approximation. From the network, chlorophylls serving as excitation sinks and sources, as well as "central" chlorophylls from a betweenness-centrality-based metric of antenna-to-P700 energy flow, were identified. Characterization of these crucial nodes can be extended to other complex photosynthetic units, as these nodes could play a critical role in the network functioning of photosynthetic energy transfer.},
	url = {https://drive.google.com/file/d/1c-k4kQO_Kzfsv_8d_wC6VfCCOBoFXJiu/view},
	author = {Ron Michael V. Acda and Francis N. C. Paraan}
}