scholarly journals Analysis of Photosynthetic Systems and Their Applications with Mathematical and Computational Models

2020 ◽  
Vol 10 (19) ◽  
pp. 6821
Author(s):  
Shyam Badu ◽  
Roderick Melnik ◽  
Sundeep Singh
Keyword(s):  
Quantum Coherence ◽  
Density Functional ◽  
Computational Models ◽  
Environmental Science ◽  
Light Harvesting ◽  
Green Sulfur Bacteria ◽  
Theoretical Background ◽  
Light Harvesting Complexes ◽  
Chlorophyll Pigments ◽  
Potential Applications

In biological and life science applications, photosynthesis is an important process that involves the absorption and transformation of sunlight into chemical energy. During the photosynthesis process, the light photons are captured by the green chlorophyll pigments in their photosynthetic antennae and further funneled to the reaction center. One of the most important light harvesting complexes that are highly important in the study of photosynthesis is the membrane-attached Fenna–Matthews–Olson (FMO) complex found in the green sulfur bacteria. In this review, we discuss the mathematical formulations and computational modeling of some of the light harvesting complexes including FMO. The most recent research developments in the photosynthetic light harvesting complexes are thoroughly discussed. The theoretical background related to the spectral density, quantum coherence and density functional theory has been elaborated. Furthermore, details about the transfer and excitation of energy in different sites of the FMO complex along with other vital photosynthetic light harvesting complexes have also been provided. Finally, we conclude this review by providing the current and potential applications in environmental science, energy, health and medicine, where such mathematical and computational studies of the photosynthesis and the light harvesting complexes can be readily integrated.

scholarly journals Local quantum uncertainty as a robust metric to characterize discord-like quantum correlations in subsets of the chromophores in photosynthetic light-harvesting complexes

2020 ◽  
Vol 66 (4 Jul-Aug) ◽  
pp. 525
Author(s):  
M. Chávez-Huerta ◽  
F. Rojas
Keyword(s):  
Quantum Coherence ◽  
Light Harvesting ◽  
Green Sulfur Bacteria ◽  
Quantum Correlations ◽  
Light Harvesting Complexes ◽  
Thermal Equilibrium State ◽  
Light Harvesting Complex ◽  
Quantum Uncertainty ◽  
Local Quantum Uncertainty ◽  
Local Quantum

Green sulfur bacteria is a photosynthetic organism whose light-harvesting complex accommodates a pigment-protein complex called Fenna-Matthews-Olson (FMO). The FMO complex sustains quantum coherence and quantum correlations between the electronic states of spatially separated pigment molecules as energy moves with nearly a 100% quantum efficiency to the reaction center. We present a method based on the quantum uncertainty associated to local measurements to quantify discord-like quantum correlations between two subsystems where one is a qubit and the other is a qudit. We implement the method by calculating local quantum uncertainty (LQU), concurrence, and coherence between subsystems of pure and mixed states represented by the eigenstates and by the thermal equilibrium state determined by the FMO Hamiltonian. Three partitions of the seven chromophores network define the subsystems: one chromophore with six chromophores, pairs of chromophores, and one chromophore with two chromophores. Implementation of the LQU approach allows us to characterize quantum correlations that had not been studied before, identify the most quantum correlated subsets of chromophores, and determine that, in the strongest associations of chromophores, the LQU is a monotonically increasing function of the coherence.

scholarly journals Parametric Mapping of Quantum Regime in Fenna–Matthews–Olson Light-Harvesting Complexes: A Synthetic Review of Models, Methods and Approaches

2020 ◽  
Vol 10 (18) ◽  
pp. 6474
Author(s):  
Bruno González-Soria ◽  
Francisco Delgado ◽  
Alan Anaya-Morales
Keyword(s):  
Quantum Coherence ◽  
Open Systems ◽  
Equations Of Motion ◽  
Green Sulfur Bacteria ◽  
Photosynthetic Performance ◽  
Physical Parameters ◽  
Main Process ◽  
Light Harvesting Complexes ◽  
Quantum Regime ◽  
Markovian Approach

Developments in ultrafast-spectroscopy techniques have revealed notably long-lived quantum coherence between electronic states in Fenna–Matthews–Olson complex bacteriochlorophylls, a group of molecules setting a nanoscale structure responsible of the coherent energy transfer in the photosynthetic process of green sulfur bacteria. Despite the experimental advances, such a task should normally be complemented with physical computer simulations to understand its complexity. Several methods have been explored to model this quantum phenomenon, mainly using the quantum open systems theory as a first approach. The traditional methods used in this approach do not take into account the memory effects of the surroundings, which is commonly approximated as a phonon bath on thermal equilibrium. To surpass such an approximation, this article applies the Hierarchical Equations of Motion method, a non-markovian approach also used to analyze the dynamic of such a complex, for the modeling of the system evolution. We perform a parametric analysis about some physical features in the quantum regime involved during the quantum excitation process in order to get a comprehension about its non-trivial dependence on operation parameters. Thus, the analysis is conducted in terms of some relevant physical parameters in the system to track the complex global behavior in aspects as coherence, entanglement, decoherence times, transference times, and efficiency of the main process of energy capturing. As a complementary analysis from the derived outcomes, we compare those features for two different species as a suggestive possible roadmap to track genetic differences in the photosynthetic performance of the complex through its biological nature.

scholarly journals Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes

2020 ◽  
Vol 22 (19) ◽  
pp. 10500-10518 ◽  
Author(s):  
Beatrix M. Bold ◽  
Monja Sokolov ◽  
Sayan Maity ◽  
Marius Wanko ◽  
Philipp M. Dohmen ◽  
...  
Keyword(s):  
Long Range ◽  
Density Functional ◽  
Light Harvesting ◽  
Tight Binding ◽  
Time Dependent ◽  
Light Harvesting Complexes ◽  
Benchmark Study ◽  
Td Dft ◽  
And Performance ◽  
Dependent Density

In the present work, we perform a benchmark study on both the isolated chromophores retinal and BChl a as well as on the biological systems, to determine the accuracy of LC-TD-DFT and LC-TD-DFTB for describing color-tuning effects.

Multiscale Modeling of Reinforced Epoxy Resins by Carbon Nanotubes and Graphene

2011 ◽  
Vol 1312 ◽  
Author(s):  
Kelvin Suggs ◽  
Vernecia Person ◽  
Chantel Nicolas ◽  
Xiao-Qian Wang
Keyword(s):  
Carbon Nanotubes ◽  
Density Functional ◽  
Computational Models ◽  
Local Density ◽  
Dynamic Structure ◽  
Supramolecular Structures ◽  
Molecular Systems ◽  
Distinct Level ◽  
Potential Applications ◽  
Nanoscale Fabrication

ABSTRACTNanocomposites are of increasing interest due to their unique structural, electronic, and thermal properties. Simultaneously, multiscale molecular modeling is becoming more robust. Therefore computational models are able to be examined with increased accuracy, complexity, and dimension. Graphene based molecules are lauded for their conductive properties as well as their architecture-like geometry which may allow bottom up nanoscale fabrication of nanoscopic structures. Furthermore, these macrocycled molecules allow high interactivity with other molecules including highly tensiled polymers that yield other novel supramolecular structures when interacted. These supramolecular structures are being investigated in lieu of a variety of potential applications. Nanocomposites of cured epoxy resin reinforced by single-walled carbon nanotubes exhibit a plethora of interesting behavior at the molecular level. A fundamental issue is how the self-organized dynamic structure of functional molecular systems affects the interactions of the nano-reinforced composites. A combination of force-field based molecular dynamics and local density-functional calculations shows that the stacking between the aromatic macrocycle and the surface of the SWNTs manifests itself via increased interfacial binding. First-principles calculations on the electronic structures further reveal that there exists distinct level hybridization behavior for metallic and semiconducting nanotubes. In addition there is a monatomic increase in binding energy with an increase in the nanotube diameter. The simulation studies suggest that graphene nanoplatelets are potentially the best fillers of epoxy matrices. The implications of these results for understanding dispersion mechanism and future nanocomposite developments are discussed.

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