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 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 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 Phonon Environment as a Design Element for Long-lived Excitonic Coherence: Dithia-anthracenophane Revisited

2022 ◽  
Author(s):  
Govind Sidhardh ◽  
Adithi Ajith ◽  
Ebin Sebastian ◽  
Mahesh Hariharan ◽  
Anil Shaji
Keyword(s):  
Quantum Coherence ◽  
Equations Of Motion ◽  
Design Element ◽  
Light Harvesting Complexes ◽  
Actual Structure ◽  
Exciton Dynamics ◽  
Design Elements ◽  
Molecular Systems ◽  
Reorganisation Energy

Excitonic energy transfer in light harvesting complexes, the primary process of photosynthesis, operates with near-unity efficiency. Experimental and theoretical studies suggest that quantum mechanical wave-like motion of excitons in the pigment-protein complex may be responsible for this quantum efficiency. Observed coherent exciton dynamics can be modelled completely only if we consider the interaction of the exciton with its complex environment. While it is known that the relative orientation of the chromophore units and reorganisation energy are important design elements, the role of a structured phonon environment is often not considered. The purpose of this study is to investigate the role of a structured immediate phonon environment in determining the exciton dynamics and the possibility of using it as an optimal design element. Through the case study of dithia-anthracenophane, a bichromophore using the Hierarchical Equations Of Motion formalism, we show that the experimentally observed coherent exciton dynamics can be reproduced only by considering the actual structure of the phonon environment. While the slow dephasing of quantum coherence in dithia-anthracenophane can be attributed to strong vibronic coupling to high-frequency modes, vibronic quenching is the source of long oscillation periods in population transfer. This study sheds light on the crucial role of the structure of the immediate phonon environment in determining the exciton dynamics. We conclude by proposing some design principles for sustaining long-lived coherence in molecular systems.

scholarly journals A Study of the Stability of a Plate-Like Load Towed beneath a Helicopter

1971 ◽  
Vol 13 (5) ◽  
pp. 330-343 ◽  
Author(s):  
D. F. Sheldon
Keyword(s):  
Equations Of Motion ◽  
Physical Parameters ◽  
Recent Experience ◽  
Wind Tunnel Testing ◽  
Stability Derivatives ◽  
Direct Indication ◽  
Metric Dimensions ◽  
Set Up ◽  
The Stability ◽  
Derivative Information

Recent experience has shown that a plate-like load suspended beneath a helicopter moving in horizontal forward flight has unstable characteristics at both low and high forward speeds. These findings have prompted a theoretical analysis to determine the longitudinal and lateral dynamic stability of a suspended pallet. Only the longitudinal stability is considered here. Although it is strictly a non-linear problem, the usual assumptions have been made to obtain linearized equations of motion. The aerodynamic derivative data required for these equations have been obtained, where possible, for the appropriate ranges of Reynolds and Strouhal number by means of static and dynamic wind tunnel testing. The resulting stability equations (with full aerodynamic derivative information) have been set up and solved, on a digital computer, to give direct indication of a stable or unstable system for a combination of physical parameters. These results have indicated a longitudinal unstable mode for all practical forward speeds. Simultaneously the important stability derivatives were found for this instability and modifications were made subsequently in the suspension system to eliminate the instabilities in the longitudinal sense. Throughout this paper, all metric dimensions are given approximately.

Vibration Analysis of a Partially Covered Double Sandwich Cantilever Beam With Concentrated Mass at the Free End

1993 ◽  
Author(s):  
C. Levy ◽  
Q. Chen
Keyword(s):  
Loss Factor ◽  
Equations Of Motion ◽  
Beam Theory ◽  
Physical Parameters ◽  
Mass Ratio ◽  
Euler Beam ◽  
Concentrated Mass ◽  
Sandwich Type ◽  
Euler Beam Theory ◽  
Two Parameters

Abstract The partially covered, sandwich-type cantilever with concentrated mass at the free end is studied. The equations of motion for the system modeled via Euler beam theory are derived and the resonant frequency and loss factor of the system are analyzed. The variations of resonance frequency and system loss factor for different geometrical and physical parameters are also discussed. Variation of these two parameters are found to strongly depend on the geometrical and physical properties of the constraining layers and the mass ratio.

Nonlinear Forced Vibration Analysis of Smart Curved CNTs Conveying Fluid

2021 ◽  
Author(s):  
Vahid Mohamadhashemi ◽  
Amir Jalali ◽  
Habib Ahmadi
Keyword(s):  
Carbon Nanotube ◽  
Velocity Vector ◽  
Multiple Scales ◽  
Fluid Velocity ◽  
Equations Of Motion ◽  
Primary Resonance ◽  
Maximum Amplitude ◽  
Beam Theory ◽  
Physical Parameters ◽  
Conveying Fluid

In this study, the nonlinear vibration of a curved carbon nanotube conveying fluid is analyzed. The nanotube is assumed to be covered by a piezoelectric layer and the Euler–Bernoulli beam theory is employed to establish the governing equations of motion. The influence of carbon nanotube curvature on structural modeling and fluid velocity vector is considered and the slip boundary conditions of CNT conveying fluid are included. The mathematical modeling of the structure is developed using Hamilton’s principle and then, the Galerkin procedure is employed to discretize the equation of motion. Furthermore, the frequency response of the system is extracted by applying the multiple scales method of perturbation. Finally, a comprehensive study is carried out on the primary resonance and piezoelectric-based parametric resonance of the system. It is shown that consideration of nanotube curvature may lead to an increase in nonlinearity. Implementing the fluid velocity vector in which nanotube curvature is included highly affects the maximum amplitude of the response and should not be ignored. Furthermore, different system parameters have evident impacts on the behavior of the system and therefore, selecting the reasonable geometrical and physical parameters of the system can be very useful to achieve a favorable response.

scholarly journals The Dynamical Behavior of a Rigid Body Relative Equilibrium Position

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
T. S. Amer
Keyword(s):  
Rigid Body ◽  
Degrees Of Freedom ◽  
Numerical Solutions ◽  
Equations Of Motion ◽  
Relative Equilibrium ◽  
Dynamical Behavior ◽  
Vertical Plane ◽  
The Body ◽  
Physical Parameters ◽  
Pendulum Model

In this paper, we will focus on the dynamical behavior of a rigid body suspended on an elastic spring as a pendulum model with three degrees of freedom. It is assumed that the body moves in a rotating vertical plane uniformly with an arbitrary angular velocity. The relative periodic motions of this model are considered. The governing equations of motion are obtained using Lagrange’s equations and represent a nonlinear system of second-order differential equations that can be solved in terms of generalized coordinates. The numerical solutions are investigated using the fourth-order Runge-Kutta algorithms through Matlab packages. These solutions are represented graphically in order to describe and discuss the behavior of the body at any instant for different values of the physical parameters of the body. The obtained results have been discussed and compared with some previous published works. Some concluding remarks have been presented at the end of this work. The importance of this work is due to its numerous applications in life such as the vibrations that occur in buildings and structures.

System-Level Optimization Model for a Snake-Inspired Robot Based on a Rectilinear Gait

2008 ◽  
Author(s):  
James K. Hopkins ◽  
Brent W. Spranklin ◽  
Satyandra K. Gupta
Keyword(s):  
Optimization Model ◽  
Equations Of Motion ◽  
Optimal Performance ◽  
System Level ◽  
Hierarchical Optimization ◽  
Physical Parameters ◽  
Optimization Approach ◽  
Gait Parameters ◽  
Robot Performance

Physical parameters of modules and gait parameters affect the overall snake-inspired robot performance. Hence the system-level optimization model has to concurrently optimize the module parameters and the gait. The equations of motion associated with the rectilinear gait are quite complex due to the changing topology of the rectilinear gait. Embedding these equations in the system-level optimization model leads to a computationally challenging formulation. This paper presents a system-level optimization model that utilizes a hierarchical optimization approach and meta-models of the pre-computed optimal gaits to reduce the complexity of the optimization model. This approach enabled us to use an experimentally validated physics-based model of the rectilinear gait and yet at the same time enabled us to create a system-level optimization model with a manageable complexity. A detailed case study is presented to show the importance of concurrently optimizing the module parameters and the gait using our model to obtain the optimal performance for a given mission.

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