Simulation Of Energy Transfer Research Articles

Predicting the future of excitation energy transfer in light-harvesting complex with artificial intelligence-based quantum dynamics

Exploring excitation energy transfer (EET) in light-harvesting complexes (LHCs) is essential for understanding the natural processes and design of highly-efficient photovoltaic devices. LHCs are open systems, where quantum effects may play a crucial role for almost perfect utilization of solar energy. Simulation of energy transfer with inclusion of quantum effects can be done within the framework of dissipative quantum dynamics (QD), which are computationally expensive. Thus, artificial intelligence (AI) offers itself as a tool for reducing the computational cost. Here we suggest AI-QD approach using AI to directly predict QD as a function of time and other parameters such as temperature, reorganization energy, etc., completely circumventing the need of recursive step-wise dynamics propagation in contrast to the traditional QD and alternative, recursive AI-based QD approaches. Our trajectory-learning AI-QD approach is able to predict the correct asymptotic behavior of QD at infinite time. We demonstrate AI-QD on seven-sites Fenna–Matthews–Olson (FMO) complex.

Fully differentiable optimization protocols for non-equilibrium steady states

In the case of quantum systems interacting with multiple environments, the time-evolution of the reduced density matrix is described by the Liouvillian. For a variety of physical observables, the long-time limit or steady state (SS) solution is needed for the computation of desired physical observables. For inverse design or optimal control of such systems, the common approaches are based on brute-force search strategies. Here, we present a novel methodology, based on automatic differentiation, capable of differentiating the SS solution with respect to any parameter of the Liouvillian. Our approach has a low memory cost, and is agnostic to the exact algorithm for computing the SS. We illustrate the advantage of this method by inverse designing the parameters of a quantum heat transfer device that maximizes the heat current and the rectification coefficient. Additionally, we optimize the parameters of various Lindblad operators used in the simulation of energy transfer under natural incoherent light. We also present a sensitivity analysis of the SS for energy transfer under natural incoherent light as a function of the incoherent-light pumping rate.

Electronic energy transfer in biomacromolecules

Electronic energy transfer is widely used as a molecular ruler to interrogate the structure of biomacromolecules, and performs a key task in photosynthesis by transferring collected energy through specialized pigment–protein complexes. Förster theory, introduced over 70 years ago, allows linking transfer rates to simple structural and spectroscopic properties of the energy‐transferring molecules. In biosystems, however, significant deviations from Förster behavior often arise due to breakdown of the ideal dipole approximation, dielectric screening effects due to the biological environment, or departure from the weak‐coupling regime. In this review, we provide a concise overview of advances in simulations of energy transfer in biomacromolecules that allow overcoming the main limitations of Förster theory. We first discuss advances in quantum chemical methods to compute electronic couplings, their extension to multiscale formulations to include screening effects, and strategies to treat the interplay between coupling fluctuations and energy transfer dynamics. We then examine the spectral overlap term, and how this quantity can be estimated from simulations of the spectral density of exciton–phonon coupling. Finally, we discuss rate theories that can describe energy transfers in situations where strong coupling leads to delocalized excitions, a common situation found in closely packed multichromophoric systems such as photosynthetic complexes and nucleic acids.This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Theoretical and Physical Chemistry > Spectroscopy

Study of energy transfer in silicon-based micro-ring resonators

Physical model, time-domain model, transmission spectra and energy transfer diagram of silicon-based micro-ring resonators based on the parallel waveguide structure are analyzed in this paper, in which transmission spectrum is obtained by Matlab, and the energy transfer process is analyzed by Rsoft. According to the analyses of the models and results, the energy transfer process in this type of resonator is clear to a great extent. The experimental results show that when the input signal is stable, the energy of the micro-ring resonator and the drop port tends to be steady after the input optical signal is coupled in the coupling region, which proves that the silicon-based micro-ring resonators can select specific optical signal if the input optical signal satisfies the resonance condition. However, if the resonance condition is not met, filtering function, optical switch function and signal selection function can be realized. Therefore, the analysis and simulation of energy transfer in silicon-based micro-ring resonators can not only enrich the silicon micro-ring resonator theory, but also provide new theoretical basis and method for the design and optimization of existing optoelectronic devices.

Energy Transfer and Fluid Flow around a Massive Astrophysical Object

In this work it is presented the modeling and simulation of energy transfer and fluid flow of a stationary spherical arrangement of particles surrounding a gravitational body such as an astrophysical object that carries the curvature of space-time continuum in general relativity, taking into account the thermodynamics of the second law. This model also predicts the drag of space and time around an astrophysical object as it rotates, with results close to the experimental data reported by other authors. To model the energy transfer of the mass and the fluid flow in the space-time, it is used a 4-dimensional system. In order to make measurements of entropy in the arrow of time (past-present), tensors in General Relativity were used to calculate this thermodynamic quantity and with this, the big bang ́s low entropy condition in phase space of coarse graining (Hawking ́s box), according to Weyl curvature hypothesis (WCH) of Roger Penrose. Contribution of this paper is presented by tensors which carry information that has to do with something as non-distortion effect in fluid flow around the astrophysical object and the low entropy condition that is believed to exist in the past, in the big bang; what leads us to search for a new physical-mathematical science to continue. At this point, the Einstein field equations are out of context, which leads us to conclude that it is necessary a mathematical science that allows us to make calculations to rescue lost information due to collapse of matter to a black hole. This math should allow us to clear up physical phenomena (like origin of the universe) and their relationship, with the objective of unifying theories that lead to a physical science without uncertainties, as at the present time. In this regard, we propose a metric in hyperbolic coodinates to build a physical wormhole shaped object where gravitational bodies can be housed that allow us to link the past entropy with the present entropy according to the second law of thermodynamics, as a kind of mathematical space or alternative model to compensate in some way, the link between WCH and the phase space volume of the Hawking's box, and the link between WCH and the quantum-mechanical state-vector reduction, , proposed by Penrose which still have not been determined by any author. Nomenclature

Numerical simulations of energy transfer in two collisionless interpenetrating plasmas

Ion stream instabilities are essential for collisionless shock formation as seen in astrophysics. Weakly relativistic shocks are considered as candidates for sources of high energy cosmic rays. Laboratory experiments may provide a better understanding of this phenomenon. High intensity short pulse laser systems are opening possibilities for efficient ion acceleration to high energies. Their collision with a secondary target could be used for collisionless shock formation. In this paper, using particle-in-cell simulations we are studying interaction of a sub-relativistic, laser created proton beam with a secondary gas target. We show that the ion bunch initiates strong electron heating accompanied by the Weibel-like filamentation and ion energy losses. The energy repartition between ions, electrons and magnetic fields are investigated. This yields insight on the processes occurring in the interstellar medium (ISM) and gamma-ray burst afterglows.

Evaluation of Coupling Factor in RF Inductively Coupled Systems

This work presents an approach for the measurement of mutual inductance on near field inductive coupling. The mutual inductance between inductive circuits allows the simulation of energy transfer from reader to tag, that can be used in RFID and powerless implantable devices. It also allows one to predict the maximum voltage in the tag of the radio-frequency system. Keywords—RFID, Inductive Coupling, Energy Transfer, Implantable Device

Mode-specific energy absorption by solvent molecules during CO2 vibrational cooling

Non-equilibrium molecular dynamics (NEMD) simulations of energy transfer from vibrationally excited CO(2) to CCl(4) and CH(2)Cl(2) solvent molecules are performed to identify the efficiency of different energy pathways into the solvent bath. Studying in detail the work performed by the vibrationally excited solute on the different solvent degrees of freedom, it is shown that vibration-to-vibration (V-V) processes are strongly dominant and controlled by those accepting modes which are close in frequency to the CO(2) bend and symmetric stretch vibration.

Simulation of energy transfer in disordered two‐dimensional mixed J‐aggregates

AbstractA theoretical model, based on numerical simulations, is provided to analyze the energy transfer in a two‐dimensional mixed J‐aggregate. The J‐aggregate is modeled as a square arrangement of parallel donor molecules in which a given concentration of acceptors is randomly substituted. The Frenkel exciton states are calculated by numerical diagonalization of the aggregate Hamiltonian including the static disorder. The scattering rates are calculated using a model of exciton‐phonon coupling. The concentration dependences of the absorption and fluorescence line shapes, the localization behavior of the exciton states and the time‐resolved fluorescence decays (configurationally averaged) are obtained. The simulations are checked against recent experimental results on mixed J‐aggregates of cyanine dyes. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Confinement on energy transfer between luminescent centers in nanocrystals

The luminescence dynamics of optical centers in nanocrystals depends critically on the phonon density of states (PDOS), which is quite distinct from that of bulk materials. It is shown that energy transfer (ET) in nanocrystals is confined by discrete PDOS as well as direct size restriction. Temperature-, concentration-, and size-dependence of the fluorescence decay from the S3/24 state of Er3+ in Y2O2S nanocrystals have been investigated using laser spectroscopic experiments and computational simulations. A set of microscopic rate equations that govern the evolution of the excitation probability Pi(t) are solved iteratively using a Monte Carlo method. The simulations of ET based on a theoretical model with five parameters are in good agreement with the experimental results. It is shown that phonon-assisted ET processes in Er3+:Y2O2S nanocrystals contribute partly to the fluorescence decay at 295 K, and is negligible at 5 K. For applications, the nanoconfinement effects on ET may significantly reduce the efficiency of sensitized or upconversion luminescence due to the lack of low-frequency phonon modes and restricted excitation migration in nanophosphors.

Dynamics of Energy Transfer in Peptide−Surface Collisions

Classical trajectory simulations are performed to study energy transfer in collisions of protonated triglycine (Gly)(3) and pentaglycine (Gly)(5) ions with n-hexyl thiolate self-assembled monolayer (SAM) and diamond [111] surfaces, for a collision energy E(i) in the range of 10-110 eV and a collision angle of 45 degrees. Energy transfer to the peptide ions' internal degrees of freedom is more efficient for collision with the diamond surface; i.e., 20% transfer to peptide vibration/rotation at E(i) = 30 eV. For collision with diamond, the majority of E(i) remains in peptide translation, while the majority of the energy transfer is to surface vibrations for collision with the softer SAM surface. The energy-transfer efficiencies are very similar for (Gly)(3) and (Gly)(5). Constraining various modes of (Gly)(3) shows that the peptide torsional modes absorb approximately 80% of the energy transfer to the peptide's internal modes. The energy-transfer efficiencies depend on E(i). These simulations are compared with recent experiments of peptide SID and simulations of energy transfer in Cr(CO)(6)(+) collisions with the SAM and diamond surfaces.

Simulation of Energy Transfer in Photosynthetic Antenna Systems with Monolayer Assemblies

To optimize the energy transfer (ET) from a mixture of 10-(1-(8-hexyl)pyrenyl)-decanoic acid, 10-(1-(6-hexyl)-pyrenyl)decanoic acid, and 10-(1-(3-hexyl)-pyrenyl)decanoic acid (HPyDA) to a mixture of 10-(3-(9-hexyl)perylenyl)-10-oxodecanoic acid and 10-(3-(10-hexyl)perylenyl)-10-oxodecanoic acid (HPeDA) in HPyDA-HPeDA mixed monolayer assemblies, fluorescence spectra of the mixed monolayers containing various compositions of HPyDA and HPeDA were measured. Efficient ET was observed in the mixed monolayers of HPeDA:HPyDA molar ratios of 1:3 - 1:300.

Simulations of energy transfer in Cr(CO) 6+ surface-induced dissociation

Classical trajectories are used to simulate energy transfer in collisions of hyperthermal Cr(CO) 6 + ions with a surface consisting of an n-hexyl thiolate [i.e. CH 3(CH 2) 5S] monolayer self-assembled on clean Au{111}. The fraction of the ion's initial translational energy E i, which transfers to internal vibrational/rotational degrees of freedom of the ion, slightly increases from 14 to 16% as E i is increased from 10 to 30 eV. This energy transfer efficiency is consistent with qualitative estimates from simple kinematic models and from experiments utilizing thermometer ions. The energy transfer found in these simulations agrees with those from previous simulations of Ne and Si(CD 3) 3 + colliding with self-assembled monolayer (SAM) surfaces.

Modelling and simulation of energy transfer in a saturated flow through a porous medium

Using the continuum theory of mixtures (a generalization of classical continuum mechanics), a model for a local description of the energy transfer in a saturated flow of a newtonian fluid through a rigid porous medium is proposed. It considers the fluid and the porous matrix as continuous constituents of a binary (solid-fluid) mixture. Both constituents coexist superposed in the whole volume of the mixture, so there exist simultaneously at each spatial point two temperatures and two velocities, giving rise to an energy generation and a momentum generation, which provide thermal and dynamical interactions, respectively. The forced convection heat transfer between the fluid and the solid constituents, when the fluid flows past a porous channel bounded by two isothermal parallel plates, is simulated by using a finite difference approach. The effects of some dimensionless parameters, such as β (relating the heat transfer between both constituents to the fluid constituent conduction), γ (relating both constituent's conduction), the aspect ratio, the fluid constituent's Péclet number, and the solid constituent's Nusselt number (at the channel's inlet and outlet) are discussed.

Simulations of energy transfer and trapping in two-dimensional disordered systems

A stochastic master equation is solved numerically to study energy transfer via dipole-dipole interactions and trapping in a two-dimensional random array of nonoverlapping donor pigments with dilute traps in the situation where the Förster transfer radii R D0 and R T0 (characterizing respectively the interactions among donors and between donor and trap) are equal (R D0 = R T0 = R 0). In the quasi-exponential, long-time regime of the calculated trapping decay , the trapping rate [Wbar] is given by the smallest eigenvalue of the associated master equation matrix and is found to vary linearly with the trap concentration C T and quadratically with the donor concentration C D in accordance with phenomenological theories of migration-accelerated quenching in the hopping approximation (i.e. R D0 ≫ R T0). At short times, is not exponential and can be conveniently characterized by e and τ, respectively the 1/e lifetime and the average lifetime of the decay. Quantitative dependences of and [Wbar] on C D, C T, R 0 and τ0 (the natural lifetime) are given and may be used to describe fluorescence quenching experiments in monolayers of pigments. For the sake of comparing the short time behaviour of our decays to the one observed in the photosynthetic unit (PSU), we have calculated fluorescence decays with parameters appropriate to chlorophyll a in vivo and found they could be easily fitted to a law of the form, exp [- At - Bt p] with p close to 1/2. The degree of nonexponentiality is found to be smaller than the one observed in the PSU, where the structure of the medium is believed to be inhomogeneous (rather than homogeneous, as assumed in the present study). Finally, we give the concentration dependence of [nbar] and h, respectively the walklength of the excitation to the trap and an effective hopping time derived from [nbar] and . The very different behaviour found for relative to other hopping times reported in the literature is explained in terms of the connectivity of the network and local concentration of the clusters visited by the excitation.

Simulation of energy transfer from a glow discharge to a solid surface

In this paper, a model simulating the energy transfer from a glow discharge to a metal surface is presented. The model takes into account separately the transfer of each excitation mode of the plasma species: vibrational, translational, rotational, electronic, ionic, secondary electrons, and atom recombination. The case studied is that of a N2 glow discharge heating a W surface. Vibrational excitation transfer appears to be the main channel for the heating of the surface. Recombination on the surface also has an important contribution to the energy transfer from the plasma to the solid. Ions and metastable molecules play a minor role.

Molecular dynamics simulations of energy transfer in shocked molecular systems

Molecular dynamics simulations of energy transfer in shocked molecular systems