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Zwischenmolekulare energiewanderung und fluoreszenz
... FRET is a non-radiative process of transferring energy from an excited donor species to an acceptor [15]. When two fluorescent molecules are considered, the interface can be modeled as a pair of interacting dipoles. ...
... b Schematic depiction of the interaction between donor and acceptor point dipoles, a point dipole with a 2D-delocalized acceptor and a 2D-delocalized donor with a 2D-delocalized acceptor [16,17] (verified, e.g., by experiment with biacetyl molecule on silver [22]), a quantum well coupled to a quasicontinuum of high-energy quantum dot states [18] (verified in a InGaN QW/CdSe QD device), and, most recently, a fluorescent molecule on Gr [20]. Swathi et al. [20] were able to derive the localized donor/graphene energy transfer rate formula analytically within the FRET effect [15]. A few computational applications of this derivation have revealed that in molecular donor/graphene heterojunctions, the competing Dexter energy transfer mechanism is negligible compared to FRET [24,25], which is the focus of current work. ...
... In the current study, we use ab initio computations to derive ground-and excited-state properties related to CT and FRET processes. Then, we apply the analytical approaches for FRET [15,26] and CT [27], allowing a direct comparison of occurrence rates of each process. We aim to assess the strength of both energy and charge transfer mechanisms at a 0D/2D interfaces consisting of planar NGs with different sizes and symmetries physisorbed on a Gr monolayer (Fig. 2). ...
The charge and energy transfer processes in photoexcited 0D/2D donor/graphene heterojunctions occur through multiple different pathways. A donor deexcitation event occurring in the most prevalent Förster energy transfer mechanism (strongly favored over Dexter transfer in van der Waals heterojunctions) prevents charge transfer from taking place, thus creating a competition between the two processes. By applying a robust computational approach, we describe the two processes from first principles and quantify their rates using Förster and Marcus theories. We consider nanojunctions where the donor are nanographenes with varying size and symmetry, and discern important trends, e.g., the symmetry-induced quenching, or the enhancement due to increased size. We observe that heterojunctions where nanographenes do not have a center of symmetry show decreased photoinduced hole and energy transfer rates, which can then be recovered by increasing the delocalization length, whereas for centrosymmetric nanographenes both hole and energy transfer processes are enhanced. Nevertheless, the hole transfer rate dominates over the energy transfer process, providing a new computation-driven design principle for obtaining a high-charge transfer junction with minimized contribution of the competing energy transfer.
... To overcome this limitation much work has been done on embedding different lanthanide ions in ligands such that the ligands (which have large absorption coefficients) absorb the pump light and subsequently transfer the absorbed energy to the lanthanide ion [45,[47][48][49][50][51][52][53][54][55][56][57][58][59][60][61]. This energy transfer is typically radiationless and can occur via several possible mechanisms: electron exchange [48,53], dipole-dipole interactions (both allowed [62][63][64][65] and unallowed transitions [48,66]), dipole-quadrapole interactions [48], and excitons [67,68]. This energy transfer has been empirically found to be most efficient if the ligand's lowest triplet energy level is between 0.23 eV and 0.62 eV greater than the lanthanide's primary luminescent state, as energy back-transfer is more likely to occur for energy differences of < 0.23 eV [51,69]. ...
... Using simple exponential fits to the data in Figures 9a and 9b we determine the lifetime as a function of Dy concentration, which is shown in Figure 8. From Figure 8 we find that as the concentration increases the lifetime becomes shorter, with the largest change occurring when going from 1 mol% to 5 mol%. The influence of concentration quenching on lanthanide luminescence lifetimes has been studied in depth [48,[62][63][64][65][66][76][77][78][79][80] with the two main mechanisms of concentration quenching in solid-state materials being: long-range Energy Transfer (LRET) [62][63][64][65]80], and short-range Dexter electron exchange [66]. These mechanisms result in different functional behavior of the lifetime as a function of concentration. ...
... Using simple exponential fits to the data in Figures 9a and 9b we determine the lifetime as a function of Dy concentration, which is shown in Figure 8. From Figure 8 we find that as the concentration increases the lifetime becomes shorter, with the largest change occurring when going from 1 mol% to 5 mol%. The influence of concentration quenching on lanthanide luminescence lifetimes has been studied in depth [48,[62][63][64][65][66][76][77][78][79][80] with the two main mechanisms of concentration quenching in solid-state materials being: long-range Energy Transfer (LRET) [62][63][64][65]80], and short-range Dexter electron exchange [66]. These mechanisms result in different functional behavior of the lifetime as a function of concentration. ...
We develop a two-color thermometry (TCT) phosphor based on [YDy(acetylacetonate)(1,10-phenanthroline)] ([YDy(acac)(phen)]) molecular crystals for use in heterogeneous materials. We characterize the optical properties of [YDy(acac)(phen)] crystals at different temperatures and Dy concentrations and find that the emission is strongly quenched by increasing temperature and concentration. We also observe a broad background emission (due to the ligands) and find that [YDy(acac)(phen)] photodegrades under 355 nm illumination with the photodegradation resulting in decreased luminescence intensity. However, while decreasing the overall emission intensity, photodegradation is not found to influence the integrated intensity ratio of the and transitions. This ratio allows us to compute the temperature of the complex Based on the temperature dependence of these ratios we calculate that [YDy(acac)(phen)] has a maximum sensitivity of 1.5 \% K and our TCT system has a minimum temperature resolution of 1.8 K. Finally, we demonstrate the use of [YDy(acac)(phen)] as a TCT phosphor by determining a dynamic temperature profile using the emission from [YDy(acac)(phen)].
... Additionally, the Otto engine is known for its robustness in various quantum thermodynamic applications, making it an excellent choice for investigating the effects of the Förster interaction and quantum entanglement in InAs quantum dots. Our objective is to examine the work performed by the heat engine by changing the external electric field in the adiabatic stages, and to study the engine's behavior against the Förster mechanism effects [22]. The Förster mechanism, also known as Förster resonance energy transfer, is a quantum mechanical process that describes the energy transfer between two chromophores (molecules that absorb light) through non-radiative dipole-dipole coupling [23]. ...
... We propose a quantum system composed of three coupled semiconductor InAs quantum dots with a small inter-dot distance, typically on the order of a few nanometers, which allows for significant dipole-dipole interactions between them [24,25], as a working substance for the quantum Otto engine (see Fig. 1). We use the excitonic electric dipole moments as a qubit in each quantum dot, under an external electric field ⃗ E , and rely on the Förster mechanism between the excitons to explain the energy transfer between the qubits [22]. ...
... with ⃗ d is the electric dipole moment associated to the exciton; it is supposed to be the same for each quantum dot, denote the Förster interaction [22] i.e. resonant energy transfer between the excitons, and ℏJ z is the static exciton-exciton dipolar interaction energy. In our Hamiltonian, the first term represents the energy associated with the excitons (electron-hole pairs) in each quantum dot. ...
Heat engines are considered a valuable resource for the modern society. The development of these systems leads to the production of heat engines with high efficiency despite their small size, called quantum heat engines. Among these, the quantum Otto cycle which is considered a fundamental thermodynamic cycle in classical heat engines, has also found applications in the realm of quantum heat engines. In this paper, we consider three InAs quantum dots as a working substance, which allows the engine to operate at very small scales, in the presence of an electric field, and the Förster mechanism, which describes the transfer of energy between quantum dots and thus affects the engine’s behavior. In this regard, we study the behavior of the work performed by the engine and the entanglement in the system as the Förster parameter is varied. We found a significant link between the engine’s work performance, the system’s entanglement, and the Förster interaction. At a critical Förster interaction value, which depends on the excitons frequencies, we observe a sharp inflection in work output. This transition coincides with the system reaching maximum entanglement after a separable state.
... However, the physically blended crystals of Cu 8 and Cu 10 clusters were still FRET inactive due to the insufficiently small intermolecular distance (Fig. 1, route I). To address this, a spatial confinement strategy, i.e., the forced cocrystallization, was exploited between Cu 8 and Cu 10 clusters, leading to a cocrystallized bicomponent Cu 8 (p-MBT) 8 (PPh 3 ) 4 @Cu 10 (p-MBT) 10 (PPh 3 ) 4 (abbreviated as Cu 8 @Cu 10 ). The overlapped emission of the Cu 8 donor and excitation of the Cu 10 acceptor, along with their controllable intermolecular distance in the cocrystallized unit cell, endowed the Cu 8 @Cu 10 cocrystal with the FRET characterization ( Fig. 1, route II). ...
... The forced cocrystallization was exploited between Cu 8 and Cu 10 clusters, giving rise to a cocrystallized bicomponent Cu 8 (p-MBT) 8 (PPh 3 ) 4 @Cu 10 (p-MBT) 10 (PPh 3 ) 4 . Before the crystallization, the ESI-MS of the mother liquid showed a mixed composition of Cu 8 and Cu 10 nanoclusters ( Supplementary Fig. 15). ...
... The precipitate was dissolved with dichloromethane, and the solution was centrifuged to remove the byproducts. The yellow crystals of Cu 8 (p-MBT) 8 (TPP) 4 were obtained by the liquid diffusion of n-hexane into the dichloromethane solution of the nanocluster for three days. ...
Understanding the fluorescence resonance energy transfer (FRET) of metal nanoparticles at the atomic level has long been a challenge due to the lack of accurate systems with definite distance and orientation of molecules. Here we present the realization of achieving FRET between two atomically precise copper nanoclusters through cocrystallization-induced spatial confinement. In this study, we demonstrate the establishment of FRET in a cocrystallized Cu8(p-MBT)8(PPh3)4@Cu10(p-MBT)10(PPh3)4 system by exploiting the overlapping spectra between the excitation of the Cu10(p-MBT)10(PPh3)4 cluster and the emission of the Cu8(p-MBT)8(PPh3)4 cluster, combined with accurate control over the confined space between the two nanoclusters. Density functional theory is employed to provide deeper insights into the role of the distance and dipole orientations of molecules to illustrate the FRET procedure between two cluster molecules at the electronic structure level.
... These molecules then power the light-dependent reactions of photosynthesis. The ATP and NADPH molecules are then used as energy sources in the light-independent reactions of photosynthesis ( Figure 2) [10]- [13]. This process then produces the sugar molecules that are necessary for plant growth. ...
... Photosynthesis is an essential process that helps maintain the balance of oxygen and carbon dioxide in the atmosphere, which is necessary to sustain life on Earth. Figure 4: Diagram of the cell membrane of a photosynthetic bacterium [4,13] When a photon interacts with the CR, it triggers an electron transfer from P to ubiquinone QB. This reduction of QB causes it to take two protons from the cytoplasm. ...
... The spectral variations linked to the presence of coupling between excitons will depend on their respective arrangement with each other. Three borderline cases have been studied in the literature [13] corresponding to geometric arrangements defined between the two chromophores: ...
These spacers can create tailor-made recognition motifs that recognize specific molecules or molecular structures. The bis-porphyrin nucleoside spacers allow for greater flexibility and accuracy in the design of recognition motifs, leading to improved molecular recognition. This makes it possible to create custom recognition motifs for various applications, such as drug target identification and drug delivery. Bis-porphyrin nucleoside spacers can also build complicated recognition motifs with many recognition sites. This allows the creation of highly precise recognition motifs for many targets, improving medication delivery and efficacy. This can drastically cut drug dosage, lowering adverse effects and expense. High stability makes recognition motifs appropriate for long-term applications. Several disorders have been treated with encouraging outcomes using this technology. It could change medicine delivery and improve focused treatments. This technology will grow more significant as more applications are developed to serve more people. It could transform the healthcare business and improve disease treatment. It could save time and money by simplifying therapies and increasing patient outcomes. It can also lower treatment costs and make them more accessible. It can also help doctors make better judgments and deliver better care by providing more accurate and timely patient insights. More dependable and accurate than traditional treatments, AI-driven medical treatments reduce errors and patient harm. Doctors and healthcare providers are increasingly using AI-driven medicinal treatments. AI-driven medical treatments are cheaper than traditional ones, saving healthcare providers money. AI-driven treatments can also speed up diagnosis and treatment, saving time and money.
... FRET is the process of energy transfer between two particles through the exchange of virtual photons in the near-field of the emitters. Typical inter-emitter separations are a few nanometers [57]- [60]. FRET goes from an initially excited donor emitter to a lower-energy acceptor, with broad overlapping emission and absorption spectra. ...
... Next we examine the one-way Förster energy transfer [57] between two emitters located at different heights within the hBN layer on the silver substrate by utilizing the large differences between the single-emitter decay rates of the donor and the acceptor. We are inspired by Ref. [42] where it is proposed to enhance of FRET with the help of localized surface plasmons in metal nanoparticles. ...
We study the collective photon decay of multiple quantum emitters embedded in a thin high-index dielectric layer such as hexagonal boron nitride (hBN), with and without a metal substrate. We first explore the significant role that guided modes including surface plasmon modes play in the collective decay of identical single-photon emitters (super- and subradiance). Surprisingly, on distances relevant for collective emission, the guided or surface-plasmon modes do not always enhance the collective emission. We identify configurations with inhibition, and others with enhancement of the dipole interaction due to the guided modes. We interpret our results in terms of local and cross densities of optical states. In the same structure, we show a remarkably favorable configuration for enhanced Förster resonance energy transfer between a donor and acceptor in the dielectric layer on a metallic substrate. We compare our results to theoretical limits for energy transfer efficiency.
... Here, we consider the phenomenon of Förster Resonance Energy Transfer (FRET) as a means for efficient nanocommunication. It is a spectroscopic process in which one molecule transfers its excitation energy non-radiatively over a distance of 1-10 nm to another molecule [9]. The FRET phenomenon has some critical communication advantages. ...
... The rate of the energy transfer and the range of it can be observed depend mainly on the overlap of the donor emission spectrum and the acceptor acceptor pair. These relationships were first measured by Förster [9], and later If the donor molecule is excited not by an external photon, but the energy comes from a chemical reaction, the phenomenon is called Bioluminescence Resonance Energy Transfer (BRET). BRET has some advantages over FRET. ...
Nano-communication has gained significant attention in the last few years, as a means to establish information transfer between future nano-machines. Comparing with other communication techniques for nano-scale (calcium ions signaling, molecular or catalytic nanomotors, pheromones propagation, bacteria-based communication), the phenomenon called Forster Resonance Energy Transfer (FRET) offers significantly smaller propagation delays and high channel throughput. In this paper, we report our recent experiments on FRET-based nano-networks performed in the Laboratory of Cell Biophysics of the Jagiellonian University, Krakow. We propose to use Alexa Fluor dyes as nano transmitters and receivers, as they enable to create multiple-input multi-output (MIMO) FRET communication channels and thus enhance FRET efficiency. We measure FRET efficiency values, calculate bit error rates for the measured scenarios and extend the calculations to consider a general case of MIMO (n,m) FRET channels.
... The problem of choosing the dielectric constant is further confounded by the expression used to describe the screening and local field effects due to the protein matrix, f. The Onsager local field factor is the oft-used local field factor [38,39], but common methods used in photosynthesis to describe f are the Förster [40] and Juzeliūnas and Andrews [41][42] methods. However, for the range of dielectrics from 2.0 -8.41 examined in this paper, the Onsager screening term only gives a slight increase in coupling strength over the traditional Förster term, and therefore the results in using these factors are expected to be almost equivalent due to their very close similarity. ...
... To robustly capture macroscopic, neuronal-level effects from electronic oscillations at the molecular level, we modeled tubulin aromatic networks from first-principles density functional theory methods and fully quantum transition dipole coupings, and then connected those results to protein-and polymer-level dynamics derived from classical or semi-classical approaches. The physical intuition for this process is visualized in Figures 2 and 3. To analyze the impact of UV photoexcitation on tubulin networks, we applied techniques from Förster resonance energy transfer, which remains the dominant theory applied in electronic energy transport to describe the coherent conveyance of electronic energy across chromophores via electrodynamic coupling of their transition electric dipole moments [40]. To compute excitonic coupling interactions for comparison with experimental data, we implemented the Schrödinger equation with a tightbinding Hamiltonian for an interacting N-body system. ...
Oxidative stress is a pathological hallmark of neurodegenerative tauopathic disorders such as Alzheimer's disease and Parkinson's disease-related dementia, which are characterized by altered forms of the microtubule-associated protein (MAP) tau. MAP tau is a key protein in stabilizing the microtubule architecture that regulates neuron morphology and synaptic strength. The precise role of reactive oxygen species (ROS) in the tauopathic disease process, however, is poorly understood. It is known that the production of ROS by mitochondria can result in ultraweak photon emission (UPE) within cells. One likely absorber of these photons is the microtubule cytoskeleton, as it forms a vast network spanning neurons, is highly co-localized with mitochondria, and shows a high density of aromatic amino acids. Functional microtubule networks may traffic this ROS-generated endogenous photon energy for cellular signaling, or they may serve as dissipaters/conduits of such energy. Experimentally, after in vitro exposure to exogenous photons, microtubules have been shown to reorient and reorganize in a dose-dependent manner with the greatest effect being observed around 280 nm, in the tryptophan and tyrosine absorption range. In this paper, recent modeling efforts based on ambient temperature experiment are presented, showing that tubulin polymers can feasibly absorb and channel these photoexcitations via resonance energy transfer, on the order of dendritic length scales. Since microtubule networks are compromised in tauopathic diseases, patients with these illnesses would be unable to support effective channeling of these photons for signaling or dissipation. Consequent emission surplus due to increased UPE production or decreased ability to absorb and transfer may lead to increased cellular oxidative damage, thus hastening the neurodegenerative process.
... The combination of unique transport properties of graphene, including ballistic transport and strong absorption of light by organic molecules, leads to the emergence of new hybrid nanostructures with great application potential for highly efficient photodetectors, biomedical sensors, and photovoltaic devices [8,9]. The observed energy transfer can be explained on the basis of two mechanisms of nonradiative energy transfer: inductive-resonant (Förster type) [14] and exchange-resonant (also called Dexter) [15] energy transfer mechanisms. Förster's mechanism describes the direct nonradiative energy transfer from the optically excited dye molecule to the carbon substrate. ...
... This part of this section is devoted to an overview of the main existing theoretical approaches. For the first time, the quantum mechanical theory of non-radiative (resonance) transfer of excitation energy from the donor (excited molecule) to the acceptor (non-excited molecule) was developed quite a long time ago in the papers of Förster [14] and Dexter [15]. For the first time, this theory was applied to calculate the rate of Förster energy transfer from an excited dye molecule to a two-dimensional structure (graphene) in the works of Sebastian K.L. and Swathi R.S. [17][18][19]. ...
Based on the first principles, we have shown that the decisive role in energy transfer from the fluorophore molecule to the carbon substrate (graphene) is played by the Förster-type inductive-resonance energy transfer mechanism. The Förster energy transfer rate can be calculated analytically via Fermi’s golden rule with the momentum-dependent initial final states of the graphene substrates and the HOMO (the highest occupied molecular orbital) and LUMO (the lowest unoccupied molecular orbital) states of the dye molecule. Combining first-principle calculations characterizing the hybrid carbon nanomaterials with tight-binding-based consideration of graphene wave functions allows us to obtain an analytical expression for the Förster energy transfer rate. We constructed graphical dependences of the Förster energy transfer rate at the distance R between substrate (graphene) and dye molecule for several materials. The results obtained can be applied to various hybrids based on carbon nanostructures and in general to the description of energy transfer processes in molecular functionalized nanostructures, once the molecular dipole moment and the substrate - molecule separation are known.
... To assess the heteromeric interactions of the selected MRGPRs, luciferase complementation (LC)-based NanoLuc binary technology (NanoBiT; Promega) was employed [332]. NanoBiT assay was validated by comparison with proximity-dependent assays based on resonance energy transfer (RET), such as bioluminescence resonance energy transfer (BRET) [333,334], and lastly, the heteromerization of MRGPRs was assessed by co-immunoprecipitation [335]. ...
... The BRET phenomenon follows Förster resonance energy transfer principles, where the donor is excited through an enzymatic reaction between the luciferase enzyme and the substrate, but not via an external excitation source as in FRET (Fluorescence resonance energy transfer). This results in improved sensitivity and a better signal-to-noise ratio in BRET compared to FRET [333,334]. Exploiting the principle of RET, where improved quantum yield of the donor is known to increase the photon-efficiency of the BRET fusion protein, we utilized NanoLuc luciferase, which has high quantum yield compared to Renilla or firefly luciferases [337]. The BRET system was developed using NanoLuc (Emmax 460 nm) as an energy donor paired with the monomeric-fluorescent protein mOrange (mOr; 26kDa; Exmax/Emmax: 548/562 nm) as an energy acceptor [340], providing a spectral resolution of ~105 nm between donor and acceptor emission peaks. ...
The largest family of membrane receptors, known as G protein-coupled receptors (GPCRs), are essential to cellular signaling and regulate physiological processes. Presently, ~35%–40% of US FDA-approved medications target GPCRs. A subfamily of GPCRs, Mas-related G protein-coupled receptors (MRGPRs), which belong to the δ-group of the rhodopsin-like GPCRs, was discovered two decades ago. MRGPRs are expressed by small non-myelinated sensory neurons of the dorsal root ganglia and trigeminal ganglia, mast cells, neutrophils, and macrophages and are known to play a role in itch, pain, and pseudo-allergic drug reactions. Moreover, MRGPRs have been identified as mediators in the renin-angiotensin system and cardiovascular biology. In addition, literature suggests that MRGPRs are also involved in inflammatory processes. Despite the fact that humans express eight MRGPRs (MRGPRD to G and X1-X4), information about their activation, signaling pathways, and role in inflammation is insufficient, and most of them are still classified as orphans. Since MRGPRs are involved in itch, pain, and inflammation, which are important physiological processes, the goal of this PhD was to: i) examine the role of MRGPRs in inflammation biology; ii) decipher the activation mechanism of MRGPRs; and iii) elucidate the oligomeric interaction of MRGPRs. Firstly, it was investigated whether β-alanine or alamandine-activated MRGPRD induces interleukin-6 (IL-6) release. It was observed that β-alanine activated MRGPRD-induced IL-6 release via the Gαq/Phospholipase C/NF-kB signaling pathway. Moreover, using IL-6 as a marker for MRGPRD activation, the mechanosensitivity of the MRGPRD and the effect of sterol derivatives, i.e., cholesterol and bile acids, on the activation of MRGPRD were established. Furthermore, it was discovered that the MRGPRD was constitutive (ligand-independent) active. In addition, it was discovered that methyl-β-cyclodextrin, which is known to remove sterols from the plasma membrane, triggered the MRGPRD-mediated IL-6 release. Secondly, in an effort to deorphanize MRGPRs, it was established that cysteine protease cathepsin S activates MRGPRD and MRGPRF. Lastly, using biophysical and biochemical techniques such as luciferase complementation, bioluminescence resonance energy transfer, and co-immunoprecipitation assays, the heteromeric interactions between MRGPRE and MRGPRF were unambiguously detected. Overall, in this doctoral thesis, the primary objective was to improve understanding of the involvement of MRGPRs in inflammatory biology, the activation mechanisms of MRGPRs, and the oligomeric interaction of MRGPRs.
... rst to articulate that the emitted light is of longer wavelength than the incident light (Valeur 2001). Calcium sulfide is, in fact, phosphorescent and the first theoretical distinction between these two processes was provided by Francis Perrin who also worked on a quantitative model of fluorescence quenching and polarized fluorescence (Valeur 2001). In 1948, Theodor Förster (1910-1974 published his quantum mechanical theory of dipole-dipole energy transfer (Sect. 5.3.4). Spectroscopy and microscopy, and our understanding of complex biological systems, would never be the same again. Three images showcasing the breadth of meaningful biological information that can be acquired through fluores ...
... A fluorophore in the first singlet excited state can variously lose its excitation energy by conversion into light (fluorescence), via thermal equilibration (vibrational relaxation), or by the formation of a non-fluorescent ground state complex with another molecule (static quenching). Yet another mechanism, first described by Theodor Förster in 1948, is a non-radiative energy transfer process that is regarded as a dynamic quenching mechanism because energy transfer occurs while the donor is in the excited state (Förster 1948). Fluorescence resonance energy transfer (FRET) is a long-range electrodynamic phenomenon that has found countless applications, particularly in biological systems in which its distance-dependence means that it can be used as a "spectroscopic ruler." ...
The study of fluorescence has revolutionized biomedical research. Since it was first described almost two centuries ago, fluorescence has transformed the scientific enterprise by facilitating unprecedented insights into the intricacies of biological systems on small and large scales. This chapter presents an overview of this curious photophysical phenomenon and the ways in which fluorescence can be harnessed to enrich our understanding of chemical and biological systems through spectroscopy and microscopy.
... The contribution of each conformation to the spectrum was broadened by a normalized gaussian function with standard deviation of k B T = 0.026 eV, k B being the Boltzmann constant. The simulated spectra were used to calculate Förster radii between dye molecules as well as radiative lifetimes [33,34]. ...
... In organic compounds, energy transfer for singlet excitons occurs via Förster Resonance Energy Transfer (FRET) [33,35], which is a non-radiative process where excitation energy is transferred from one molecule to the other given the existence of overlap between the fluorescence and absorption spectra of the donor and acceptor molecules, respectively. Its rate, k F , is calculated as ...
Photodynamic therapy (PDT) and photothermal therapy (PTT) are promising candidates for cancer treatment and their efficiency can be further enhanced by using a combination of both. While chloroaluminum phthalocyanine (AlClPc) has been studied extensively as a photosensitizer in PDT, nanographene oxide (nGO) has shown promise in PTT due to its high absorption of near-infrared radiation. In this work, we investigate the energy transport between AlClPc and nGO for their combined use in phototherapies. We use density functional theory (DFT) and time-dependent DFT to analyze the electronic structure of AlClPc and its interaction with nGO. Based on experimental parameters, we model the system's morphology and implement it in Kinetic Monte Carlo (KMC) simulations to investigate the energy transfer mechanism between the compounds. Our KMC calculations show that the experimentally observed fluorescence quenching requires modeling both the energy transfer from dyes to nGO and a molecular aggregation model. Our results provide insights into the underlying mechanisms responsible for the fluorescence quenching observed in AlClPc/nGO aggregates, which could impact the efficacy of photodynamic therapy.
... Förster resonance energy transfer (FRET) (Förster 1948;Lakowicz 2006;Sener et al. 2011) and excitonic (Agranovich and Galanin 1982;Sener et al. 2011) theories were used to determine the PBS → PS II and PBS → OCP R energy transfer rates, respectively. Theoretical calculations of energy transfer and quenching were based on the molecular architecture model of the OCP-PBS-PS II supercomplex previously developed in silico from the X-ray crystal structures of APC trimers stacked in cylinders (Zlenko et al. 2017), the PS II dimer ) and the red carotenoid protein (RCP) identical to the N-terminal domain of OCP R (Leverenz et al. 2015) directly involved in the interaction with PBS. ...
... It is implicitly assumed that PBS transfers the absorbed energy to PS II via the FRET mechanism, which is characterized by the notion of the Förster radius (R 0 ) (Förster 1948;Lakowicz 2006;Kawakami et al. 2022): ...
The chromophorylated PBLcm domain of the ApcE linker protein in the cyanobacterial phycobilisome (PBS) serves as a bottleneck for Förster resonance energy transfer (FRET) from the PBS to the antennal chlorophyll of photosystem II (PS II) and as a redirection point for energy distribution to the orange protein ketocarotenoid (OCP), which is excitonically coupled to the PBLcm chromophore in the process of non-photochemical quenching (NPQ) under high light conditions. The involvement of PBLcm in the quenching process was first directly demonstrated by measuring steady-state fluorescence spectra of cyanobacterial cells at different stages of NPQ development. The time required to transfer energy from the PBLcm to the OCP is several times shorter than the time it takes to transfer energy from the PBLcm to the PS II, ensuring quenching efficiency. The data obtained provide an explanation for the different rates of PBS quenching in vivo and in vitro according to the half ratio of OCP/PBS in the cyanobacterial cell, which is tens of times lower than that realized for an effective NPQ process in solution.
... FRET was described by Theodor Förster in 1948 and refers to the non-radiative transfer of energy from an excited donor fluorophore to an acceptor fluorophore [17]. The process begins when a donor fluorophore absorbs a photon, promoting its electrons to a higher energy state. ...
Förster Resonance Energy Transfer combined with Fluorescence Lifetime Imaging Microscopy (FRET-FLIM) is revolutionizing plant biology, by enabling the study of protein–protein interactions (PPIs) within live cells. This manuscript describes the principles of FRET and the practical application of FRET acceptor photobleaching (FRET-APB) in exploring PPIs in vivo . It mainly focuses on the superior characteristics of FRET-FLIM and details the materials and methods for implementing this technique in plants. It provides a profound overview about the required instruments, protocols for sample preparation, methods for calibration and acquisition, and pipelines for data analyses including novel analyses for binding and FRET efficiencies. Furthermore, it discusses the potential pitfalls and challenges related to the sample autofluorescence, protein expression heterogeneity, and acquisition photodamage or bleaching. This works aims to highlight the great prospects of FRET-FLIM in advancing our understanding of PPIs in living plant cells.
... Exciting the donor fluorophore may result in energy transfer to the nearby acceptor dye. According to T. Förster [12][13][14] the energy transfer efficiency between a donor and an acceptor fluorophore depends on several factors, e.g. the distance, the transition dipole moment orientations, the fluorescence quantum yield, the fluorescence lifetime of the donor or quenching processes of the fluorophores by the local environment. The donor excited state lifetime of a FRET-labeled protein depends on two competing radiative processes beside nonradiative decay pathways, i.e. the fluorescence decay and the energy transfer in the presence of an acceptor dye. ...
ATP synthases utilize a proton motive force to synthesize ATP. In reverse, these membrane-embedded enzymes can also hydrolyze ATP to pump protons over the membrane. To prevent wasteful ATP hydrolysis, distinct control mechanisms exist for ATP synthases in bacteria, archaea, chloroplasts and mitochondria. Single-molecule F\"orster resonance energy transfer (smFRET) demonstrated that the C-terminus of the rotary subunit epsilon in the Escherichia coli enzyme changes its conformation to block ATP hydrolysis. Previously we investigated the related conformational changes of subunit F of the A1AO-ATP synthase from the archaeon Methanosarcina mazei G\"o1. Here, we analyze the lifetimes of fluorescence donor and acceptor dyes to distinguish between smFRET signals for conformational changes and potential artefacts.
... A fast conversion is important since any delay would increase the chances of relaxation mechanisms to channel energy into heating instead of chemical potentials. Early explanations of the energy transport, based on incoherent and dipole-dipole-mediated excitation hopping between molecular sites (Förster, 1948), failed to explain the observed transfer rates. Delocalization and coherent exciton coupling between the closely packed antenna pigments were therefore suggested as the most likely explanation, with experimental support rapidly growing throughout recent years. ...
Quantum physics and biology have long been regarded as unrelated disciplines, describing nature at the inanimate microlevel on the one hand and living species on the other hand. Over the last decades the life sciences have succeeded in providing ever more and refined explanations of macroscopic phenomena that were based on an improved understanding of molecular structures and mechanisms. Simultaneously, quantum physics, originally rooted in a world view of quantum coherences, entanglement and other non-classical effects, has been heading towards systems of increasing complexity. The present perspective article shall serve as a pedestrian guide to the growing interconnections between the two fields. We recapitulate the generic and sometimes unintuitive characteristics of quantum physics and point to a number of applications in the life sciences. We discuss our criteria for a future quantum biology, its current status, recent experimental progress and also the restrictions that nature imposes on bold extrapolations of quantum theory to macroscopic phenomena.
... This work will focus on the area of non-radiative energy transfer (NRET) of energy absorbed by QDs [17][18][19]. Förster-type NRET is a dipole-dipole interaction between resonant donor and acceptor species and has a well-defined distance dependence [20]. NRET has been demonstrated in a large range of material systems, with potential for LED [9,[21][22][23][24][25] and light harvesting applications [2,3,13,[26][27][28][29][30][31][32][33]. ...
Ag nanoparticles in the form of colloids and ordered arrays are used to demonstrate plasmon-mediated non-radiative energy transfer from quantum dots to quantum wells with varying top barrier thicknesses. Plasmon-mediated energy transfer efficiencies of up to ~25% are observed with the Ag colloids. The distance dependence of the plasmon-mediated energy transfer is found to follow the same d^{-4} dependence as the direct quantum dot to quantum well energy transfer. There is also evidence for an increase in the characteristic distance of the interaction, thus indicating that it follows a F\"orster-like model with the Ag nanoparticle-quantum dot acting as an enhanced donor dipole. Ordered Ag nanoparticle arrays display plasmon-mediated energy transfer efficiencies up to ~21%. To explore the tunability of the array system, two arrays with different geometries are presented. It is demonstrated that changing the geometry of the array allows a transition from overall quenching of the acceptor quantum well emission to enhancement, as well as control of the competition between the quantum dot donor quenching and energy transfer rates.
... The original quantum derivations by Oppenheimer and Förster [4][5][6] appealed to the "golden rule" of quantum mechanics [8]. However, Physics textbooks present that result in a way that seems applicable only for transitions to or from a continuum of states-not the discrete electron energy levels of donor and acceptor fluorophores. ...
Resonance energy transfer has become an indispensable experimental tool for single-molecule and single-cell biophysics. Its physical underpinnings, however, are subtle: It involves a discrete jump of excitation from one molecule to another, and so we regard it as a strongly quantum-mechanical process. And yet, its kinetics differ from what many of us were taught about two-state quantum systems; quantum superpositions of the states do not seem to arise; and so on. Although J. R. Oppenheimer and T. F\"orster navigated these subtleties successfully, it remains hard to find an elementary derivation in modern language. The key step involves acknowledging quantum decoherence. Appreciating that aspect can be helpful when we attempt to extend our understanding to situations where F\"orster's original analysis is not applicable.
... When the interaction with the environment (internal vibrations, solvent, etc.) is much stronger than the resonant excitation transfer interaction, the excitation becomes more or less localized on one monomer and the transfer is no longer described by coherent exciton motion but it becomes an incoherent hopping process. Förster derived an elegant formula for the rate constants for transport of excitation from one monomer to the other 23,24 . This rate is proportional to the overlap of the donor emission spectrum and the absorption spectrum of the acceptor molecule and depends on the inverse sixth power of the distance between donor and acceptor. ...
Organic molecules store the energy of absorbed light in the form of charge-neutral molecular excitations -- Frenkel excitons. Usually, in amorphous organic materials, excitons are viewed as quasiparticles, localized on single molecules, which diffuse randomly through the structure. However, the picture of incoherent hopping is not applicable to some classes of molecular aggregates -- assemblies of molecules that have strong near field interaction between electronic excitations in the individual subunits. Molecular aggregates can be found in nature, in photosynthetic complexes of plants and bacteria, and they can also be produced artificially in various forms including quasi-one dimensional chains, two-dimensional films, tubes, etc. In these structures light is absorbed collectively by many molecules and the following dynamics of molecular excitation possesses coherent properties. This energy transfer mechanism, mediated by the coherent exciton dynamics, resembles the propagation of electromagnetic waves through a structured medium on the nanometer scale. The absorbed energy can be transferred resonantly over distances of hundreds of nanometers before exciton relaxation occurs. Furthermore, the spatial and energetic landscape of molecular aggregates can enable the funneling of the exciton energy to a small number of molecules either within or outside the aggregate. In this review we establish a bridge between the fields of photonics and excitonics by describing the present understanding of exciton dynamics in molecular aggregates.
... Calcium signaling, molecular and catalytic nanomotors, pheromones propagation, and information transfer using bacteria as carriers have already been studied, but these mechanisms are slow and characterized by large propagation delays: the encoded data travels with a speed of several dozens of micrometers per second at maximum [2]. Comparing with these techniques, a mechanism based on the phenomenon of Förster Resonance Energy Transfer (FRET) is more promising, especially having in mind its low propagation delay [3][4][5][6]. FRET is a process in which a molecule, known as a donor, is able to non-radiatively (i.e. without releasing a photon) transfer its energy to another molecule, called an acceptor. ...
Nanocommunications, understood as communications between nanoscale devices, is commonly regarded as a technology essential for cooperation of large groups of nanomachines and thus crucial for development of the whole area of nanotechnology. While solutions for point-to-point nanocommunications have been already proposed, larger networks cannot function properly without routing. In this article we focus on the nanocommunications via Forster Resonance Energy Transfer (FRET), which was found to be a technique with a very high signal propagation speed, and discuss how to route signals through nanonetworks. We introduce five new routing mechanisms, based on biological properties of specific molecules. We experimentally validate one of these mechanisms. Finally, we analyze open issues showing the technical challenges for signal transmission and routing in FRET-based nanocommunications.
... A large number of problems in physics and chemistry require very significant dipole-dipole interaction which includes fundamental interactions such as van der Waals forces and vacuum friction [1,2], Förster (radiative) energy transfer (FRET) [3,4], radiative heat transfer [2,5], quantum information protocols like the realization of CNOT gates [6][7][8], pairwise excitation of atoms [9][10][11], and Rydberg blockade [12,13]. In the last decades numerous plasmonic and metamaterial platforms have been developed to enhance the dipole-dipole interaction significantly. ...
Currently epsilon near zero materials (ENZ) have become important for controlling the propagation of light and enhancing by several orders of magnitude the Kerr and other nonlinearities. Given this advance it is important to examine the quantum electrodynamic processes and information tasks near ENZ materials. We study the entanglement between two two-level systems near ENZ materials and compare our results with the case where the ENZ material is replaced by a metal. It is shown that with ENZ materials substantial entanglement can be achieved over larger distances than for metal films. We show that this entanglement over large distances is due to the fact that one can not only have large emission rates but also large energy transmission rates at the epsilon-nearzero wavelength. This establishes superiority of ENZ materials for studying processes specifically important for quantum information tasks.
... In 1948, Theodor Förster introduced an equation that quanties the efficiency of electronic excitation transfer between an energy donor (D) and acceptor (A). 159 CDs are frequently utilized as donors. Currently, there are primarily two types of FRET-based CD probes. ...
The study on the synthesis of carbon dots, sensing mechanisms, conditions associated with glucose imbalance, and potential applications as promising materials for glucose sensors.
... To obtain high sensitivity, the hairpin DNA was used to construct Föster resonance energy transfer (FRET) detection strategy [18]. FRET is a non-radiative energy transfer phenomenon through longrange dipole-dipole interactions between donors and acceptors [19]. FRET system can be influenced by three crucial elements including the distance between fluorescent acceptor and donor molecules, degree of spectral overlap and dipole orientation of donor and acceptor [20,21]. ...
The expression of aflD gene plays a significant role in the biosynthesis of aflatoxin, aflD structural genes can be served as a good biomarker of aflatoxigenic strains. The detection of the aflD gene is a promising method to control the further spread of aflatoxins. In this research, a rapid fluorescence biosensor targeting aflatoxigenic biosynthesis-related genes aflD was developed based on nitrogen-doped carbon quantum dots (NCQDs) and AuNPs as fluorescence donors and quenchers respectively. This sensor was fabricated by immobilization of NCQDs and AuNPs on the two ends of hairpin DNA. In the absence of the aflD gene, NCQDs were closed to AuNPs to trigger the fluorescence resonance energy transfer leading to a quenching and showed the fluorescent signal “off”. In the presence of the aflD gene, NCQDs and AuNPs were separated by the target aflD gene complementary matching with the loop of the hairpin structure, which caused to the recovery of fluorescence signal and performance the fluorescent signal “on”. It was shown that the biosensor provided an excellent limit of detection (LOD) of 1.95 nM (3σ / k) with a liner range of 10–150 nM. Besides, this biosensor performed the satisfied selectivity through the comparison between aflD gene and mismatched DNA sequences. The feasibility of this biosensor was examined in rice contaminated by Aspergillus flavus. Therefore, it could potentially be used as a feasible tool for preventing aflatoxin in grain and its products.
... As seen in Figure 3a, the alignment of the PL spectrum of the CdSe/ZnS CSQDs with the absorbance spectrum of the MEH−PPV serves as compelling evidence of energy transfer from the QDs to MEH−PPV. This phenomenon is in line with the Föster mechanism [23][24][25][26][27][28]. There is a notable absence of a substantial overlap between the PL spectrum of MEH−PPV and the absorbance spectrum of QDs (Figure 3b). ...
This study investigates the energy transfer mechanism between the organic polymer poly(2-methoxy-5(2’-ethyl)heroxyphenylenevinylene) (MEH−PPV) and CdSe/ZnS core-shell quantum dots (CdSe/ZnS CSQDs). Additionally, a hybrid ZnO-based photodetector (PD) is fabricated using the composite of MEH−PPV and CdSe/ZnS CSQDs, aiming to gain deeper insights. The combination of MEH−PPV and CdSe/ZnS CSQDs facilitates a broad spectral response in PDs, spanning from the ultraviolet (UV) to the visible range. In particular, PDs with QDs in the composite demonstrate notably excellent photosensitivity to both ultraviolet (UV) light (365 nm) (~5 fold) and visible light (505 nm) (~3 fold).
... From a physical perspective, following excitation of a fluorophore or a pigment, the energy depletes via various pathways, whether radiatively via emitting a fluorescence photon (Rad), or non-radiatively (NR), such as via the release of heat (H), the transfer of excitation energy to a nearby fluorophore, known as electronic excitation energy transfer (EET), through, for instance, the Förster resonance energy transfer (FRET) mechanism [10], or through the induction of a photochemical (P) reaction. Each of the above de-excitation processes per a given fluorophore has a given efficiency, also known as its quantum yield (QY), which is the ratio of the rate of that process and the sum of all de-excitation processes (Eqn 1). ...
Phytoplankton are a major source of primary productivity. Their photosynthetic fluorescence are unique measures of their type, physiological state, and response to environmental conditions. Changes in phytoplankton photophysiology are commonly monitored by bulk fluorescence spectroscopy, where gradual changes are reported in response to different perturbations, such as light intensity changes. What is the meaning of such trends in bulk parameters if their values report ensemble averages of multiple unsynchronized cells? To answer this, we developed an experimental scheme that enables tracking fluorescence intensities, brightnesses, and their ratios, as well as mean photon nanotimes equivalent to mean fluorescence lifetimes, one cell at a time. We monitored three different phytoplankton species during diurnal cycles and in response to an abrupt increase in light intensity. Our results show that we can define specific subpopulations of cells by their fluorescence parameters for each of the phytoplankton species, and in response to varying light conditions. Importantly, we identify the cells undergo well‐defined transitions between these subpopulations. The approach shown in this work will be useful in the exact characterization of phytoplankton cell states and parameter signatures in response to different changes these cells experience in marine environments, which will be applicable for monitoring marine‐related environmental effects.
... The reweighted distance distributions were then converted to potentials of mean force by Boltzmann inversion (Fig. 1f, Supplementary Fig. 5). The fluorescence relaxation times, τ cd , from nsFCS, combined with the reweighted distance distributions, and the known distance dependence of the FRET efficiency according to Förster's theory 46 fully define the dynamics of the chain in the framework of diffusion in a potential of mean force 5,8,39 (SI, Methods); the dynamics can be characterized either by the effective end-to-end diffusion coefficient or the chain reconfiguration time, τ r (Supplementary Table 4). The numerical values of τ cd and τ r are very similar, which is expected 39 , because the average transfer efficiencies probed here correspond to distances near R 0 (Fig. 1g, Supplementary Table 4). ...
The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, and nanophotonic enhancement to determine the conformational ensembles and rapid chain dynamics of short single-stranded nucleic acids in solution. To interpret the experimental results in terms of end-to-end distance dynamics, we utilize the hierarchical chain growth approach, simple polymer models, and refinement with Bayesian inference to generate structural ensembles that closely align with the experimental data. The resulting chain reconfiguration times are exceedingly rapid, in the 10-ns range. Solvent viscosity-dependent measurements indicate that these dynamics of single-stranded nucleic acids exhibit negligible internal friction and are thus dominated by solvent friction. Our results provide a detailed view of the conformational distributions and rapid dynamics of single-stranded nucleic acids.
... 3, and the total number of acceptor ( ) and donor ( ) photons (after corrections) generated by specifically the 515 nm excitation source (fig 2b, bottom). Here, of course, the values report on the distance between the two fluorophores in a manner governed by Förster resonance energy transfer (Forster 1948). ...
The 3ʹ end of the hepatitis C virus genome is terminated by a highly conserved, 98-nucleotide sequence called 3′X. This untranslated structural element is thought to regulate several essential RNA-dependent processes associated with infection. 3′X has two proposed conformations comprised of either three- or two stem-loop structures that result from different base pairing interactions within the first 55 nucleotides. Here, we used single-molecule FRET spectroscopy to monitor the conformational status of fluorescently labeled constructs that isolate this region of the RNA (3′X55). We observed that 3′X55 can adopt both proposed conformations and the relative abundance of them can be modulated by either solution conditions or nucleotide deletions. Furthermore, interconversion between the two conformations is slow and takes place over the course of several hours. The simultaneous existence of two slowly interconverting conformations may help prime individual copies of the viral genome for either viral protein or RNA synthesis, thereby minimizing conflicts between these two competing processes.
... Taking after photosystems present in plants, a vital part of these systems are chromophores, molecules that can be excited by the absorption of light. When this process occurs in precisely ordered systems, electronic energy transfer between the dye molecules may occur [4] following either Förster [5] or Dexter [6] mechanism creating nanoscale antennae that can act as a donor for appropriately arranged accepting reaction center causing photoinduced electron transfer leading [7] to a gradient of redox potential between them [8]. Such a process is crucial not only to the photovoltaics but for the light-emitting diodes and supercapacitors as well [9,10]. ...
In this paper, we present a facile method of synthesis and modification of poly(glycidyl methacrylate) brushes with 6-aminofluorescein (6AF) molecules. Polymer brushes were obtained using surface-grafted atom transfer radical polymerization (SI-ATRP) and functionalized in the presence of triethylamine (TEA) acting both as a reaction catalyst and an agent preventing aggregation of chromophores. Atomic force microscopy (AFM), FTIR, X-ray photoelectron spectroscopy (XPS) were used to study the structure and formation of obtained photoactive platforms. UV/Vis absorption and emission spectroscopy and confocal microscopy were conducted to investigate photoactivity of chromophores within the macromolecular matrix. Owing to the simplicity of fabrication and good ordering of the chromophore in a thin nanometric layer, the proposed method may open new opportunities for obtaining light sensors, photovoltaic devices, or other light-harvesting systems.
... The most common strategy is to design a biomarker-responsive quencher-modified linker as an energy acceptor to quench the afterglow luminescence that is restored upon biomarker-mediated cleavage of the quencher to release it from the nanoparticle surface 56,57 . However, due to the large distance between the afterglow donor and the quenching acceptor via nanoparticle surface modifications (>10 nm) 58,59 , the energy transfer is relatively inefficient, thus hampering the quenching efficiency and thereafter the imaging contrast versus biomarkers. Therefore, an activatable afterglow approach that breaks such harsh distance limitation of energy transfer is urgently needed to expand versatility and improve sensing capability. ...
Activatable afterglow luminescence nanoprobes enabling switched “off-on” signals in response to biomarkers have recently emerged to achieve reduced unspecific signals and improved imaging fidelity. However, such nanoprobes always use a biomarker-interrupted energy transfer to obtain an activatable signal, which necessitates a strict distance requisition between a donor and an acceptor moiety (<10 nm) and hence induces low efficiency and non-feasibility. Herein, we report organic upconversion afterglow luminescence cocktail nanoparticles (ALCNs) that instead utilize acidity-manipulated singlet oxygen (¹O2) transfer between a donor and an acceptor moiety with enlarged distance and thus possess more efficiency and flexibility to achieve an activatable afterglow signal. After in vitro validation of acidity-activated afterglow luminescence, ALCNs achieve in vivo imaging of 4T1-xenograft subcutaneous tumors in female mice and orthotopic liver tumors in male mice with a high signal-to-noise ratio (SNR). As a representative targeting trial, Bio-ALCNs with biotin modification prove the enhanced targeting ability, sensitivity, and specificity for pulmonary metastasis and subcutaneous tumor imaging via systemic administration of nanoparticles in female mice, which also implies the potential broad utility of ALCNs for tumor imaging with diverse design flexibility. Therefore, this study provides an innovative and general approach for activatable afterglow imaging with better imaging performance than fluorescence imaging.
... In the following discussion, we will consider dipole-dipole mechanism of energy migration within the set of donors. For this physical process, the transfer rate is given by w DD 23 . In this formula, τ 0D is a donor lifetime in the absence of other molecules, R DD 0 is the critical radius (distance) for energy transfer. ...
Theory of multistep excitation energy migration within the set of chemically identical chromophores distributed on the surface of a spherical nanoparticle is presented. The Green function solution to the master equation is expanded as a diagrammatic series. Topological reduction of the series leads to the expression for emission anisotropy decay. The solution obtained behaves very well over the whole time range and it remains accurate even for a high number of the attached chromophores. Emission anisotropy decay depends strongly not only on the number of fluorophores linked to the spherical nanoparticle but also on the ratio of critical radius to spherical nanoparticle radius, which may be crucial for optimal design of antenna-like fluorescent nanostructures. The results for mean squared excitation displacement are provided as well. Excellent quantitative agreement between the theoretical model and Monte–Carlo simulation results was found. The current model shows clear advantage over previously elaborated approach based on the Padé approximant.
... where is the probability of resonance energy transfer, as described by Förster theory (53), and fT is the fraction of fluorophores that exist as traps as defined earlier. This expression assumes that an excited molecule only undergoes FRET to its nearest-neighbour, justified by multiple studies (33,36). ...
It is important to understand the behaviours of fluorescent molecules because, firstly, they are often utilized as probes in biophysical experiments and, secondly, they are crucial cofactors in biological processes such as photosynthesis. A phenomenon called ‘fluorescence quenching’ occurs when fluorophores are present at high concentrations but the mechanisms for quenching are debated. Here, we used a technique called ‘in-membrane electrophoresis’ to generate concentration gradients of fluorophores within a supported lipid bilayer (SLB), across which quenching was expected to occur. Fluorescence lifetime imaging microscopy (FLIM) provides images where the fluorescence intensity in each pixel is correlated to fluorescence lifetime: the intensity provides information about the location and concentration of fluorophores and the lifetime reveals the occurrence of energy-dissipative processes. FLIM was used to compare the quenching behaviour of three commonly-used fluorophores: Texas Red (TR), nitrobenzoaxadiazole (NBD) and 4,4-difluoro-4-bora-3a,4a-diaza- s -indacene (BODIPY). FLIM images provided evidence of quenching in regions where the fluorophores accumulated but the degree of quenching varied between the different fluorophores. The relationship between quenching and concentration was quantified and the ‘critical radius for trap formation’, representing the relative quenching strength, was calculated as 2.70, 2.02 and 1.14 nm, for BODIPY, TR and NBD, respectively. The experimental data supports the theory that quenching takes place via a ‘transfer-to-trap’ mechanism which proposes, firstly, that excitation energy is transferred between fluorophores and may reach a ‘trap site’ resulting in immediate energy dissipation and, secondly, that trap sites are formed in a concentration-dependent manner. Some previous work suggested that quenching occurs only when fluorophores aggregate, or form long-lived dimers, but our data and this theory argues that traps may be ‘statistical pairs’ of fluorophores that exist only transiently. Our findings should inspire future work to assess whether these traps can be charge-transfer states, excited state dimers or something else.
... Fluorescence anisotropy values were determined for fluorescently labelled variants using polarisation-sensitive detection in the single-molecule instrument 59 , and were between 0.04 and 0.14 both for the monomeric proteins and the proteins in complex with DNA, indicating sufficiently rapid orientational averaging of the fluorophores to justify the approximation κ 2 ≈ 2/3 used in Förster theory 60 . ...
More than 1600 human transcription factors orchestrate the transcriptional machinery to control gene expression and cell fate. Their function is conveyed through intrinsically disordered regions (IDRs) containing activation or repression domains but lacking quantitative structural ensemble models prevents their mechanistic decoding. Here we integrate single-molecule FRET and NMR spectroscopy with molecular simulations showing that DNA binding can lead to complex changes in the IDR ensemble and accessibility. The C-terminal IDR of pioneer factor Sox2 is highly disordered but its conformational dynamics are guided by weak and dynamic charge interactions with the folded DNA binding domain. Both DNA and nucleosome binding induce major rearrangements in the IDR ensemble without affecting DNA binding affinity. Remarkably, interdomain interactions are redistributed in complex with DNA leading to variable exposure of two activation domains critical for transcription. Charged intramolecular interactions allowing for dynamic redistributions may be common in transcription factors and necessary for sensitive tuning of structural ensembles.
... empirical understanding of the microscopic lanthanide-to-lanthanide interaction in upconversion. According to the classic theories developed by Förster 39 and Dexter 40 , direct long-range energy transfer (from a few up to ten nanometres) is conceivable as a result of the long-lived metastable states of the lanthanide ions. However, the significance of this process in lanthanide upconversion remains uncharted. ...
Optical upconversion from lanthanide-doped nanoparticles is promising for a variety of applications ranging from bioimaging, optogenetics, nanothermometry, super-resolution nanoscopy and volumetric displays to solar cells. Despite remarkable progress made in enhancing upconversion to fuel these applications, achieving luminescence of upconversion nanoparticles (UCNPs) that is comparable to or higher than the bulk counterparts has been challenging due to nanoscale-induced quenching effects. Here we demonstrate a size-dependent lanthanide energy transfer effect in a conceptual design of hexagonal sodium yttrium fluoride (NaYF4) core–shell–shell NaYF4@NaYF4:Yb/Tm@NaYF4 UCNPs with depleted surface quenching. We show that precise control over the domain size (or the thickness of the middle shell doped with ytterbium (Yb) and thulium (Tm) from 1.2 to 13 nm) increases the lanthanide energy transfer efficiency (from 30.2 to 50.4%) and amplifies the upconversion quantum yield to a high value of 13.0 ± 1.3% in sub-50 nm UCNPs (excitation: 980 nm, 100 W cm⁻²), which is around fourfold higher than the micrometre-scale hexagonal NaYF4:Yb/Tm bulk counterparts. Spectroscopic studies and theoretical microscopic modelling reveal that long-range lanthanide energy transfer (>9.5 nm) takes place and underlies the observed size-dependent phenomena. Demonstration of size-dependent lanthanide energy transfer and upconversion quantum yields at the nanoscale transforms our long-existing conceptual understanding of lanthanide energy transfer (size independence), thereby having important implications for applications of lanthanide nanophotonics and biophotonics.
... Fluorescence anisotropy values were determined for fluorescently labelled variants using polarisation-sensitive detection in the single-molecule instrument 59 , and were between 0.04 and 0.14 both for the monomeric proteins and the proteins in complex with DNA, indicating sufficiently rapid orientational averaging of the fluorophores to justify the approximation κ 2 ≈ 2/3 used in Förster theory 60 . ...
... We apply a high-throughput assay based on fluorescent activated cell sorting (FACS) of Escherichia coli cells to select top candidates from a library of 3750 putative de novo proteins (Figure 1 a-b). The design of the assay, based on previous work by philipps˙fret-based˙2003, makes use of Förster resonance energy transfer (FRET) between two fluorescent proteins with spectral overlap (Förster 1948). Efficiency of the transfer is inversely dependent on the distance of the fluorescent proteins, thereby offering a way to measure proximity of two molecules or to study intramolecular conformation states. ...
De novo genes emerge from previously non-coding stretches of the genome. Their encoded de novo proteins are generally expected to be similar to random sequences and,
accordingly, with no stable tertiary fold and high predicted disorder. However, structural properties of de novo proteins and whether they differ during the stages of emergence and
fixation have not been studied in depth and rely heavily on predictions. Here we generated a library of short human putative de novo proteins of varying lengths and ages and
sorted the candidates according to their structural compactness and disorder propensity. Using Forster resonance energy transfer (FRET) combined with Fluorescence-activated
cell sorting (FACS) we were able to screen the library for most compact protein structures, as well as most elongated and flexible structures. Compact de novo proteins are
on average slightly shorter and contain lower predicted disorder than less compact ones. The predicted structures for most and least compact de novo proteins correspond to
expectations in that they contain more secondary structure content or higher disorder content, respectively. Our experiments indicate that older de novo proteins have higher
compactness and structural propensity compared to young ones. We discuss possible evolutionary scenarios and their implications underlying the age-dependencies of compactness and structural content of putative de novo proteins.
... FRET, the non-radiative dipole-dipole energy exchange between two fluorophores (a donor and an acceptor) [1][2][3][4], typically plays a pivotal role in complex molecular assemblies [5]. It monitors the nanoscale dynamics of proteins [6,7] and is involved in the photosynthetic processes of plants and bacteria [8,9]. ...
Fluorescence resonance energy transfer (FRET) was found strongly enhanced by plasmon resonance. In this work, Nanoporous Gold with small amount of residual silver was used to form Nanoporous Gold / Organic molecular layer compound with PSS and PAH. The ratio of its specific gold and silver content is achieved by controlling the time of its dealloying. Layered films of polyelectrolyte multilayers were assembled between the donor-acceptor pairs and NPG films to control distance. The maximum of FRET enhancement of 80-fold on the fluorescence intensity between the donor-acceptor pairs (CFP-YFP) is observed at a distance of ~10.5 nm from the NPG film. This Nanoporous Gold with small amount of residual silver not only enhanced FRET 4-fold more than nanoporous gold of only gold content almost, but also effectively realized the regulation of FRET enhancement. The ability to precisely measure and regulate the enhancement of FRET enables the rational selection of plasmonic nanotransducer dimensions for the particular biosensing application.
... FRET, a physical phenomenon in which dipole-dipole resonance interaction leads to the energy transfer from an excited donor to an acceptor chromophore, has been widely used to detect molecular interactions or molecules in biomedical and chemical research, such as molecular and cellular processes, signal transduction, medical diagnostics, and optical imaging. The FRET phenomena and energy transfer efficiency were first proposed by a German scientist, Theodor Förster, in 1948 [16]. The interaction of two fluorophores, either genetic or organic molecule, occurs between oscillating dipoles with overlapped emission and excitation resonance frequencies and depends on geometric properties of the donor-acceptor pair. ...
Protein–protein interactions and enzyme-catalyzed reactions are the fundamental processes in life, and the quantification and manipulation, kinetics determination, and ether activation or inhibition of these processes are critical for fully understanding physiological processes and discovering new medicine. Various methodologies and technologies have been developed to determine the parameters of these biological and medical processes. However, due to the extreme complexity of these processes, current methods and technologies can only determine one or a few parameters. The recent development of quantitative Förster resonance energy transfer (qFRET) methodology combined with technology aims to establish a high-throughput assay platform to determine protein interaction affinity, enzymatic kinetics, high-throughput screening, and pharmacological parameters using one assay platform. The FRET assay is widely used in biological and biomedical research in vitro and in vivo and provides high-sensitivity measurement in real time. Extensive efforts have been made to develop the FRET assay into a quantitative assay to determine protein–protein interaction affinity and enzymatic kinetics in the past. However, the progress has been challenging due to complicated FRET signal analysis and translational hurdles. The recent qFRET analysis utilizes cross-wavelength correlation coefficiency to dissect the sensitized FRET signal from the total fluorescence signal, which then is used for various biochemical and pharmacological parameter determination, such as K D , K cat , K M , K i , IC 50, and product inhibition kinetics parameters. The qFRET-based biochemical and pharmacological parameter assays and qFRET-based screenings are conducted in 384-well plates in a high-throughput assay mode. Therefore, the qFRET assay platform can provide a universal high-throughput assay platform for future large-scale protein characterizations and therapeutics development.
Graphical Abstract
... Using the virtual lens processing of the same data, surface fields of the unperturbed resonance could potentially also have been retrieved. Measuring the near-field at resonance without probe-induced perturbations could help to uncover scattering and loss mechanisms which limit higher quality resonances, while offering avenues to explore more complex nearfield interactions such as Förster resonance energy transfer (FRET) 53 . ...
Imaging with resolutions much below the wavelength λ – now common in the visible spectrum – remains challenging at lower frequencies, where exponentially decaying evanescent waves are generally measured using a tip or antenna close to an object. Such approaches are often problematic because probes can perturb the near-field itself. Here we show that information encoded in evanescent waves can be probed further than previously thought, by reconstructing truthful images of the near-field through selective amplification of evanescent waves, akin to a virtual superlens that images the near field without perturbing it. We quantify trade-offs between noise and measurement distance, experimentally demonstrating reconstruction of complex images with subwavelength features down to a resolution of λ/7 and amplitude signal-to-noise ratios < 25dB between 0.18–1.5 THz. Our procedure can be implemented with any near-field probe, greatly relaxes experimental requirements for subwavelength imaging at sub-optical frequencies and opens the door to non-invasive near-field scanning.
... Förster resonant energy transfer (FRET) is a non-radiative electromagnetic process that, via non-contact near field coupling, enables the transfer of excitation energy from a photo-excited object (donor) to another unexcited one (acceptor) in close proximity (typically apart by a distance of few to tens of nm) [1][2][3][4][5] . Since FRET is not a radiative process mediated by real photons, the rate of FRET is not restricted by the slow spontaneous radiative decay of the donor and finite optical cross section of the acceptor. ...
We present a theoretical investigation of exciton-mediated Förster resonant energy transfers (FRET’s) from photoexcited quantum dots (QD’s) to transition-metal dichalcogenide monolayers (TMD-ML’s), implemented by the quantum theory of FRET on the base of first-principles-calculated exciton fine structures. With the enhanced electron-hole Coulomb interactions, atomically thin TMD-MLs are shown to serve as an exceptional platform for FRET that are mediated purely by excitons and take full advantage of the superior excitonic properties. Remarkably, the energy-transfer responses of atomically thin TMD-ML’s are shown to be dictated by the momentum-forbidden dark excitons rather than the commonly recognized bright ones. Specifically, the longitudinal dark exciton states following the exchange-driven light-like linear band dispersion play a key role in grading up the efficiency and robustness of FRET of TMD-ML against the inhomogeneity of QD-donor ensembles. With the essential involvement of dark excitons, the FRET responses of TMD-ML’s no longer follow the distance power law as classically predicted and, notably, cannot manifest the dimensionality of the donor-acceptor system.
... FRET and BRET have been used for studies of GPCR signalling for more than two decades (Bunemann et al., 2003;Digby et al., 2006;Gales et al., 2005). RET techniques are based on the non-radiative transfer of energy from an excited fluorophore (donor) to another, closely located (2-10 nm), fluorophore with lower excitation energy (acceptor) which emits fluorescence (Förster, 1948). RET can be used for the detection of molecular proximity and conformational changes within a molecule at high temporal resolution. ...
The GPCR signalling cascade is a key pathway responsible for the signal transduction of a multitude of physical and chemical stimuli, including light, odorants, neurotransmitters, and hormones. Understanding the structural and functional properties of the GPCR cascade requires direct observation of signalling processes in high spatial and temporal resolution with minimal perturbation to endogenous systems. Optical microscopy and spectroscopy techniques are uniquely suited to this purpose because they excel at multiple spatial and temporal scales and can be used in living objects. Here, we review recent developments in microscopy and spectroscopy technologies which enable new insights into GPCR signalling. We focus on advanced techniques with high spatial and temporal resolution, single-molecule methods, labelling strategies, and approaches suitable for endogenous systems and large living objects. This review aims to assist researchers in choosing appropriate microscopy and spectroscopy approaches for a variety of applications in the study of cellular signalling.
Plastic scintillators, segmented into small, optically isolated voxels, are used for detecting elementary particles and provide reliable particle identification with nanosecond time resolution. Building large detectors requires the production and precise alignment of millions of individual units, a process that is time-consuming, cost-intensive, and difficult to scale. Here, we introduce an additive manufacturing process chain capable of producing plastic-based scintillator detectors as a single, monolithic structure. Unlike previous manufacturing methods, this approach consolidates all production steps within one machine, creating a detector that integrates and precisely aligns its voxels into a unified structure. By combining fused deposition modeling with an injection process optimized for fabricating scintillation geometries, we produced an additively manufactured fine-granularity plastic scintillator detector with performance comparable to the state of the art, and demonstrated its capabilities for 3D tracking of elementary particles and energy-loss measurement. This work presents an efficient and economical production process for manufacturing plastic-based scintillator detectors, adaptable to various sizes and geometries.
Lanthanide (Ln)-doped upconverting nanocrystals (LnNPs) exhibit suitable features as energy donors for Förster resonance energy transfer (FRET). The sensitivity of biosensors can be improved by optically active materials with anti-Stokes emission, narrowband absorption and emission spectral lines, and long luminescence lifetimes. In contrast to energy reabsorption, energy transfer between the upconversion nanocrystals (UCNPs) and organic dyes attached to their surface can be observed through donor emission quenching and acceptor emission and decreases in the luminescence lifetimes of donors. Although the emission spectra confirmed that FRET occurred from the Er 3+ ions to the Rose Bengal acceptor, the luminescence lifetimes were generally not affected by the presence of the acceptor. The Ln 3+ dopant in LnNPs, which typically has 20-100 % Yb 3+ sensitizer ions and 0.2-2% activator (Er 3+ /Tm 3+ /Ho 3+) ions, results in hundreds to thousands of Ln 3+ ions in a single UCNP. The interaction between multiple Ln 3+ ions results in significant energy migration and storage in the Yb 3+ sensitizer network, which is often recharged with the energy of the Er 3+ ions when they emit and nonradiatively transfer their energy to acceptor species. However, the energy transfer mechanisms could not be unambiguously determined through spectroscopic data due to the nature the upconversion process. Studies confirmed that the energy migration distance was significantly shortened when the LnNP surface contained acceptors; this affected the energy storage and 'recharging' capability of the Yb 3+ sensitizer network within the UCNPs. These results provide hints on the future use of LnNP as effective FRET probes, in which the highest possible absorption cross section and possibly lowest dopant concentration should be maintained.
Colloidal semiconducting nanoplatelets are known for their remarkable optical properties. Several applications involving them are being studied in the fields of optoelectronics, photovoltaics and quantum computing. To that extent, it's important to anticipate the collective properties that arise from their interactions when assembled. In this work, I was able to use micro-photoluminescence to study linear chains of self-assembled CdSe nanoplatelets in which FRET energy transfers have been shown. We first observed temporal fluctuations in the fluorescence of several chains, reminiscent of the blinking of isolated nanoplatelets. We explain these fluctuations by the inhibition from a defective quencher nanoplatelet of an emitting area of up to 35 nanoplatelets and driven by FRET interactions, faster than other excitonic effects. An analytical random walk model has been developed to support this explanation. On the other hand, we observed an acceleration in chain decay dynamics compared to the behaviour of single isolated nanoplatelets, as well as the presence of a delayed emission component. We explain these effects by FRET interactions between nanoplatelets which lead to excitons diffusion along a chain to two particular sites: a quencher site, where fast non-radiative recombination occurs, or a charge trap site. Finally, the possibility of observing superradiance in these samples was investigated through a semi-classical description of the phenomenon.
It is important to understand the behaviors of fluorescent molecules because, firstly, they are often utilized as probes in biophysical experiments and, secondly, they are crucial cofactors in biological processes such as photosynthesis. A phenomenon called “fluorescence quenching” occurs when fluorophores are present at high concentrations, but the mechanisms for quenching are debated. Here, we used a technique called “in-membrane electrophoresis” to generate concentration gradients of fluorophores within a supported lipid bilayer, across which quenching was expected to occur. Fluorescence lifetime imaging microscopy (FLIM) provides images where the fluorescence intensity in each pixel is correlated to fluorescence lifetime: the intensity provides information about the location and concentration of fluorophores and the lifetime reveals the occurrence of energy-dissipative processes. FLIM was used to compare the quenching behavior of three commonly used fluorophores: Texas Red (TR), nitrobenzoaxadiazole (NBD), and 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY). FLIM images provided evidence of quenching in regions where the fluorophores accumulated, but the degree of quenching varied between the different fluorophores. The relationship between quenching and concentration was quantified and the “critical radius for trap formation,” representing the relative quenching strength, was calculated as 2.70, 2.02, and 1.14 nm, for BODIPY, TR, and NBD, respectively. The experimental data support the theory that quenching takes place via a “transfer-to-trap” mechanism which proposes, firstly, that excitation energy is transferred between fluorophores and may reach a “trap site,” resulting in immediate energy dissipation, and, secondly, that trap sites are formed in a concentration-dependent manner. Some previous work suggested that quenching occurs only when fluorophores aggregate, or form long-lived dimers, but our data and this theory argue that traps may be “statistical pairs” of fluorophores that exist only transiently. Our findings should inspire future work to assess whether these traps can be charge-transfer states, excited-state dimers, or something else.
G protein‐coupled receptor (GPCR) oligomerization is a highly debated topic in the field. While initially believed to function as monomers, current literature increasingly suggests that these cell surface receptors, spanning almost all GPCR families, function as homo‐ or hetero‐oligomers. Yet, the functional consequences of these oligomeric complexes remain largely unknown. Adhesion GPCRs (aGPCRs) present an intriguing family of receptors characterized by their large and multi‐domain N‐terminal fragments (NTFs), intricate activation mechanisms, and the prevalence of numerous splice variants in almost all family members. In the present study, bioluminescence energy transfer (BRET) and Förster resonance energy transfer (FRET) were used to study the homo‐oligomerization of adhesion G protein‐coupled receptor G1 (ADGRG1; also known as GPR56) and to assess the involvement of NTFs in these receptor complexes. Based on the results presented herein, we propose that ADGRG1 forms 7‐transmembrane‐driven homo‐oligomers on the plasma membrane. Additionally, Stachel motif interactions appear to influence the conformation of these receptor complexes.
Förster resonance energy transfer (FRET) is a widely-used and versatile technique for the structural characterization of biomolecules. Here, we introduce FRETpredict, an easy-to-use Python software to predict FRET efficiencies from ensembles of protein conformations. FRETpredict uses a rotamer library approach to describe the FRET probes covalently bound to the protein. The software efficiently and flexibly operates on large conformational ensembles such as those generated by molecular dynamics simulations to facilitate the validation or refinement of molecular models and the interpretation of experimental data. We provide access to rotamer libraries for many commonly used dyes and linkers and describe a general methodology to generate new rotamer libraries for FRET probes. We demonstrate the performance and accuracy of the software for different types of systems: a rigid peptide (polyproline 11), an intrinsically disordered protein (ACTR), and three folded proteins (HiSiaP, SBD2, and MalE). FRETpredict is open source (GPLv3) and is available at github.com/KULL-Centre/FRETpredict and as a Python PyPI package at pypi.org/project/FRETpredict .
In situ identification of aptamer-binding targets on living cell membrane surfaces is of considerable interest, but a major challenge, specifically, when advancing recognition to the level of membrane receptor subunits. Here we propose a novel nanometal surface energy transfer (NSET) based nanoruler with a single-nucleobase resolution (SN-nanoruler), in which FAM-labeled aptamers and single-sized gold nanoparticle (GNP) antibody conjugates act as a donor and an acceptor. A single nucleobase resolution of the SN-nanoruler was experimentally illustrated by molecular size, orientation, quenching nature, and other dye-GNP pairs. The SN-nanoruler provides high reproducibility and precision for measuring molecule distance on living cell membranes at the nanometer level owing to only the use of single-sized antibody-capped GNPs. In situ identification of the aptamer binding site was advanced to the protein subunit level on the living cell membrane for the utilization of this SN-nanoruler. The results suggest that the proposed strategy is a solid step towards the wider application of optical-based rulers to observe the molecular structural configuration and dynamic transitions on the membrane surface of living cells.
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