Structural Analysis of Peptides of PSⅡ Light-harvesting Complexes in Siphonous Green Algae, Codium fragile

Peptide composition and arrangement of 4 major light-harvesting complexes LHCP 1-3 and LHCP 3′ isolated from siphonous green algae (Codium fragile (Sur.) Hariot.) were investigated. LHCP 1 showed five main peptides, 34.4, 31.5, 29.5, 28.2 and 26.5 kD in SDS-PAGE, the 34.4 and 31.5 kD peptides were never found in higher plants. LHCP 3 contained the other four kinds of LHCP 1 peptides except 34.4 kD, while LHCP 3′ consisted of only 28.2 and 26.5 kD peptides. We found that 34.4, 28.2 and 26.5 kD peptides were easy to decompose from LHCP 1 when subjected to SDS-PAGE without pretreatment. They might be located at the exterior of LHCP 1, while the 31.5 and 29.5 kD peptides were at the central part. The 28.2 and 26.5 kD peptides often occurred in CPa, the center complex of PSⅡ. They are possibly the LHCⅡ peptides tightly associated with CCⅡ. According to the results described above, a peptide map of LHCP 1 was sketched.

Long-Lived Coherence Originating from Electronic-Vibrational Couplings in Light-Harvesting Complexes

We theoretically investigate the evolutions of two-dimensional, third-order, nonlinear photon echo rephasing spectra with population time by using an exact numerical path integral method. It is shown that for the same system, the coherence time and relaxation time of excitonic states are short, however, if the couplings of electronic and intra-pigment vibrational modes are considered, the coherence time and relaxation time of this vibronic states are greatly extended. It means that the couplings between electronic and vibrational modes play important roles in keeping long-lived coherence in light-harvesting complexes. Particularly, by using the method we can fix the transition path of the energy transfer in bio-molecular systems.

Energy transfer between two aggregates in light-harvesting complexes

Energy transfer processes between two aggregates in a coupled chromophoric-pigment （protein） system are studied via the standard master equation approach. Each pigment of the two aggregates is modeled as a two-level system. The excitation energy is assumed to be transferred from the donor aggregate to the acceptor aggregate. The model can be used to theoretically simulate many aspects of light-harvesting complexes （LHCs）. By applying the real bio-parameters of photosynthesis, we numerically investigate the efficiency of energy transfer （EET） between the two aggregates in terms of some factors, e.g., the initial coherence of the donor aggregate, the coupling strengthes between the two aggregates and between different pigments, and the effects of noise from the environment. Our results provide evidence for that the actual numbers of pigments in the chromophoric tings of LHCs should be the optimum parameters for a high EET. We also give a detailed analysis of the effects of noise on the EET.

Theoretical study on the exciton dynamics of coherent excitation energy transfer in the phycoerythrin 545 light-harvesting complex

The experimental observation of long-lived quantum coherence in the excitation energy transfer(EET)process of the several photosynthetic light-harvesting complexes at low and room temperatures has aroused hot debate.It challenges the common perception in the field of complicated pigment molecular systems and evokes considerable theoretical efforts to seek reasonable explanations.In this work,we investigate the coherent exciton dynamics of the phycoerythrin 545(PE545)complex.We use the dissipation equation of motion to theoretically investigate the effect of the local pigment vibrations on the population transfer process.The result indicates that the realistic local pigment vibrations do assist the energy transmission.We demonstrate the coherence between different pigment molecules in the PE545 system is an essential ingredient in the EET process among various sites.The coherence makes the excitation energy delocalized,which leads to the redistribution of the excitation among all the chromophores in the steady state.Furthermore,we investigate the effects of the complex high-frequency spectral density function on the exciton dynamics and find that the high-frequency Brownian oscillator model contributes most to the exciton dynamic process.The discussions on the local pigment vibrations of the Brownian oscillator model suggest that the local heterogeneous protein environments and the effects of active vibration modes play a significant role in coherent energy transport.

Self-assembly of biomimetic light-harvesting complexes capable of hydrogen evolution

Biomimetics provides us a new perspective to understand complex biological process and strategy to fabricate functional materials. However,a great challenge still remains to design and fabricate biomimetic materials using a facile but effective method. Here, we develop a biomimetic light harvesting architecture based on one-step co-assembly of amphiphilic amino acid and porphyrin. Amphiphilic amino acid can self-assemble into nanofibers via π-stacking and hydrogen binding interactions. Negatively charged porphyrin adsorbs on the surface of the assembled nanofibers through electrostatic force, and the nanofibers further organize into porous urchin-like microspheres induced presumably by hydrophobic interaction. The assembled amphiphilic amino acid nanofibers work as a template to tune the organization of porphyrin with an architecture principle analogous to natural light harvesting complex. The co-assembled microspheres exhibit enhanced light capture due to the light reflection in the porous structure. Reaction center(platinum nanoparticles) can be effectively coupled with the light harvesting microspheres via photoreduction. After visible light illumination, hydrogen evolution occurs on the hybrid microspheres.

Characteristics and phylogeny of light-harvesting complex gene encoded proteins from marine red alga Griffithsia japonica

Six genes encoding light-harvesting complex (LHC) protein have been characterized in the multicellular red alga Griffithsia japonica EST analysis. Three of them were full sequences while others were partial sequences with 3'-UTRs. The cleavage sites between signal peptide and mature LHC protein were analyzed on these three full sequences. The sequence characteristics, calculated molecular weights and isoelectric point (pI) values and hydrophobicity of the mature proteins were deduced and analyzed. Comparing the LHC sequences of G. japonica with higher plant, Chlorophyta, chromophytes and other red algae, the high conservation of the chlorophyll (Chl) binding site among chromophytes and red algae were revealed. Phylogenetic analysis on LHC proteins from higher plant, green algae, euglena, brown algae, diatom, cryptomonad, Raphidophyte and red algae reveals that (1) there are two distinct groups of Chl a/b and Chl a/c -binding LHC; (2) Chl a binding proteins of red algae share greater similarities with the Chl a/c-binding proteins of the chromophytes and dinoflagellate than with the Chl a/b - binding proteins of the green algae and higher plants; (3) chromophyte's LHC is supposed to be evolved from red algae LHC.

Effect of the mutation of carotenoids on the dynamics of energy transfer in light-harvesting complexes （LH2） from Rhodobacter sphaeroides 601 at room temperature

Energy transfers in two kinds of peripheral light-harvesting complexes （LH2） of Rhodobacter sphaeroides （RS） 601 are studied by using femtosecond pump^probe spectroscopy with tunable laser wavelength at room temperature. These two complexes are native LH2 （RS601） and green carotenoid mutated LH2 （GM309）. The obtained results demonstrate that, compared with spheroidenes with ten conjugated double bonds in native RS601, carotenoid in GM309 containing neurosporenes with nine conjugated double bonds can lead to a reduction in energy transfer rate in the B800-to-B850 band and the disturbance in the energy relaxation processes within the excitonic B850 band.

Component spectroscopic properties of light-harvesting complexes with DFT calculations

Photosynthesis is a fundamental process in biosciences and biotechnology that influences profoundly the research in other disciplines.In this paper,we focus on the characterization of fundamental components,present in pigment-protein complexes,in terms of their spectroscopic properties such as infrared spectra,nuclear magnetic resonance,as well as nuclear quadrupole resonance,which are of critical importance for many applications.Such components include chlorophylls and bacteriochlorophylls.Based on the density functional theory method,we calculate the main spectroscopic characteristics of these components for the Fenna-Matthews-Olson light-harvesting complex,analyze them and compare them with available experimental results.Future outlook is discussed in the context of current and potential applications of the presented results.

Novel Evidence for a Reversible Dissociation of Light-harvesting Complex II from Photosystem II Reaction Center Complex Induced by Saturating Light Illumination in Soybean Leaves

After saturating light illumination for 3 h the potential photochemical efficiency of photosystem Ⅱ （PSII） （FJF,, the ratio of variable to maximal fluorescence） decreased markedly and recovered basically to the level before saturating light illumination after dark recovery for 3 h in both soybean and wheat leaves, indicating that the decline in FJ/Fm is a reversible down-regulation. Also, the saturating light illumination led to significant decreases in the low temperature （77 K） chlorophyll fluorescence parameters F685 （chlorophyll a fluorescence peaked at 685 nm） and F685/F735 （F735, chlorophyll a fluorescence peaked at 735 nm） in soybean leaves but not in wheat leaves. Moreover, trypsin （a protease） treatment resulted in a remarkable decrease in the amounts of PsbS protein （a nuclear gene psbS-encoded 22 kDa protein） in the thylakoids from saturating light-illuminated （SI）, but not in those from darkadapted （DT） and dark-recovered （DRT） soybean leaves. However, the treatment did not cause such a decrease in amounts of the PsbS protein in the thylakoids from saturating light-illuminated wheat leaves. These results support the conclusion that saturating light illumination induces a reversible dissociation of some light-harvesting complex Ⅱ （LHClI） from PSII reaction center complex in soybean leaf but not in wheat leaf.

Decoherence-and Dimerization-assisted Energy Transport in Protomer of Light-Harvesting Complexes

We have investigated the dynamics of a protomer coupled to two different decoherent environments,each in a configuration called the spin star configuration.Using the quantum mechanics method,in different situations,we obtain the analytical expressions for the transition probability in the protomer system.In thermal equilibrium,there exist well-defined ranges of parameters for which decoherent interaction between the protomer and the environment assists energy transfer in the protomer system,while in pure quantum mechanics states,the decoherent interaction assists energy transfer for an eigenstate but against energy transfer for quantum mechanics averages.In particular,we also find that the dimerization of two bacteriochlorophylls in protomer can always assist energy transfer in certain parameter range,and in the appropriate spin bath energy,the efficiency of energy transport is sensitively depended on the temperature of environments.

Light-harvesting Complex Ⅱ Sensitized Oxide Photoanodes with Organic Acceptor Molecule as Electron Transfer Mediator

Dye sensitized solar cell（DSSC） is a promising thin film solar cell that has been widely investigated after its birth because of its advantages,such as flexibility,low-cost,easyfabrication and so on[1-3].For DSSCs,sensitizers play a core role due to their responsibility for the generation of the photo carriers resulted from light absorption and the transfer of the photo-generated electrons into semiconductor photoanodes[4].Keywords：Light-harvesting complex Ⅱ; Anthraquinone 2-carboxylic acid; ZnO; TiO2 nanostructure; Solar cell

Energy Transfer in the Light-Harvesting Complexes of Purple Bacteria

In this paper, we use a nonlinear decohering quantum model to study the initial step of photosynthesis which is an ultrafast transfer process of absorption the sunlight by light-harvesting complexes and electronic excitation transfer to the reaction center(RC). In this decohering model, the Hamiltonian of the system commutes with the systemenvironment interaction. We take B850 ring of light-harvesting complex II(LH-II) in purple bacteria as an example to calculate the efficiency of the energy transfer as a function of time. We find that the environmental noise can make the LH-II have stable energy transfer efficiency over a long time. This is to say that the environmental noise which is the decohering source has advantage of the energy transfer in the process of photosynthesis.

Cloning and Sequence Analysis of a Full-length cDNA Encoding Light-harvesting Complexes of Photosystem II in Phyllostachys edulis

The light-harvesting chlorophyll a/b-protein complex plays an important role in photosynthesis of plants. A full-length cDNA of light-harvesting chlorophyll a/b （cab） gene was cloned from the first strand of Moso （Phyllostachys edulis） cDNA through RT-PCR and RACE methods, named as cabPhEIO （cab gene 10 from Ph. edulis）. The length of cab- PhEIO （GenBank accession number： EU118754） is 1 151 bp, which contains an open reading frame encoding 283 amino acids from 81st to 932nd position. The bioinformatics analysis indicated that the protein encoded by cab-PhElO had a chlorophll a/b binding domain （83rd -247th position）, two protein kinase C-phosphorylation sites, three Nmyristoylation sites and a yia A/B double helix domain.The amino acid sequence of cab-PhElO showed high similarity with the cab genes of Oryza sativa, Zea mays, Hordeum vulgare, and Vitis vinifera, more than 80%, respectively, which indicated that cab-PhElO gene belongs to lhcb5 gene family.

Ultrafast excitation relaxation in light-harvesting complex LH2 from Rb.sphaeroides 601

The energy relaxation and kinetic evolution of transient spectra of bacteriochloro- phylls (BChls) in light-harvesting complex LH2 from Rb. sphaeroides 601 were investigated using femtosecond pump-probe technique. Upon 783 nm excitation, the energy at B800 BChls ex-periences an intramolecular redistribution with 0.35 ps time constant before transferring to B850 BChls. With tuning the excitation wavelength, the dynamical evolution of excited BChls was clearly observed, which indicates an obvious competition between the ground state bleaching and excited state absorption (ESA) of BChls involved and an isosbestic point near 818 nm, and also demonstrates that from the lower electronic excited state of B800 BChls to the higher exci-tonic state of B850 BChls is an efficient routine for energy transfer. The excitation energy in higher excitonic states of B850 BChls relaxes rapidly to the next lowest excitonic state by inter-conversion, delocalization to adjacent molecular, populating the lowest excitonic state and the change of molecular conformation.

Excited-state dynamics in light-harvesting complex of Rhodobacter sphaeroides

Photodynamics of peripheral antenna complexes,light-harvesting complex (LH2) of Rhodobacter (Rb) Sphaeroides 601,was studied using femtosecond pump-probe technique at different laser wavelengths. The obtained results reveal dramatic dynamical evolutions within B800 and B850 absorption bands of antenna complexes LH2. At excitation wavelength around 835 nm,a sharp photobleaching signal was observed which was assigned to the contribution of the two-exciton state,which was further confirmed by the power dependence measurement. Rate equations with eight-level scheme were used to calculate the population evolution in LH2 and the transient dynamics under femtosecond pulse excitation. The research results prove that not only the transition from ground state to one-exciton state but also that from one-exciton state to two-exciton state contribute to the photodynamics of B850.

Identification of Light-Harvesting Chlorophyll a/b-Binding Protein Genes of Zostera marina L.and Their Expression Under Different Environmental Conditions

Photosynthesis includes the collection of light and a/b-binding （LHC） proteins. In high plants, the LHC gene family constituting the light-harvesting complex ofphotosystems I and II. the transfer of solar energy using light-harvesting chlorophyll includes LHCA and LHCB sub-families, which encode proteins Zostera marina L. is a monocotyledonous angiosperm and inhab- its submerged marine environments rather than land environments. We characterized the Lhca and Lhcb gene families of Z. marina from the expressed sequence tags （EST） database. In total, 13 unigenes were annotated as ZmLhc, 6 in Lhca family and 7 in ZmLhcb family. ZmLHCA and ZmLHCB contained the conservative LHC motifs and amino acid residues binding chlorophyll. The average similarity among mature ZmLHCA and ZmLHCB was 48.91% and 48.66%, respectively, which indicated a high degree of diver- gence within ZmLHChc gene family. The reconstructed phylogenetic tree showed that the tree topology and phylogenetic relation- ship were similar to those reported in other high plants, suggesting that the Lhc genes were highly conservative and the classification of ZmLhc genes was consistent with the evolutionary position of Z. marina. Real-time reverse transcription （RT） PCR analysis showed that different members of ZmLhca and ZmLhcb responded to a stress in different expression patterns. Salinity, temperature, light intensity and light quality may affect the expression of most ZmLhca and ZmLhcb genes. Inorganic carbon concentration and acidity had no obvious effect on ZmLhca and ZmLhcb gene expression, except for ZmLhca6.

Incorporating porphyrin-Pt in light-harvesting metal-organic frameworks for enhanced visible light-driven hydrogen production

Molecular catalysts for H2-evolution are of interest for their integration into light-harvesting complexes for photocatalytic water splitting.Here,we report the meso-tetra(4-carboxyphenyl)porphine[(TCPP)Pt^(Ⅱ)]complex as a molecular H2-evolving photocatalyst using chloranilic acid(CA)as a sacrificial electron donor,the choice of which is critical to the stability of the photocatalyst.When triethanolamine was used,[(TCPP)Pt^(Ⅱ)]decomposed to form Pt nanoparticles.Density functional theory calculations together with evidence from electrochemical and spectroscopic analyses suggested that the catalysis was possibly initiated by a proton-coupled electron transfer(PCET)to form[(TCPP)Pt^(Ⅰ)]-N-H,followed by another electron injection and protonation to form a[(TCPP)Pt^(Ⅱ)-hydride]-N-H intermediate that can release H2.As the whole catalytic cycle involves the injection of multiple electrons,a light-harvesting network should be helpful by providing multiple photo-induced electrons.Thus,we integrated this molecular catalyst into a light-harvesting metal-organic framework to boost its activity by~830 times.This work presents a mechanistic study of the photocatalytic H2 evolution and energy transfer and highlights the importance of a light-harvesting network for multiple electron injections.

Modeling time-dependent mechanical behavior of hard rock considering excavation-induced damage and complex 3D stress states

To investigate the long-term stability of deep rocks,a three-dimensional(3D)time-dependent model that accounts for excavation-induced damage and complex stress state is developed.This model comprises three main components:a 3D viscoplastic isotropic constitutive relation that considers excavation damage and complex stress state,a quantitative relationship between critical irreversible deformation and complex stress state,and evolution characteristics of strength parameters.The proposed model is implemented in a self-developed numerical code,i.e.CASRock.The reliability of the model is validated through experiments.It is indicated that the time-dependent fracturing potential index(xTFPI)at a given time during the attenuation creep stage shows a negative correlation with the extent of excavationinduced damage.The time-dependent fracturing process of rock demonstrates a distinct interval effect of the intermediate principal stress,thereby highlighting the 3D stress-dependent characteristic of the model.Finally,the influence of excavation-induced damage and intermediate principal stress on the time-dependent fracturing characteristics of the surrounding rocks around the tunnel is discussed.

Saturation Estimation with Complex Electrical Conductivity for Hydrate-Bearing Clayey Sediments:An Experimental Study

Clays have considerable influence on the electrical properties of hydrate-bearing sediments.It is desirable to understand the electrical properties of hydrate-bearing clayey sediments and to build hydrate saturation(S_(h))models for reservoir evaluation and monitoring.The electrical properties of tetrahydrofuran-hydrate-bearing sediments with montmorillonite are characterized by complex conductivity at frequencies from 0.01 Hz to 1 kHz.The effects of clay and Sh on the complex conductivity were analyzed.A decrease and increase in electrical conductance result from the clay-swelling-induced blockage and ion migration in the electrical double layer(EDL),respectively.The quadrature conductivity increases with the clay content up to 10%because of the increased surface site density of counterions in EDL.Both the in-phase conductivity and quadrature conductivity decrease consistently with increasing Sh from 0.50 to 0.90.Three sets of models for Sh evaluation were developed.The model based on the Simandoux equation outperforms Archie’s formula,with a root-mean-square error(E_(RMS))of 1.8%and 3.9%,respectively,highlighting the clay effects on the in-phase conductivity.The fre-quency effect correlations based on in-phase and quadrature conductivities exhibit inferior performance(E_(RMS)=11.6%and 13.2%,re-spectively)due to the challenge of choosing an appropriate pair of frequencies and intrinsic uncertainties from two measurements.The second-order Cole-Cole formula can be used to fit the complex-conductivity spectra.One pair of inverted Cole-Cole parameters,i.e.,characteristic time and chargeability,is employed to predict S_(h) with an E_(RMS) of 5.05%and 9.05%,respectively.

A novel complex-high-order graph convolutional network paradigm:ChyGCN

In recent years,there has been a growing interest in graph convolutional networks(GCN).However,existing GCN and variants are predominantly based on simple graph or hypergraph structures,which restricts their ability to handle complex data correlations in practical applications.These limitations stem from the difficulty in establishing multiple hierarchies and acquiring adaptive weights for each of them.To address this issue,this paper introduces the latest concept of complex hypergraphs and constructs a versatile high-order multi-level data correlation model.This model is realized by establishing a three-tier structure of complexes-hypergraphs-vertices.Specifically,we start by establishing hyperedge clusters on a foundational network,utilizing a second-order hypergraph structure to depict potential correlations.For this second-order structure,truncation methods are used to assess and generate a three-layer composite structure.During the construction of the composite structure,an adaptive learning strategy is implemented to merge correlations across different levels.We evaluate this model on several popular datasets and compare it with recent state-of-the-art methods.The comprehensive assessment results demonstrate that the proposed model surpasses the existing methods,particularly in modeling implicit data correlations(the classification accuracy of nodes on five public datasets Cora,Citeseer,Pubmed,Github Web ML,and Facebook are 86.1±0.33,79.2±0.35,83.1±0.46,83.8±0.23,and 80.1±0.37,respectively).This indicates that our approach possesses advantages in handling datasets with implicit multi-level structures.