Special Pair Research Articles

Water Soluble Chlorophyll-Binding Proteins of Plants: Structure, Properties and Functions

Water soluble chlorophyll-binding proteins (WSCPs) of higher plants differ from most proteins containing chlorophyll orbacteriochlorophyll in that they are soluble in watr and are neither embedded in the lipid membrane nor directly involved in the process of photosynthesis. Chlorophyll molecules in WSCPs ensembles are packed in dimers within the hydrophobic zone of the protein matrix, similar to the structure of a chlorophyll "special pair" in the reaction centers of phototrophs. This fact together with the detected photosensitizing activity of WSCPs makes it possible to consider these proteins as a promising object for modelling the evolutionary prototypes of the photosynthetic apparatus, as well as for developing the artificial solar energy converters. There are two classes of proteins in the WSCP family, class I and class II the representatives of these classes have a weak degree of homology in the primary structure, but a high degree of similarity in the tertiary and quaternary structure. One of the features of class I WSCPs is photoconversion, that is, to change the structure and spectral properties of the chromophore under the action of light. The functions of WSCPs in the plant are thought to be associated with stress protection.

An INS-Aided Cycle Slip Detection and Repair Method Based on IF and WL Combinations

Cycle slips often occur in carrier phase observations due to the problem of the obstruction, low signal-to-noise ratio, or high receiver dynamics. An effective INS(inertial navigation system)-aided cycle slip detection and repair method is presented, which is based on PPP/INS integrated system. It utilizes high-precision INS information instead of a pseudorange to remove the satellite-receiver geometric range in the wide-lane and ionospheric-free phase combinations, cooperates with satellite and epoch differential processing, and creates INS-aided wide-lane model and INS-aided ionospheric-free model. The INS-aided ionospheric-free model is unaffected by the dramatic changes in the ionosphere but cannot detect the special pairs of cycle slips. The INS-aided wide-lane model has a long wavelength. However, it is insensitive to the equal cycle slips on dual frequencies. So their combination can achieve mutual complementary advantages. The results show that this method can effectively detect and repair various types of cycle slips. Moreover, when it comes to the cycle slip after a GPS interruption, the method can realize the instantaneous correction.

Mixed Local-Nonlocal Vector Schrödinger Equations and Their Breather Solutions**Supported by the Natural Science Foundation of Liaoning Province of China under Grant No. 201602678

To the best of our knowledge, all nonlinearities in the known nonlinear integrable systems are either local or nonlocal. A natural problem is whether there exist some nonlinear integrable systems with both local and nonlocal nonlinearities, and how to solve this kinds of spectral nonlinear integrable systems with both local and nonlocal nonlinearities. Recently, some novel mixed local-nonlocal vector Schrödinger equations are presented, which are different from the single local and nonlocal coupled Schrödinger equation. We investigate the Darboux transformation of mixed local-nonlocal vector Schrödinger equations with a spectral problem. Starting from a special Lax pairs, the mixed local-nonlocal vector Schrödinger equations are constructed. We obtain the one- and two- and N-soliton solution formulas of the mixed local-nonlocal vector Schrödinger equations with N-fold Darboux transformation. Based on the obtained solutions, the propagation and interaction structures of these multi-solitons are shown, the evolution structures of the one-solitons are exhibited, the overtaking elastic interactions among the two-breather solitons are considered. We find that unlike the local and nonlocal cases, the mixed local-nonlocal vector Schrödinger equations have some novel results. The results in this paper might be helpful for understanding some physical phenomena described in plasmas.

Parameter extraction method for the twisted pair cable with rectangular connectors.

Cables play an important role in transmitting energy and information. In this article, in order to obtain the S-parameters of the special twisted pair cable with rectangular connectors, a de-embedding method of the transmission matrix is proposed to deal with the two adapters ends of the cable. According to the frequency-dependent RLGC(f) model, the cable characteristics are extracted in the frequency range of 10 MHz to 200 MHz through conventional and modified methods respectively. The frequency-domain analysis shows that the inherent capacity of modified method can decrease the errors especially due to the discontinuities of hyperbolic functions. This research supplies an advantageous modelling approach for the cable to improve its robustness against disturbances in the S-parameters measurement that cannot be decreased with the calibration procedure.

A document level neural model integrated domain knowledge for chemical-induced disease relations

BackgroundThe effective combination of texts and knowledge may improve performances of natural language processing tasks. For the recognition of chemical-induced disease (CID) relations which may span sentence boundaries in an article, although existing CID systems explored the utilization for knowledge bases, the effects of different knowledge on the identification of a special CID haven’t been distinguished by these systems. Moreover, systems based on neural network only constructed sentence or mention level models.ResultsIn this work, we proposed an effective document level neural model integrated domain knowledge to extract CID relations from biomedical articles. Basic semantic information of an article with respect to a special CID candidate pair was learned from the document level sub-network module. Furthermore, knowledge attention depending on the representation of the article was proposed to distinguish the influences of different knowledge on the special CID pair and then the final representation of knowledge was formed by aggregating weighed knowledge. Finally, the integrated representations of texts and knowledge were passed to a softmax classifier to perform the CID recognition. Experimental results on the chemical-disease relation corpus proposed by BioCreative V show that our proposed system integrated knowledge achieves a good overall performance compared with other state-of-the-art systems.ConclusionsExperimental analyses demonstrate that the introduced attention mechanism on domain knowledge plays a significant role in distinguishing influences of different knowledge on the judgment for a special CID relation.

Ionization by an Oscillating Field: Resonances and Photons

We describe new exact results for a model of ionization of a bound state in a 1d delta function potential, induced by periodic oscillations of the potential of period $$2\pi /\omega $$ . In particular we have obtained exact expressions, in the form of Borel summed transseries for the energy distribution of the emitted particle as a function of time, $$\omega $$ and strength $$\alpha $$ of the oscillation of the potential. These show peaks in the energy distribution, separated by $$\hbar \omega $$ , which look like single or multi-photon absorption. The peaks are very sharp when the time is large and the strength of the oscillating potential is small but are still clearly visible for large fields, and even for time-periods of a few oscillations. These features are similar to those observed in laser induced electron emission from solids or atoms (Phys Rev Lett 105:257601, 2010). For large $$\alpha $$ the model exhibits peak-suppression. The ionization probability is not monotone in the strength of the oscillating potential: there are windows of much slower ionization at special pairs $$(\alpha ,\omega )$$ . This shows that ionization processes by time-periodic fields exhibit universal features whose mathematical origin are resonances which pump energy into the system represented by singularities in the complex energy plane. All these features are proven in our simple model system without the use of any approximations.

Electronic Interactions in the Bacterial Reaction Center Revealed by Two-Color 2D Electronic Spectroscopy.

The bacterial reaction center (BRC) serves as an important model system for understanding the charge separation processes in photosynthesis. Knowledge of the electronic structure of the BRC is critical for understanding its charge separation mechanism. While it is well-accepted that the "special pair" pigments are strongly coupled, the degree of coupling among other BRC pigments has been thought to be relatively weak. Here we study the W(M250)V mutant BRC by two-color two-dimensional electronic spectroscopy to correlate changes in the Q x region with excitation of the Q y transitions. The resulting Q y-Q x cross-peaks provide a sensitive measure of the electronic interactions throughout the BRC pigment network and complement one-color 2D studies in which such interactions are often obscured by energy transfer and excited-state absorption signals. Our observations should motivate the refinement of electronic structure models of the BRC to facilitate improved understanding of the charge separation mechanism.

Special Pairs of SURD Equations

Special Pairs of SURD Equations

Electron-Phonon Coupling in Cyanobacterial Photosystem I.

One of the fundamental problems in biophysics is whether the protein medium at room temperature can be properly treated as a fluid dielectric or whether its dynamics is determined by a highly ordered molecular structure resembling the properties of crystalline and amorphous solids. Here, we measured the recombination between reduced A1 and the oxidized chlorophyll special pair P700 over a wide temperature range using preparations of photosystem I from the cyanobacterium Synechococcus sp. PCC 7002 depleted of the iron-sulfur clusters. We found that the dielectric properties of the protein matrix in early electron transfer reactions of photosystem I resemble the behavior of solids that require an implicit treatment of electron-phonon coupling even at ambient temperatures. The quantum effects of electron-phonon coupling in proteins could account for a variety of phenomena, such as the weak sensitivity of electron transfer in pigment-protein complexes to changing environmental conditions including temperature, driving force, polarity, and chemical composition.

New Insights into the Mechanism of Uphill Excitation Energy Transfer from Core Antenna to Reaction Center in Purple Photosynthetic Bacteria.

The uphill excitation energy transfer (EET) from the core antenna (LH1) to the reaction center (RC) of purple photosynthetic bacteria was investigated at room temperature by comparing the native LH1-RC from Thermochromatium ( Tch.) tepidum with the hybrid LH1-RC from a mutant strain of Rhodobacter ( Rba.) sphaeroides. The latter protein with chimeric Tch-LH1 and Rba-RC exhibits a substantially larger RC-to-LH1 energy difference (Δ E = 630 cm-1) of 3-fold thermal energy (3 kB T). The spectroscopic and kinetics results are discussed on the basis of the newly reported high-resolution structures of Tch. tepidum LH1-RC, which allow us to propose the existence of a passage formed by LH1 BChls that facilitates the LH1 → RC EET. The semilogarithmic plot of the EET rate against Δ E was found to be linear over a broad range of Δ E, which consolidates the mechanism of thermal activation as promoted by the spectral overlap between the LH1 fluorescence and the special pair absorption of RC.

Synthesis, Optical Resolution, and Circularly Polarized Luminescence of an Axially Chiral Porphyrin Dimer

AbstractMotivated by the chiral supramolecular structures of chlorophylls in photosynthesis proteins, i. e., special pairs present in purple photosynthetic bacteria, photosystems‐I, and ‐II, a chiral porphyrin dimer was designed, synthesized, and resolved to give optically pure forms. Synthesis of the dimer was achieved by using 5,10‐diarylporphyrin as the starting material. The stereochemistry of the dimer was speculated by comparing experimentally and theoretically obtained circular dichroism spectra. Clear circularly polarized luminescence spectra were obtained at 636 nm with dimensionless Kuhn's anisotropy value of ∼2.0 × 10−3.

Primary processes in the bacterial reaction center probed by two-dimensional electronic spectroscopy

In the initial steps of photosynthesis, reaction centers convert solar energy to stable charge-separated states with near-unity quantum efficiency. The reaction center from purple bacteria remains an important model system for probing the structure-function relationship and understanding mechanisms of photosynthetic charge separation. Here we perform 2D electronic spectroscopy (2DES) on bacterial reaction centers (BRCs) from two mutants of the purple bacterium Rhodobacter capsulatus, spanning the Q y absorption bands of the BRC. We analyze the 2DES data using a multiexcitation global-fitting approach that employs a common set of basis spectra for all excitation frequencies, incorporating inputs from the linear absorption spectrum and the BRC structure. We extract the exciton energies, resolving the previously hidden upper exciton state of the special pair. We show that the time-dependent 2DES data are well-represented by a two-step sequential reaction scheme in which charge separation proceeds from the excited state of the special pair (P*) to P+HA- via the intermediate P+BA- When inhomogeneous broadening and Stark shifts of the B* band are taken into account we can adequately describe the 2DES data without the need to introduce a second charge-separation pathway originating from the excited state of the monomeric bacteriochlorophyll BA*.

Excitonic Interactions in Bacteriochlorin Homo-Dyads Enable Charge Transfer: A New Approach to the Artificial Photosynthetic Special Pair.

Excitonically coupled bacteriochlorin (BC) dimers constitute a primary electron donor (special pair) in bacterial photosynthesis and absorbing units in light-harvesting antenna. However, the exact nature of the excited state of these dyads is still not fully understood. Here, we report a detailed spectroscopic and computational investigation of a series of symmetrical bacteriochlorin dimers, where the bacteriochlorins are connected either directly or by a phenylene bridge of variable length. The excited state of these dyads is quenched in high-dielectric solvents, which we attribute to photoinduced charge transfer. The mixing of charge transfer with the excitonic state causes accelerated (within 41 ps) decay of the excited state for the directly linked dyad, which is reduced by orders of magnitude with each additional phenyl ring separating the bacteriochlorins. These results highlight the origins of the excited-state dynamics in symmetric BC dyads and provide a new model for studying the primary processes in photosynthesis and for the development of artificial, biomimetic systems for solar energy conversion.

Primary and Higher Order Structure of the Reaction Center from the Purple Phototrophic Bacterium Blastochloris viridis: A Test for Native Mass Spectrometry.

The reaction center (RC) from the phototrophic bacterium Blastochloris viridis was the first integral membrane protein complex to have its structure determined by X-ray crystallography and has been studied extensively since then. It is composed of four protein subunits, H, M, L, and C, as well as cofactors, including bacteriopheophytin (BPh), bacteriochlorophyll (BCh), menaquinone, ubiquinone, heme, carotenoid, and Fe. In this study, we utilized mass spectrometry-based proteomics to study this protein complex via bottom-up sequencing, intact protein mass analysis, and native MS ligand-binding analysis. Its primary structure shows a series of mutations, including an unusual alteration and extension on the C-terminus of the M-subunit. In terms of quaternary structure, proteins such as this containing many cofactors serve to test the ability to introduce native-state protein assemblies into the gas phase because the cofactors will not be retained if the quaternary structure is seriously perturbed. Furthermore, this specific RC, under native MS, exhibits a strong ability not only to bind the special pair but also to preserve the two peripheral BCh's.

Proposal for verifying dipole properties of light-harvesting antennas

For light harvesters with a reaction center complex (LH1-RC complex) of three types, we propose an experiment to verify our analysis based upon antenna theories that automatically include the required structural information. Our analysis conforms to the current understanding of light-harvesting antennas in that we can explain known properties of these complexes. We provide an explanation for the functional roles of the notch at the light harvester, a functional role of the polypeptide called PufX or W at the opening, a functional role of the special pair, a reason that the cross section of the light harvester must not be circular, a reason that the light harvester must not be spherical, reasons for the use of dielectric bacteriochlorophylls instead of conductors to make the light harvester, a mechanism to prevent damage from excess sunlight, an advantage of the dimeric form, and reasons for the modular design of nature. Based upon our analysis we provide a mechanism for dimerization. We predict that the dimeric form of light-harvesting complexes is favored under intense sunlight. We further comment upon the classification of the dimeric or S-shape complexes. The S-shape complexes should not be considered as the third type of light harvester but simply as a composite form.

Spatio-temporal asymmetry of local wind fields and its impact on short-term wind forecasting.

The massive amounts of spatio-temporal data collected in today's wind farms have created a necessity for accurate spatio-temporal models. Despite the growing recognition for non-separable spatio-temporal models, a significant reliance on separable, symmetric models is still the norm in today's renewable industry. We discover that the broad use of separable models is due to the handling of wind data in a setting that does not reveal their fine-scale spatio-temporal structure. The contribution of this research is two-fold. First, we devise a special pair of spatio-temporal "lens" that allows us to see the fine-scale spatio-temporal variations and interactions, and subsequently, we conclude that local wind fields exhibit strong signs of non-separability and asymmetry. Using one year of turbine-specific wind measurements, we show that asymmetry can in fact be detected in more than 93% of the time. Second, making use of the spatio-temporal lens, we propose an enhanced procedure for short-term wind speed forecast. Substantial improvements in forecast accuracy in both wind speed and wind power were observed. When combined with certain intelligent methods such as support vector machine, additional improvements are possible.

Eyelid Drive System: An Assistive Technology Employing Inductive Sensing of Eyelid Movement.

This paper presents the design, development, and validation of the eyelid drive system (EDS), an assistive technology comprising a specialized pair of glasses and millimeter-sized passive resonators, attached to the user's eyelids, that transduce eyelid movement (blinking and winking) through inductive sensing. The theory of operation and design optimization with simulations are presented. A proof-of-concept prototype EDS was constructed using a pair of nonprescription glasses and commercial-off-the-shelf components. In benchtop tests with model eyelids, the EDS demonstrated basic functionality. Initial trials were performed involving six human subjects interacting with custom designed graphical user interfaces on a computer. A group mean accuracy of 96.3% was achieved using a set of four different commands at a response rate of 3 s. A mean information transfer rate (ITR) of 56.1 b/min over all subjects was achieved with a set of six different commands at a response rate of 1.5 s. This proof-of-concept device consumes 51.6mW of power. The EDS compares favorably with related eye-interfacing assistive technologies and provides a unique combination of advantages, including high accuracy and ITR, wearability, insensitivity to lighting and noise conditions, obviation of facial electrodes, and the use of nonexaggerated gestures.

Photoresponsive Electrodes Modified with DNA Duplexes Possessing a Porphyrin Dimer.

This work describes the formation of a porphyrin (Por) dimer using a DNA duplex as a scaffold and photocurrent generation from electrodes modified with a monolayer of Por-DNA conjugates. The solid-phase click reaction between an azide-porphyrin and oligonucleotide labeled with an ethynyl group on CPG support was utilized to conjugate the Por to the DNA. UV/Vis absorption and circular dichroism (CD) spectral studies revealed that the Por dimer can be formed through DNA hybridization and that through-space electronic interactions, characterized from the exciton-coupled absorption and the bisignate CD, can occur between the two Por molecules. Photoelectrochemical experiments were performed for the electrodes functionalized with a monolayer composed of the Por-DNA conjugates. It was found that the Por dimer on the electrode, which was designed to resemble the special pair in natural photosynthesis, shows efficient photocurrent generation in the presence of electron-acceptor reagents compared with the Por monomer. These findings strongly support the idea that the DNA structures could be useful to construct Por arrays, which is essential for the design of photo- and bio-electronic devices.

Projector approach to the general linear equation with variables from the subring of the rational functions and a factorable coefficient

The problem of finding two rational, linearly related functions with poles in the half-planes is considered. A new approach to this theory is proposed. The problem with factorable rational coefficients is formulated and solved. The method is based on the theory that is derived from previous research by the second author. The result is used for the corresponding abstract equations in the ring, with a special factorization pair of subrings. The formulas of solutions and illustrative examples are given. The procedure does not involve Fourier integral, Cauchy integral theory, or the Hölder function.

Decomposition of the Experimental Raman and Infrared Spectra of Acidic Water into Proton, Special Pair, and Counterion Contributions.

Textbooks describe excess protons in liquid water as hydronium (H3O+) ions, although their true structure remains lively debated. To address this question, we have combined Raman and infrared (IR) multivariate curve resolution spectroscopy with ab initio molecular dynamics and anharmonic vibrational spectroscopic calculations. Our results are used to resolve, for the first time, the vibrational spectra of hydrated protons and counterions and reveal that there is little ion-pairing below 2 M. Moreover, we find that isolated excess protons are strongly IR active and nearly Raman inactive (with vibrational frequencies of ∼1500 ± 500 cm-1), while flanking water OH vibrations are both IR and Raman active (with higher frequencies of ∼2500 ± 500 cm-1). The emerging picture is consistent with Georg Zundel's seminal work, as well as recent ultrafast dynamics studies, leading to the conclusion that protons in liquid water are primarily hydrated by two flanking water molecules, with a broad range of proton hydrogen bond lengths and asymmetries.