The photodissociation dynamics and ultrafast electron diffraction image of cyclobutanone from the surface hopping dynamics simulation.

The comprehension of nonadiabatic dynamics in polyatomic systems relies heavily on the simultaneous advancements in theoretical and experimental domains. The gas-phase ultrafast electron diffraction (UED) technique has attracted significant attention as a unique tool for monitoring photochemical and photophysical processes at the all-atomic level with high temporal and spatial resolutions. In this work, we simulate the UED spectra of cyclobutanone using the trajectory surface hopping method at the extended multi-state complete active space second order perturbation theory (XMS-CASPT2) level and thereby predict the results of the upcoming UED experiments in the Stanford Linear Accelerator Laboratory. The simulated results demonstrate that a few pathways, including the C2 and C3 dissociation channels, as well as the ring opening channel, play important roles in the nonadiabatic reactions of cyclobutanone. We demonstrate that the simulated UED signal can be directly interpreted in terms of atomic motions, which provides a unique way of monitoring the evolution of the molecular structure in real time. Our work not only provides numerical data that help to determine the accuracy of the well-known surface hopping dynamics at the high XMS-CASPT2 electronic-structure level but also facilitates the understanding of the microscopic mechanisms of the photoinduced reactions in cyclobutanone.

The development of the QM/MM interface and its application for the on-the-fly QM/MM nonadiabatic dynamics in JADE package: Theory, implementation, and applications.

Understanding the nonadiabatic dynamics of complex systems is a challenging task in computational photochemistry. Herein, we present an efficient and user-friendly quantum mechanics/molecular mechanics (QM/MM) interface to run on-the-fly nonadiabatic dynamics. Currently, this interface consists of an independent set of codes designed for general-purpose use. Herein, we demonstrate the ability and feasibility of the QM/MM interface by integrating it with our long-term developed JADE package. Tailored to handle nonadiabatic processes in various complex systems, especially condensed phases and protein environments, we delve into the theories, implementations, and applications of on-the-fly QM/MM nonadiabatic dynamics. The QM/MM approach is established within the framework of the additive QM/MM scheme, employing electrostatic embedding, link-atom inclusion, and charge-redistribution schemes to treat the QM/MM boundary. Trajectory surface-hopping dynamics are facilitated using the fewest switches algorithm, encompassing classical and quantum treatments for nuclear and electronic motions, respectively. Finally, we report simulations of nonadiabatic dynamics for two typical systems: azomethane in water and the retinal chromophore PSB3 in a protein environment. Our results not only illustrate the power of the QM/MM program but also reveal the important roles of environmental factors in nonadiabatic processes.

On-the-fly simulation of time-resolved fluorescence spectra and anisotropy.

We combine on-the-fly trajectory surface hopping simulations and the doorway-window representation of nonlinear optical response functions to create an efficient protocol for the evaluation of time- and frequency-resolved fluorescence (TFRF) spectra and anisotropies of the realistic polyatomic systems. This approach gives the effective description of the proper (e.g., experimental) pulse envelopes, laser field polarizations, and the proper orientational averaging of TFRF signals directly from the well-established on-the-fly nonadiabatic dynamic simulations without extra computational cost. To discuss the implementation details of the developed protocol, we chose cis-azobenzene as a prototype to simulate the time evolution of the TFRF spectra governed by its nonadiabatic dynamics. The results show that the TFRF is determined by the interplay of several key factors, i.e., decays of excited-state populations, evolution of the transition dipole moments along with the dynamic propagation, and scaling factor of the TFRF signals associated with the cube of emission frequency. This work not only provides an efficient and effective approach to simulate the TFRF and anisotropies of realistic polyatomic systems but also discusses the important relationship between the TFRF signals and the underlining nonadiabatic dynamics.

Ultrasensitive miRNA Detection Based on Magnetic Upconversion Nanoparticle Enhancement and CRISPR/Cas13a-Driven Signal Amplification.

MicroRNAs (miRNAs), a class of small molecules with important regulatory functions, have been widely used in the field of biosensing as biomarkers for the early diagnosis of various diseases. Therefore, it is crucial to develop an miRNA detection platform with high sensitivity and specificity. Here, we have designed a CRISPR/Cas13-based enzymatic cyclic amplification system and regarded the magnetic upconversion nanoparticles (MUCNPs) as a biosensor of outputting the detection signal for the highly sensitive and high-fidelity detection of miRNAs. MUCNPs were composed of UCNPs (fluorescence donors) and Fe3O4@AuNPs (fluorescence acceptors) through double-stranded DNA hybrid coupling. The target miRNA acted as an activator, which could activate the trans-cleavage activity of Cas13a to the well-designed Trigger containing two uracil ribonucleotides (rU) in its loop and trigger a strand displacement reaction to generate a large amount of single-stranded DNA, resulting in the release of the UCNPs from MUCNPs. Benefiting from the high fidelity and high selectivity of CRISPR/Cas13a, the great effect of triggered enzymatic cycle amplification, and the high-intensity luminescent signal of MUCNPs, this method possessed miRNA detection capability with high sensitivity and specificity even in the complex environment with 10% fetal bovine serum (FBS) and a serum sample. Meanwhile, the detection limit could be as low as 83.2 fM. In addition, this method effectively reduced the effect of photobleaching and maintained high stability, which was expected to achieve efficient and sensitive miRNA detection.

Studies of nonadiabatic dynamics in the singlet fission processes of pentacene dimer via tensor network method.

Singlet fission (SF) is a very significant photophysical phenomenon and possesses potential applications. In this work, we try to give a rather detailed theoretical investigation of the SF process in the stacked polyacene dimer by combining the high-level quantum chemistry calculations and the quantum dynamics simulations based on the tensor network method. Starting with the construction of the linear vibronic coupling model, we explore the pure electronic dynamics and the vibronic dynamics in the SF processes. The role of vibrational modes in nonadiabatic dynamics is addressed. The results show that the super-exchange mechanism mediated by the charge-transfer state is found in both pure electronic dynamics and the nonadiabatic dynamics. Particularly the vibrational modes with the frequencies resonance with the adiabatic energy gap play very import roles in the SF dynamics. This work not only provides a deep and detailed understanding of the SF process but also verifies the efficiency of the tensor network method with the train structure that can serve as the reference dynamics method to explore the dynamics behaviors of complex systems.

Genome-Wide mRNA and Long Non-Coding RNA Analysis of Porcine Trophoblast Cells Infected with Porcine Reproductive and Respiratory Syndrome Virus Associated with Reproductive Failure.

Porcine reproductive and respiratory syndrome (PRRS) is a vertically transmitted reproductive disorder that is typically characterized by miscarriage, premature birth, and stillbirth in pregnant sows after infection. Such characteristics indicate that PRRSV can infect and penetrate the porcine placental barrier to infect fetus piglets. The porcine trophoblast is an important component of the placental barrier, and secretes various hormones, including estrogen and progesterone, to maintain normal pregnancy and embryonic development during pregnancy. It is conceivable that the pathogenic effects of PRRSV infection on porcine trophoblast cells may lead to reproductive failure; however, the underlying detailed mechanism of the interaction between porcine trophoblast (PTR2) cells and PRRSV is unknown. Therefore, we conducted genome-wide mRNA and long non-coding RNA (lncRNA) analysis profiling in PRRSV-infected PTR2. The results showed that 672 mRNAs and 476 lncRNAs were significantly different from the control group after viral infection. Target genes of the co-expression and co-location of differential mRNAs and lncRNAs were enriched by GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, revealing that most of the pathways were involved in cell nutrient metabolism, cell proliferation, and differentiation. Specifically, the estrogen signaling pathway, the PI3K (PhosphoInositide-3 Kinase)-Akt (serine/threonine kinase) signaling pathway, and the insulin secretion related to embryonic development were selected for analysis. Further research found that PRRSV inhibits the expression of G-protein-coupled estrogen receptor 1 (GPER1), thereby reducing estrogen-induced phosphorylation of AKT and the mammalian target of rapamycin (mTOR). The reduction in the phosphorylation of AKT and mTOR blocks the activation of the GPER1- PI3K-AKT-mTOR signaling pathway, consequently restraining insulin secretion, impacting PTR2 cell proliferation, differentiation, and nutrient metabolism. We also found that PRRSV triggered trophoblast cell apoptosis, interrupting the integrity of the placental villus barrier. Furthermore, the interaction network diagram of lncRNA, regulating GPER1 and apoptosis-related genes, was constructed, providing a reference for enriching the functions of these lncRNA in the future. In summary, this article elucidated the differential expression of mRNA and lncRNA in trophoblast cells infected with PRRSV. This infection could inhibit the PI3K-AKT-mTOR pathway and trigger apoptosis, providing insight into the mechanism of the vertical transmission of PRRSV and the manifestation of reproductive failure.

The principal component analysis of the ring deformation in the nonadiabatic surface hopping dynamics.

The analysis of the leading active molecular motions in the on-the-fly trajectory surface hopping simulation provides the essential information to understand the geometric evolution in nonadiabatic dynamics. When the ring deformation is involved, the identification of the key active coordinates becomes challenging. A "hierarchical" protocol based on the dimensionality reduction and clustering approaches is proposed for the automatic analysis of the ring deformation in the nonadiabatic molecular dynamics. The representative system keto isocytosine is taken as the prototype to illustrate this protocol. The results indicate that the current hierarchical analysis protocol is a powerful way to clearly clarify both the major and minor active molecular motions of the ring distortion in nonadiabatic dynamics.

Investigation of nonadiabatic dynamics in the photolysis of methyl nitrate (CH3ONO2) by on-the-fly surface hopping simulation.

The photolysis mechanism of methyl nitrate (CH3ONO2) was studied using the on-the-fly surface hopping dynamics at the XMS-CASPT2 level. Several critical geometries, including electronic state minima and conical intersections, were obtained, which play essential roles in the nonadiabatic dynamics of CH3ONO2. The ultrafast nonadiabatic decay dynamics to the ground state were simulated, which gives a proper explanation on the broad and structureless absorption spectra of CH3ONO2. The photodissociation channels, including CH3O + NO2, CH3O + NO + O, and others, as well as their branching ratios, were identified. When the dynamics starts from the lowest two electronic states (S1 and S2), the CH3O + NO2 channel is the dominant photolysis pathway, although we observed the minor contributions of other channels. In contrast, when the trajectories start from the third excited state S3, both CH3O + NO2 and CH3O + NO + O channels become important. Here the CH3O-NO2 bond dissociation takes place first, and then for some trajectories, the N-O bond of the NO2 part breaks successively. The quasi-degeneracy of electronic states may exist in the dissociation limits of both CH3O + NO2 and CH3O + NO + O channels. The current work provides valuable information in the understanding of experimental findings of the wavelength-dependent photolysis mechanism of CH3ONO2.

Analysis of bath motion in MM-SQC dynamics via dimensionality reduction approach: Principal component analysis.

The system-plus-bath model is an important tool to understand the nonadiabatic dynamics of large molecular systems. Understanding the collective motion of a large number of bath modes is essential for revealing their key roles in the overall dynamics. Here, we applied principal component analysis (PCA) to investigate the bath motion in the basis of a large dataset generated from the symmetrical quasi-classical dynamics method based on the Meyer-Miller mapping Hamiltonian nonadiabatic dynamics for the excited-state energy transfer in the Frenkel-exciton model. The PCA method clearly elucidated that two types of bath modes, which either display strong vibronic coupling or have frequencies close to that of the electronic transition, are important to the nonadiabatic dynamics. These observations were fully consistent with the physical insights. The conclusions were based on the PCA of the trajectory data and did not involve significant pre-defined physical knowledge. The results show that the PCA approach, which is one of the simplest unsupervised machine learning dimensionality reduction methods, is a powerful one for analyzing complicated nonadiabatic dynamics in the condensed phase with many degrees of freedom.

Study of the exciton dynamics in perylene bisimide (PBI) aggregates with symmetrical quasiclassical dynamics based on the Meyer-Miller mapping Hamiltonian.

The exciton dynamics in one-dimensional stacked PBI (Perylene Bisimide) aggregates was studied with SQC-MM dynamics (Symmetrical Quasiclassical Dynamics based on the Meyer-Miller mapping Hamiltonian). Based on linear vibronic coupling models, one-dimensional PBI aggregates with different lengths were investigated. Based on an investigation of short PBI aggregates (10 sites and 80-140 modes) using both the SQC-MM and ML-MCTDH (multilayer multiconfigurational time-dependent Hartree) methods, we showed that SQC-MM dynamics give a reasonable description of the exciton dynamics for organic PBI aggregates composed of 101 sites and 808 modes. This allows us to employ SQC-MM dynamics in the explicit study of exciton diffusion for long one-dimensional PBI aggregates based on models with different site-site coupling strengths with/without static disorder by including all the involved electronic and vibrational degrees of freedom.

Predictors and one-year outcomes of patients with delayed graft function after deceased donor kidney transplantation.

BACKGROUND: Delayed graft function (DGF) is closely associated with the use of marginal donated kidneys due to deficits during transplantation and in recipients. We aimed to predict the incidence of DGF and evaluate its effect on graft survival. METHODS: This retrospective study on kidney transplantation was conducted from January 1, 2018, to December 31, 2019, at the Second Xiangya Hospital of Central South University. We classified recipients whose operations were performed in different years into training and validation cohorts and used data from the training cohort to analyze predictors of DGF. A nomogram was then constructed to predict the likelihood of DGF based on these predictors. RESULTS: The incidence rate of DGF was 16.92%. Binary logistic regression analysis showed correlations between the incidence of DGF and cold ischemic time (CIT), warm ischemic time (WIT), terminal serum creatine (Scr) concentration, duration of pretransplant dialysis, primary cause of donor death, and usage of LifePort. The internal accuracy of the nomogram was 83.12%. One-year graft survival rates were 93.59 and 99.74%, respectively, for the groups with and without DGF (P < 0.05). CONCLUSION: The nomogram established in this study showed good accuracy in predicting DGF after deceased donor kidney transplantation; additionally, DGF decreased one-year graft survival.

Performance of trajectory surface hopping method in the treatment of ultrafast intersystem crossing dynamics.

We carried out extensive studies to examine the performance of the fewest-switches surface hopping method in the description of the ultrafast intersystem crossing dynamic of various singlet-triplet (S-T) models by comparison with the results of the exact full quantum dynamics. Different implementation details and some derivative approaches were examined. As expected, it is better to perform the trajectory surface hopping calculations in the spin-adiabatic representation or by the local diabatization approach, instead of in the spin-diabatic representation. The surface hopping method provides reasonable results for the short-time dynamics in the S-T model with weak spin-orbital coupling (diabatic coupling), although it does not perform well in the models with strong spin-orbital coupling (diabatic coupling). When the system accesses the S-T potential energy crossing with rather high kinetic energy, the trajectory surface hopping method tends to produce a good description of the nonadiabatic intersystem crossing dynamics. The impact of the decoherence correction on the performance of the trajectory surface hopping is system dependent. It improves the result accuracy in many cases, while its influence may also be minor for other cases.

Thiazoloisoindigo: A Building Block that Merges the Merits of Thienoisoindigo and Diazaisoindigo for Conjugated Polymers.

Thiazoloisoindigo, a novel structural variation of isoindigo, is for the first time utilized to synthesize conjugated polymers. The polymer based on thiazoloisoindigo merges the advantages of the one based on thienoisoindigo and diazaisoindigo; it not only exhibits a greatly redshifted UV/Vis absorption to the near-infrared region owing to its strong tendency to form quinoidal structures, similar to that based on thienoisoindigo, but also shows excellent ambipolar mobility (hole: 3.93, electron: 1.07 cm2 V-1 s-1 ) in organic field-effect transistors (OFETs), superior to that based on diazaisoindigo, showing the strong electron-withdrawing capability of thiazoloisoindigo.

Phosphorus and chlorine co-doped carbon dots with strong photoluminescence as a fluorescent probe for ferric ions.

Usually, carbon dots (CDs) display a relatively weak fluorescence quantum yield (QY). In order to obtain brighter CDs, phosphorus and chlorine co-doped CDs (P,Cl-CDs) were prepared via hydrothermal treatment of maltose in the presence of phosphoric and hydrochloric acids. The new CDs are highly monodispersed in water solution, have high fractions of P (14.4 atomic%) and Cl (8.9 atomic%), and exhibited yellow fluorescence with a QY of 15%. This is higher than that of monoatomic doped CDs (8.7 and 9.3% for P-CDs and Cl-CDs, respectively). The P,Cl-CDs are highly photostable, and fluorescence is strongly (statically) quenched by Fe(III). Fluorescence decreases with increasing concentration of Fe(III) in the range from 0.1-8.0 µmol⋅L-1, with a 60 nmol⋅L-1 detection limit. The doped CDs are shown to be a viable nanoprobe for the fluorometric determination of Fe(III) in spiked serum and water samples. Graphical abstract Schematic presentation of one-step synthesis of phosphorus and chlorine co-doped carbon dots with high photoluminescence for the detection of ferric ions.

Postbiotic properties of exopolysaccharide produced by Levilactobacillus brevis M-10 isolated from natural fermented sour porridge through in vitro simulated digestion and fermentation.

The simulated digestion and fermentation characteristics in vitro of exopolysaccharide (EPS) of Levilactobacillus brevis M-10 were studied to evaluate its postbiotic properties. The simulated digestion results showed that EPS could not be degraded in saliva but could be very slightly degraded in gastric juice and could be degraded in intestinal juice. The results of simulated fermentation demonstrated that EPS could lower the intestine pH and be utilized by gut microbes to produce short-chain fatty acids such as propionic acid and butyric acid. Meanwhile, EPS significantly raised the diversity of human gut microbiota, and the relative abundances of Phascolarctobacterium were significantly increased, whereas Fusobacterium and Morganella significantly decreased. In conclusion, EPS from L. brevis M-10 was a good postbiotic as inulin. This was the first report about EPS as the postbiotic of L. brevis M-10 screened from broomcorn millet sour porridge in northwestern Shanxi Province, China.

Tilapia head gelatins to stabilize fish oil emulsions and the effect of extraction methods.

The preparation and use of gelatins from fish by-products have attracted much attention in the field of food science. Herein, four types of tilapia head gelatins were extracted and characterized: hot water-pretreated gelatin (HWG), acetic acid-pretreated gelatin (AAG), sodium hydroxide-pretreated gelatin (SHG), and pepsin enzyme-pretreated gelatin (PEG). The gel strength values followed the order: PEG (74 ± 1 Bloom) > AAG (66 ± 1) > HWG (59 ± 1) > SHG (34 ± 1). The foaming properties, fish oil emulsion viscosity, emulsion activity, and emulsion stabilization ability followed this order: PEG > HWG ≥ AAG > SHG. The effect mechanisms of extraction methods and gelatin concentrations on the emulsion stability involved the interfacial tension, emulsion viscosity, and fat-binding capacity. This work provided important knowledge for analyzing the relations between the structure and function of gelatin. It also provided a high-value application method of fish wastes.

An electrochemiluminescent dual-signal immunosensor based on a Ru(bpy)32+-doped silica nanoparticle/copper nanocluster composite for okadaic acid detection.

In this study, a sensitive dual-signal electrochemiluminescence (ECL) immunosensor was developed for okadaic acid (OA) detection utilizing copper nanoclusters (CuNCs) and Ru(bpy)32+-doped silica nanoparticles (RuSiNPs). Interestingly, the CuNCs could simultaneously enhance both cathodic (-0.95 V) and anodic (+1.15 V) ECL signals of RuSiNPs, forming a dual-signal ECL sensing platform. Further, RuSiNPs@CuNCs were used as immunomarkers by covalently conjugating them with an anti-OA monoclonal antibody (mAb) to form probes. Finally, dual ECL signals of the immunosensor were fabricated and showed good linear relationships with OA concentrations in the range of 0.05-70 ng mL-1, having a median inhibitory concentration (IC50) of 1.972 ng mL-1 and a limit of detection of 0.039 ng mL-1. Moreover, the constant ratio of the cathodic and anodic ECL peaks achieved self-calibration of the detection signal and improved the reliability of the results. Finally, we successfully applied the ECL sensor to detect OA in spiked oyster samples.

Effects of gelatin type and concentration on the preparation and properties of freeze-dried fish oil powders.

The effects of gelatin type (porcine skin gelatin, PSG; bovine skin gelatin, BSG; fish gelatin, FG; or cold-water fish skin gelatin, CFG) and concentration on the preparation and properties of fish oil powders were investigated in this work. The oil powders were prepared using the combination method of gelatin-sodium hexametaphosphate complex coacervation with starch sodium octenyl succinate (SSOS)-aided freeze-drying. Compared with the other gelatins, CFG-with an unobvious isoelectric point, a lower molecular weight, more hydrogen bonds, and longer gel formation time-could not form complex coacervates, which are necessary to prepare oil powders. For oil powders obtained from the other gelatins, gelatin type and concentration did not have obvious effects on microscale morphologies; they did, however, have significant effects on physicochemical properties. The highest peroxide values of the oil powders were mainly dependent on the gelatins, expressed in the following manner: PSG (153 ± 5 - 168 ± 3 meq/Kg oil) < BSG (176 ± 5 - 188 ± 1 meq/Kg oil) < FG (196 ± 11 - 201 ± 22 meq/Kg oil). Acidic and neutral pH could not dissolve the complex coacervates. However, the oil powders could be quickly dissolved to form emulsion droplets in the gastric phase, and that SSOS increased coacervate stability and promoted oil digestion during the in vitro gastrointestinal process. In sum, this study contributes fundamental information to understanding the development of fish oil solid encapsulation preparations.

Molecular modification of low-dissolution soy protein isolates by anionic xanthan gum, neutral guar gum, or neutral konjac glucomannan to improve the protein dissolution and stabilize fish oil emulsion.

Herein, the effects of anionic xanthan gum (XG), neutral guar gum (GG), and neutral konjac glucomannan (KGM) on the dissolution, physicochemical properties, and emulsion stabilization ability of soy protein isolate (SPI)-polysaccharide conjugates were studied. The SPI-polysaccharide conjugates had better water dissolution than the insoluble SPI. Compared with SPI, SPI-polysaccharide conjugates had lower ß-sheet (39.6 %-56.4 % vs. 47.3 %) and α-helix (13.0 %-13.2 % vs. 22.6 %) percentages, and higher ß-turn (23.8 %-26.5 % vs. 11.0 %) percentages. The creaming stability of SPI-polysaccharide conjugate-stabilized fish oil-loaded emulsions mainly depended on polysaccharide type: SPI-XG (Creaming index: 0) > SPI-GG (Creaming index: 8.1 %-21.2 %) > SPI-KGM (18.1 %-40.4 %). In addition, it also depended on the SPI preparation concentrations, glycation times, and glycation pH. The modification by anionic XG induced no obvious emulsion creaming even after 14-day storage, which suggested that anionic polysaccharide might be the best polysaccharide to modify SPI for emulsion stabilization. This work provided useful information to modify insoluble proteins by polysaccharides for potential application.

Fish oil-loaded multicore submillimeter-sized capsules prepared with monoaxial electrospraying, chitosan-tripolyphosphate ionotropic gelation, and Tween blending.

In order to load fish oil for potential encapsulation of fat-soluble functional active substances, fish oil-loaded multicore submillimeter-sized capsules were prepared with a combination method of three strategies (monoaxial electrospraying, chitosan-tripolyphosphate ionotropic gelation, and Tween blending). The chitosan-tripolyphosphate/Tween (20, 40, 60, and 80) capsules had smaller and evener fish oil cores than the chitosan-tripolyphosphate capsules, which resulted from that Tween addition induced smaller and evener fish oil droplets in the emulsions. Tween addition decreased the water contents from 56.6 % to 35.0 %-43.4 %, increased the loading capacities from 10.4 % to 12.7 %-17.2 %, and increased encapsulation efficiencies from 97.4 % to 97.8 %-99.1 %. In addition, Tween addition also decreased the highest peroxide values from 417 meq/kg oil to 173-262 meq/kg oil. These properties' changes might result from the structural differences between the chitosan-tripolyphosphate and chitosan-tripolyphosphate/Tween capsules. All the results suggested that the obtained chitosan-tripolyphosphate/Tween capsules are promising carriers for fish oil encapsulation. This work also provided useful knowledge to understand the preparation, structural, and physicochemical properties of the chitosan-tripolyphosphate capsules.