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We have theoretically investigated the hydrodesulphurisation (HDS) mechanism of hydrogenated thiophene over Cu–Mo-modified FAU zeolite using a two-layer ONIOM (our Own N-layered Integrated molecular Orbital and molecular Mechanics) study. The thiophene is hydrogenated to 2,3-dihydrothiophene (2,3-DHT), 2,5-dihydrothiophene (2,5-DHT) and tetrahydrothiophene (THT) due to moderate free energy barriers. Hydrogenolysis desulphurisation (HYD) and concerted direct desulphurisation (DDS) are discussed. Ring-opening, hydrogen transfer and C−S bond cleavage steps of thiophene derivatives are involved in the HYD process. The rate-determining steps are the hydrogen transfer step for 2,5-DHT and C−S bond cracking step for 2,3-DHT and THT. The concerted DDS pathway is probably more favourable than the HYD pathway in the desulphurisation of 2,5-DHT. The difference charge density (DCD) analysis reveals that for the ring-opening process, the electrons are migrated from the organic chain to the Cu–Mo catalytic centre. The reduced density gradient (RDG) plots indicate that both steric hindrance and a weak van der Waals (VDW) interaction exist between organic fragment and catalytic centre for all transition states (TSs). The localised orbital locator (LOL) maps suggest that there are strong covalent interactions and weak VDW interactions between the atoms in the forming chemical bonds.

The complex conformations of the cyclic moieties impact the physical and chemical properties of the molecules. In this work, we chose 22 molecules of four-, five-, and six-membered rings and performed a thorough conformational sampling using Cremer-Pople coordinates. We sampled hundreds or thousand of conformational structures including all well-known and many less well-known conformers for each molecule. We tried to represent the potential energy surfaces (PESs) by fitting the data to common analytical force field functional forms. Although the general features of PESs can be described by the essential force field functional forms, the accuracy of representation can be improved remarkably by including the torsion-bond and torsion-angle coupling terms. The best fit yields R-squared (R2) values close to 1.0 and mean absolute errors (MAEs) in energy less than 0.3 kcal/mol.

Retinal ganglion cell apoptotic death is the main pathological characteristic of glaucoma, which is the leading cause of irreversible blindness. Disruption of Ca

AIM: To study the changes of the red blood cell volume distribution width(RDW)level and the correlation between them in patients with primary angle-closure glaucoma(PACG).METHODS: Retrospective case-control study was conducted. A total of 306 PACG patients in Eye & ENT Hospital of Fudan University from February 2019 to October 2020 were selected as the case group and 126 healthy patients who received physical examination at the hospital during the same period were selected as the control group. The PACG patients were divided into three subgroups according to the mean defect of visual field(MD): mild(MD≤6dB), moderate(612dB). The detailed eye and physical examinations information of the two groups were collected from the medical data platform of Eye & ENT Hospital of Fudan University. The blood sample parameters were detected by automated hematology and biochemistry analyzers. Independent sample t-test, Chi-square test, one-way ANOVA test, Pearson correlation analyses and multiple linear regression analyses were performed in this research. RESULTS: There was no significant difference between the PACG group and the control group in age, gender, body mass index and blood pressure(P>0.05). Based on the laboratory results, the mean RDW level was significantly higher(t=2.132, P=0.034)in the PACG group(12.64%±0.96%)than that in the control group(12.45%±0.49%). Moreover, the mean RDW level and the mean hemoglobin(HG)level was significantly lower(P

With the rapid development of molecular biology technologies such as whole-genome testing in the past decade, non-coding RNA has been deeply explored. Circular RNA(circRNA)gradually becomes a hot topic in recent years, which plays an important role in the occurrence and development of a variety of diseases, and relevant studies have been carried out in ophthalmological diseases. This article will review the mechanism, basic research, and clinical findings of circRNA in various ophthalmic diseases, and briefly discuss the potential clinical significance of circRNA in ophthalmic diseases.

We have parametrized an AMBER force field in a TEAMFF database to accurately represent intra- and intermolecular interactions of cellulose. Parameters are obtained by fitting quantum mechanics (QM) energetic data on a training set of 12 simple and substituted heterocycles, alcohols, ethers, and saccharides. The temperature-dependent Lennard–Jones parameters were optimized by fitting experimental data of 23 molecular liquids at different temperatures using molecular dynamics (MD) simulations. Validation on cellobiose, the monomer of cellulose, exhibits excellent agreement between the data obtained by molecular mechanics calculations using the present force field and QM calculations in terms of conformational energies, structures, and vibrational frequencies. The MD simulation results of cellulose Iβ crystal agree well with the experimental data, showing a 0.1% deviation in density and less than 1% deviations in all the cell parameters.

We have theoretically studied the hydrodesulphurisation (HDS) mechanism of thiophene and its hydrogenated derivatives over sulphided Co–Mo catalysts supported by four zeolites (ZSM-5, FAU, Beta, MCM-22) by a two-layer ONIOM (our Own N-layered Integrated molecular Orbital and molecular Mechanics) method. Due to low energy barriers, the thiophene can be hydrogenated to 2,3-dihydrothiophene (2,3-DHT), 2,5-dihydrothiophene (2,5-DHT) and tetrahydrothiophene (THT). Direct desulphurisation (DDS) and hydrogenolysis desulphurisation (HYD) pathways were investigated in detail. The calculated results show that in DDS mechanism of thiophene, the rate-determining step is the C–S bond cleavage. In HYD mechanisms of 2,5-DHT, 2,3-DHT and THT, the rate-determining step is hydrogen transfer on ZSM-5, FAU and Beta zeolites except MCM-22 zeolite. The HYD of 2,3-DHT and THT should occur by the stepwise pathway. But for the 2,5-DHT, the concerted pathway is probably more favourable than the stepwise pathway. The reduced density gradient (RDG), differential charge density (DCD), and local orbital locator (LOL) maps show that for all transition states (TSs), there are complicated van der Waals (VDW) and electrostatic interactions between the organic fragment and the catalytic centre.

This work proposes a state-of-the-art hybrid kernel to calculate molecular similarity. Combined with Gaussian process models, the performance of the hybrid kernel in predicting molecular properties is comparable to that of the directed message-passing neural network (D-MPNN). The hybrid kernel consists of a marginalized graph kernel (MGK) and a radial basis function (RBF) kernel that operate on molecular graphs and global molecular features, respectively. Bayesian optimization was used to obtain the optimal hyperparameters for both models. The comparisons are performed on 11 publicly available data sets. Our results show that their performances are similar, their prediction errors are correlated, and the ensemble predictions of the two models perform better than either of them. Through principal component analysis, we found that the molecular embeddings of the hybrid kernel and the D-MPNN are also similar. The advantage of D-MPNN lies in the computational efficiency and scalability of large-scale data, while the advantage of the graph kernel models lies in the accurate uncertainty quantification.

The rubber tree, Hevea brasiliensis, produces natural rubber that serves as an essential industrial raw material. Here, we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing (SMRT) and Hi-C technologies to anchor the ∼1.47-Gb genome assembly into 18 pseudochromosomes. The chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution, since the common paleopolyploid event occurred before the split of Hevea and Manihot. We show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last 10 million years, leading to the massive expansion by ∼65.88% (∼970 Mbp) of the whole rubber tree genome since the divergence from Manihot. We identify large-scale expansion of genes associated with whole rubber biosynthesis processes, such as basal metabolic processes, ethylene biosynthesis, and the activation of polysaccharide and glycoprotein lectin, which are important properties for latex production. A map of genomic variation between the cultivated and wild rubber trees was obtained, which contains ∼15.7 million high-quality single-nucleotide polymorphisms. We identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history of rubber tree, some of which are involved in rubber biosynthesis. This genome assembly represents key resources for future rubber tree research and breeding, providing novel targets for improving plant biotic and abiotic tolerance and rubber production.

The pressure-dependent viscosity of 2,2,4-trimethylhexane is predicted using all-atom TEAM force field and the non-equilibrium periodic perturbation (PP) method. The viscosities predicted using the PP method do not show Newtonian plateau in the precision range of prediction for high-viscosity fluids. Using four alkane molecules as test cases, we found that our previously published force field, developed for ambient pressure conditions, is inaccurate for predicting viscosities under elevated pressures. Two approaches were attempted to enhance the pressure transferability of the force field: one involves moving the non-bond interaction site of hydrogen closer to that of attached carbon, which smooths the van der Waals (vdW) surface of molecule, and the other involves replacing the LJ-12-6 function by LJ-9-6, making the repulsion softer. Both approaches enhanced the pressure transferability; however, the former works well below 500 MPa, while the latter is valid under pressures up to 1 GPa.

It has long remained elusive whether ${\mathrm{CuCo}}_{2}{\mathrm{S}}_{4}$ thiospinel shows bulk superconductivity (SC). Here we clarify the issue by studying the samples of sulfur-deficient ${\mathrm{CuCo}}_{2}{\mathrm{S}}_{3.7}$ and sulfurized ${\mathrm{CuCo}}_{2}{\mathrm{S}}_{4}$. The sample ${\mathrm{CuCo}}_{2}{\mathrm{S}}_{3.7}$ has a smaller lattice constant of $a=9.454$ \AA{}, and it is not superconducting down to 1.8 K. After a full sulfurization, the $a$ axis of the thiospinel phase increases to 9.475 \AA{}, and the thiospinel becomes nearly stoichiometric ${\mathrm{CuCo}}_{2}{\mathrm{S}}_{4}$, although a secondary phase of slightly Cu-doped ${\mathrm{CoS}}_{2}$ forms. Bulk SC at 4.2 K and Pauli paramagnetism have been demonstrated for the sulfurized ${\mathrm{CuCo}}_{2}{\mathrm{S}}_{4}$ by the measurements of electrical resistivity, magnetic susceptibility, and specific heat.

This work proposes a state-of-the-art hybrid kernel to calculate molecular similarity. Combining with Gaussian process models, the performance of the hybrid kernel in predicting molecular properties is comparable to that of the Directed Message Passing Neural Network (D-MPNN). The hybrid kernel consists of a marginalized graph kernel (MGK) and a radial basis function (RBF) kernel that operates on molecular graphs and global molecular features, respectively. Bayesian optimization was used to get the optimal hyperparameters for both models. The comparisons are performed on 11 publicly available data sets. Our results show that the predictions of both models are correlated with similar performance, and the ensemble prediction of both models performs better than either of them. Through principal component analysis, we found that the features extracted by the hybrid kernel are similar to those extracted by D-MPNN. The advantage of D-MPNN lies in computational efficiency, while the advantage of the graph kernel models lies in the inherent uncertainty quantification and accurate uncertainty quantification. All codes for graph kernel machines used in this work can be found at https://github.com/Xiangyan93/Chem-Graph-Kernel-Machine.

This work presents a Gaussian process regression (GPR) model on top of a novel graph representation of chemical molecules that predicts thermodynamic properties of pure substances in single, double, and triple phases. A transferable molecular graph representation is proposed as the input for a marginalized graph kernel, which is the major component of the covariance function in our GPR models. Radial basis function kernels of temperature and pressure are also incorporated into the covariance function when necessary. We predicted three types of representative properties of pure substances in single, double, and triple phases, i.e., critical temperature, vapor-liquid equilibrium (VLE) density, and pressure-temperature density. The data is collected from Knovel Data Analysis Beta: NIST ThermoDynamics Pure Compounds. The accuracy of the models is nearly identical to the precision of the experimental measurements. Moreover, the reliability of our predictions can be quantified on a per-sample basis using the posterior uncertainty of the GPR model. We compare our model against Morgan fingerprints and a graph neural network to further demonstrate the advantage of the proposed method. The marginalized graph kernel is computed using GraphDot package at https://github.com/yhtang/GraphDot. All codes used in this work can be found at https://github.com/Xiangyan93/Chem-Graph-Kernel-Machine.

AIM: To determine whether glaucoma patients exhibit an abnormal melatonin concentration in serum and the effects of psychiatric disorders caused by glaucoma in melatonin secretion. METHODS: A sample of 80 primary angle-closure glaucoma (PACG) patients, 120 primary open angle glaucoma (POAG) patients, and 120 normal controls were enrolled in this study. All the participants were asked to complete the following questionnaires: Pittsburgh sleep quality index (PSQI), self-rating anxiety scale (SAS), and self-rating depression scale (SDS). Variance analysis was used to compare the subscores between the groups. After that, we chose 58 patients with primary glaucoma and 20 non-glaucoma control patients to collect their serum samples at 7-10 a.m. Serum melatonin levels were measured using enzyme linked immunosorbent assay (ELISA). RESULTS: Of all participants, the scores of PSQI, SAS, and SDS in PACG and POAG group were 9.38±0.40, 46.08±8.99, 51.11±10.72 and 7.43±0.35, 45.42±9.87, 49.04±12.24 respectively, significantly higher than those in control group (4.16±0.28, 35.49±9.18, 40.31±13.08). The serum melatonin levels in PACG (37.29±2.99 pg/mL) and POAG (35.97±3.64 pg/mL) were significantly higher than the controls (29.96±3.94 pg/mL) (P

An automatic high-throughput computing (HTC) procedure is implemented for calculating vapor-liquid equilibrium (VLE) curves of binary systems using molecular dynamics simulation and coarse-grained force field. The HTC procedure builds simulation models, carries out the simulations, and validates the simulations automatically. The procedure is demonstrated by calculating the VLE curves for 16 binary mixtures of carbon dioxide and n-alkanes on 856 state points in the temperature range of 277.2–420.0 K and pressure range of 0.3–25.0 MPa. The averaged uncertainties in predictions are 0.119 MPa for pressure, 0.007 and 0.029 for liquid and vapor CO 2 molar fractions, and 0.005 and 0.010 for liquid and vapor densities respectively. The Validation against experiment data on 10 binary systems and 316 state points shows that the predictions are accurate with average deviation of about 5% for CO 2 mole fraction and 3.5% for saturated density at pressure range to P P c . This automatic procedure can only be used for the prediction of the vapor-liquid equilibrium. The computed data can be obtained from http://sun.sjtu.edu.cn/msd .

The mechanisms of aluminophosphate oligomerization were investigated using density functional theory with the SMD solvation model. Two aluminum species, Al(OH)4(-) and Al(H2O)6(3+), and four phosphorus species, H3PO4, H2PO4(-), HPO4(2-), and PO4(3-), were considered as the monomers for polycondensation reactions. It was found that the most favorable pathway to dimerization was a Lewis acid-base reaction: the aprotic oxygen of phosphoric acid (P═O) performs a nucleophilic attack on the central aluminum atom of Al(OH)4(-). Using this mechanism as a pattern, plausible dimerization mechanisms were investigated by varying the proticity and hydration of the phosphorus and aluminum monomers, respectively. The relative reaction rates of each mechanism were estimated under different pH conditions. The chain growth of aluminophosphates to trimers, tetramers, and pentamers and the cyclization of a linear tetramer were also investigated. For oligomerization reactions beyond dimer formation, it is found that cluster growth favors the addition of the phosphoric monomers rather than aluminum monomers.

The Hilbert-Huang transform (HHT) is an adaptive data analysis method that can accommodate the variety of data generated by nonlinear and nonstationary processes in nature. In this paper, we focus on the small geomagnetically induced current (GIC) at the local substations in low-latitude power grid of China, responding to a moderate storm on 14–18 July 2012. The HHT is applied to analyze the neutral point currents (NPCs) of transformers measured at different substations, and the GIC indices converted from local geomagnetic field measurements. The original data are decomposed into intrinsic mode functions (IMFs) using the ensemble empirical mode decomposition. After removal of the quasi-diurnal components related with the solar quiet variation, the IMFs representing storm disturbances are transformed into Hilbert energy spectra. The results show that some transformers have more or less responses to the moderate storm in the form of Hilbert energy spectra with the frequency around 2–3 mHz. A comparison on the amplitude changes of the spectra total energy of NPCs' perturbation during storm time intervals at different sites suggests that a shell type of three-phase single transformer group seems to be more vulnerable in the storm. Although the low-latitude power grids usually show very small GIC, these can be used to investigate the potential risk of space weather to the system.

A superconductive Ba2Ti2Fe2As4O oxypnictide sample was synthesized following a solid-state reaction route. X-ray diffraction followed by Rietveld analysis was used for checking the phase content. 57Fe Mossbauer spectroscopy in transmission geometry was used for characterizing the hyperfine parameters of the iron site. Ba2Ti2Fe2As4O is paramagnetic at least down to 77 K in contrast to the BaFe2As2 parent phase, which exhibits a spin-density order below ∼ 140 K. Fitting the isomer shift and spectral absorption data with the Debye model yielded Debye temperatures of 280–320 K.

An activity called Purple Dragons and Yellow Toadstools, originally reported in 1987 as a training activity for jurors, was adapted as a priming exercise for a unit on teaching research ethics with undergraduate students. In this activity, learners develop skills for building negotiated consensus. The procedure involves individuals' ranking 10-15 moral transgressions and/or legal violations followed by a small group discussion in order to arrive at an agreed-upon ranking by the team. The framework has proved to be quite flexible, adaptable to different subject areas and with different populations of students.

The surface-bulk partition of nonionic surfactants was predicted by calculating chemical potential differences using two simulation boxes representing the surface and the bulk phases separately. A published coarse grained force field was modified and validated for this application. Thermodynamic integration (TI) was applied to compute excess chemical potentials. The high concentration surface was stabilized by applying an external harmonic potential, and the bulk was treated as ideal solution, which was confirmed by simulation using a lattice model at conditions near the critical micelle concentration (∼10(-5) mol/L). Based on the calculated chemical potential differences with precision of ca. 1 kJ/mol, the equilibria of surface-bulk concentration was predicted well in comparison with the experimental data.

EphB1, expressed in Müller cells, and ephrinB2, expressed in both Müller cells and retinal ganglion cells (RGCs), constitute an EphB/ephrinB reverse signaling in RGCs. Whether and how this reverse signaling is involved in RGC apoptosis in a rat chronic ocular hypertension (COH) model was investigated. In the COH model, both EphB1 and ephrinB2 were significantly increased and the reverse signaling was activated, which was accompanied by increased protein levels of phosphorylated (p) src, GluA2, and p-GluA2. Intravitreal injection of EphB2-Fc, an activator of ephrinB2, induced an increase in TUNEL-positive signals in normal retinae. A coimmunoprecipitation assay demonstrated direct interactions among ephrinB2, p-src, and GluA2. Moreover, in COH rats the expression of GluA2 proteins on the surface of retinal cells was decreased. Such GluA2 endocytosis could be prevented by preoperational intravitreal injection of 4-amino-3-(4-chlorophenyl)-1-(t-butyl)-1H-pyrazolo [3,4-d] pyrimidine (PP2), an inhibitor of src family tyrosine kinases, and possibly involved the protein interacting with C kinase 1 and phosphorylation of GluA2. In normal rats, intravitreal injection of EphB2-Fc caused changes in these protein levels similar to those observed in COH rats, which all could be avoided by preinjection of PP2. Patch-clamp experiments further showed that the current–voltage relationship of AMPA receptor-mediated EPSCs of RGCs exhibited stronger inward rectification in EphB2-Fc-injected rats. Furthermore, preinjection of PP2 orN-[3-[[4-[(3-aminopropyl)amino]butyl]amino]propyl]-1-naphthaleneacetamide trihydrochloride) (Naspm), a Ca2+-permeable GluA2-lacking AMPA receptor inhibitor, remarkably inhibited RGC apoptosis in either EphB2-Fc-injected or COH rats. Together, elevated GluA2 trafficking induced by activated EphB2/ephrinB2 reverse signaling likely contributes to RGC apoptosis in COH rats.

The roles of the iris microvasculature have been increasingly recognised in the pathogenesis of glaucoma and cataract; however limited information exists regarding the iris microvasculature and its endothelium. This study quantitatively assessed the iris microvascular network and its endothelium using intra-luminal micro-perfusion, fixation, and staining of the porcine iris. The temporal long posterior ciliary artery of 11 isolated porcine eyes was cannulated, perfusion-fixed and labelled using silver nitrate. The iris microvasculature was studied for its distribution, orders and endothelial morphometrics. The density of three layers of microvasculature was measured. Endothelial cell length and width were measured for each vessel order. The iris has an unusual vascular distribution which consisted of abundant large vessels in the middle of the iris stroma, branching over a relatively short distance to the microvasculature located in the superficial and deep stroma as well as the pupil edge. The average vascular density of the middle, superficial, and deep layers were 38.9 ± 1.93%, 10.9 ± 1.61% and 8.0 ± 0.79% respectively. Multiple orders of iris vessels (capillary, 6 orders of arteries, and 4 orders of veins) with relatively large capillary and input arteries (319.5 ± 25.6 μm) were found. Significant heterogeneity of vascular diameter and shape of the endothelia was revealed in different orders of the iris vasculature. Detailed information of topography and endothelium of the iris microvasculature combined with unique structural features of the iris may help us to further understand the physiological and pathogenic roles of the iris in relevant ocular diseases.

Coarse-grained force field (CGFF) methods were applied to study the self-assembly of sodium dodecyl sulfate with fragrance additives. The CGFF parameters were parameterized and validated using experimental and all-atom simulation data. Direct molecular dynamics simulations were carried out to characterize the initial aggregation, partitioning of fragrances, and chemical potentials of the surfactant and fragrance molecules in aggregates of different sizes. The equilibrium critical micelle concentrations (CMCs) and micelle size distributions, which could not be obtained by direct simulation, were predicted using the calculated chemical potentials in combination with a thermodynamic model. The predicted partitioning of fragrances, CMCs, micelle sizes, and micelle structures agree well with previously reported experimental data. Graphical abstract Enhancement of micelle size distribution using thermodynamic model.

The surface-bulk partition of surfactants is a piece of important information for understanding the performance of surfactants. In this work, we predicted surface-bulk partitions for three ionic surfactants (sodium hexyl sulfate, sodium nonyl sulfate, sodium dodecyl sulfate) using molecular dynamics simulations and a coarse-grained force field. The simulations were performed with the bilayer model that represents thin films. By setting initial configurations using chemical potentials calculated for infinitely dilute solutions, we obtained a sufficient number of independent samples for each simulation which ran at least 2 μs. Predicted surface concentrations and surface tensions are in good agreement with the experimental data. The surface adsorption isotherms, surface structures, and critical micelle concentrations (CMCs) derived from the simulated data are in reasonable agreement with the experimental data and previously calculated data. For surfactants with a short alkyl chain (SHS), stable oligomers are formed before micelles in the bulk.

We develop here the methodology for dramatically accelerating the ReaxFF reactive force field based reactive molecular dynamics (RMD) simulations through use of the bond boost concept (BB), which we validate here for describing hydrogen combustion. The bond order, undercoordination, and overcoordination concepts of ReaxFF ensure that the BB correctly adapts to the instantaneous configurations in the reactive system to automatically identify the reactions appropriate to receive the bond boost. We refer to this as adaptive Accelerated ReaxFF Reactive Dynamics or aARRDyn. To validate the aARRDyn methodology, we determined the detailed sequence of reactions for hydrogen combustion with and without the BB. We validate that the kinetics and reaction mechanisms (that is the detailed sequences of reactive intermediates and their subsequent transformation to others) for H_2 oxidation obtained from aARRDyn agrees well with the brute force reactive molecular dynamics (BF-RMD) at 2498 K. Using aARRDyn, we then extend our simulations to the whole range of combustion temperatures from ignition (798 K) to flame temperature (2998K), and demonstrate that, over this full temperature range, the reaction rates predicted by aARRDyn agree well with the BF-RMD values, extrapolated to lower temperatures. For the aARRDyn simulation at 798 K we find that the time period for half the H_2 to form H_2O product is 538 s, whereas the computational cost was just 1289 ps, a speed increase of 0.42 trillion (10^(12)) over BF-RMD. In carrying out these RMD simulations we found that the ReaxFF-COH2008 version of the ReaxFF force field was not accurate for such intermediates as H_3O. Consequently we reoptimized the fit to a quantum mechanics (QM) level, leading to the ReaxFF–OH2014 force field that was used in the simulations.

Grand Canonical Monte Carlo (GCMC) simulations with ab initio force field were used to predict the adsorption isotherms of n-C6F14 in BCR-704 faujasite (calcium type) zeolite. The force field parameters were derived using the vapor–liquid equilibrium data for the adsorbate molecules, and ab initio data for the adsorbent (zeolite) with argon as a testing particle. The interactions between the adsorbate molecules and the zeolite were represented by using the Lorentz–Berthelot combining rule. Based on a comparison of ab initio and experimental data obtained for methane absorbed on calcium and sodium type zeolites, it was found that the exposed, non-framework calcium cations (Ca2+) must be partially hydroxylated. As the force field parameters were determined using ab initio data, we were able to estimate the percentage of hydroxylation without interference from the force field parameters by using the experimental adsorption data of argon and nitrogen. The hydroxylation ratio of calcium cations was estimated to be 63%. Based on this model and the combined force field parameters, the adsorption isotherm of n-C6F14 on BCR-704 zeolite was predicted and the results are in reasonable agreement with the experimental data.

Using force field parameters developed and validated for zeolitic imidazolate frameworks (ZIFs) and carbon dioxide (CO2) independently from adsorption data, we predicted CO2/ZIFs adsorption isotherms using the Grand Canonic Monte Carlo (GCMC) method. The results are in sharp contradiction: the calculated adsorption data agree well with the experimental data for SOD-type ZIF-8, but are more than 100% higher than the experimental data for GME-type ZIFs. Using non-equilibrium molecular dynamics simulations and potential of mean force (PMF) calculations, we reveal that the discrepancies are due to the kinetic blockage which is significant for ZIF-68 but negligible for ZIF-8. This study demonstrates that a force field developed independently from the adsorption data can be used to predict the adsorptions accurately; and the kinetic factor must be considered if the bottlenecks exist in the adsorption paths due to geometric and energetic features of adsorbate and adsorbent. It could be very misleading if the force field parameters are adjusted by fitting the GCMC simulation data to experimental data without considering the kinetic factors.

Purpose: Our previous study indicated that mitochondrial DNA (mtDNA) damage and mutations are crucial to the progressive loss of retinal ganglion cells (RGCs) in a glaucomatous rat model. In this study, we examined whether high pressure could directly cause mtDNA alterations and whether the latter could lead to mitochondrial dysfunction and RGC death. Methods: Primary cultured rat RGCs were exposed to 30 mm Hg of hydrostatic pressure (HP) for 12, 24, 48, 72, 96 and 120 h. mtDNA alterations and mtDNA repair/replication enzymes OGG1, MYH and polymerase gamma (POLG) expressions were also analyzed. The RGCs were then infected with a lentiviral small hairpin RNA (shRNA) expression vector targeting POLG (POLG-shRNA), and mtDNA alterations as well as mitochondrial function, including complex I/III activities and ATP production were subsequently studied at appropriate times. Finally, RGC apoptosis and the mitochondrial-apoptosis pathway-related protein cleaved caspase-3 were detected using a Terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL) assay and western blotting, respectively. Results: mtDNA damage was observed as early as 48 h after the exposure of RGCs to HP. At 120 h after HP, mtDNA damage and mutations significantly increased, reaching >40% and 4.8 ± 0.3-fold, respectively, compared with the control values. Twelve hours after HP, the expressions of OGG1, MYH and POLG mRNA in the RGCs were obviously increased 5.02 ± 0.6-fold (p < 0.01), 4.3 ± 0.2-fold (p < 0.05), and 0.8 ± 0.09-fold (p < 0.05). Western blot analysis showed that the protein levels of the three enzymes decreased at 72 and 120 h after HP (p < 0.05). After interference with POLG-shRNA, the mtDNA damage and mutations were significantly increased (p < 0.01), while complex I/III activities gradually decreased (p < 0.05). Corresponding decreases in membrane potential and ATP production appeared at 5 and 6 days after POLG-shRNA transfection respectively (p < 0.05). Increases in the apoptosis of RGCs and cleaved caspase-3 protein expression were observed after mtDNA damage and mutations. Conclusions: High pressures could directly cause mtDNA alterations, leading to mitochondrial dysfunction and RGC death.

At a temperature over the decomposition point (375 °C) of MgH2, the formation of Mg2Ni is greatly enhanced from the 2MgH2+Ni system, as compared to the 2Mg+Ni system. In support of this finding, in-situ observation of X-ray absorption fine structure of the two systems indicates that MgNi bonds form faster in the 2MgH2+Ni system than in the 2Mg+Ni system. Furthermore, theoretical modeling also shows that Mg atoms are readily released from MgH2 using much less energy and thus are more available to react with Ni once the dehydrogenation of MgH2 occurs, as compared to normal Mg.

Thermal conductivities of graphene-like silicon and carbon hybrid nanostructures with silicon atom percentages varying from 0 % (graphene) to 100 % (silicene) are investigated using the reserve non-equilibrium molecular dynamic (RNEMD) method and Tersoff bond order potentials. The thermal conductivity of graphene is dramatically reduced with increasing silicon concentration, and the reduction appears to be related more to the topological structures formed than the amount of doped silicon atoms present. The reduction is collectively contributed to by reduced phonon group velocities (v), phonon free paths (l∞), and the specific heat capacity (c) of the material. For systems with high symmetry, thermal conductivity is mainly influenced by v and c. For systems with low symmetry, thermal conductivity is dominated by l∞; such materials are also more direction-dependent on thermal flux than highly symmetric materials.

Molecular dynamics (MD) simulations were applied to investigate the liquid–liquid equilibria of water and dipropylene glycol dimethyl ether (DMM) based on all-atom OPLS force fields and simple point charge (SPC) water model. The default combining rules (geometric means) for describing interactions between water and ether molecules were modified by fitting hydration free energies of dimethyl ether and diethyl ether. The difference of Gibbs free energies (ΔG) was calculated using the thermodynamic integration (TI) method. Extensive simulations were carried out in order to reach high precision in the predicted free energies. The average uncertainties in calculated ΔG are 0.8 kJ/mol for DMM and 0.3 kJ/mol for water. From the calculated ΔGmix, the mutual solubility of the binary mixture was predicted using the double tangent method at four temperatures ranging from 283 K to 353 K and 1 atm.

Molecular simulation, as a powerful tool for investigating science of matter at a molecular level, is widely applied in interdisciplinary fields between chemistry, physics, biology, engineering and...