CHARMM36 all‐atom additive protein force field: Validation based on comparison to NMR data

Protein structure and dynamics can be characterized on the atomistic level with both nuclear magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here, we quantify the ability of the recently presented CHARMM36 (C36) force field (FF) to reproduce various NMR observables using MD simulations. The studied NMR properties include backbone scalar couplings across hydrogen bonds, residual dipolar couplings (RDCs) and relaxation order parameter, as well as scalar couplings, RDCs, and order parameters for side‐chain amino‐ and methyl‐containing groups. It is shown that the C36 FF leads to better correlation with experimental data compared to the CHARMM22/CMAP FF and suggest using C36 in protein simulations. Although both CHARMM FFs contains the same nonbond parameters, our results show how the changes in the internal parameters associated with the peptide backbone via CMAP and the χ₁ and χ₂ dihedral parameters leads to improved treatment of the analyzed nonbond interactions. This highlights the importance of proper treatment of the internal covalent components in modeling nonbond interactions with molecular mechanics FFs. © 2013 Wiley Periodicals, Inc.     

Mechanistic Simulation Studies on Viscous-Elastic Polymer Flooding in Petroleum Reservoirs

Based on the theory and application developments of polymer flooding on enhancing oil recovery, an improved mathematical model has been developed to simulate the mechanism of viscous-elastic polymer flooding. IMPES method has been presented to solve the polymer flooding model considering the viscosifying effect of elasticity, the effect of decreasing residual oil and the degradation of polymer molecules. The validation of the model is approved by an experiment. A simulation example was carried out using the developed numerical simulator. The enhanced oil recovery mechanism was discussed for viscous-elastic polymer flooding, and corresponding influencing factors were also studied.     

TargetATPsite: A template‐free method for ATP‐binding sites prediction with residue evolution image sparse representation and classifier ensemble

Understanding the interactions between proteins and ligands is critical for protein function annotations and drug discovery. We report a new sequence‐based template‐free predictor (TargetATPsite) to identify the Adenosine‐5′‐triphosphate (ATP) binding sites with machine‐learning approaches. Two steps are implemented in TargetATPsite: binding residues and pockets predictions, respectively. To predict the binding residues, a novel image sparse representation technique is proposed to encode residue evolution information treated as the input features. An ensemble classifier constructed based on support vector machines (SVM) from multiple random under‐samplings is used as the prediction model, which is effective for dealing with imbalance phenomenon between the positive and negative training samples. Compared with the existing ATP‐specific sequence‐based predictors, TargetATPsite is featured by the second step of possessing the capability of further identifying the binding pockets from the predicted binding residues through a spatial clustering algorithm. Experimental results on three benchmark datasets demonstrate the efficacy of TargetATPsite. © 2013 Wiley Periodicals, Inc.     

Improvement in Uranium Adsorption Properties of Amidoxime-Based Adsorbent Through Cografting of Amine Group

Amidoxime (AO)/amine co-functionalized polypropylene fiber adsorbents were prepared. The all-polymeric structures were characterized by using Fourier transform infrared spectroscopy (FTIR), optical microscope, contact angle meter and electron spin resonance (ESR) analysis methods, confirming the grafting, modification, and amidoximation stages gravimetrically, spectroscopically, and visually. The properties for the removal of uranyl(VI) from aqueous solutions were investigated. For amidoxime (AO) fiber, high adsorption rate was observed within the first 30 minutes and the plateau value of 40.6% uranium loading (0.0812 mg/g) was reached at around 30 minutes. The adsorption equilibrium for AO/amine fiber was attained within 20 minutes, resulting in the adsorption of 92.6% uranium loading (0.185 mg/g). The percentage of adsorption increases with increasing pH value (2–6), reaches a maximum at pH 6.0 and then remains almost constant for AO/amine fiber, whereas reduces slightly for AO fiber.     

Preparation and characterization of nanosized TiO2 powder as an inorganic adsorbent for aqueous radionuclide Co(II) ions

In this research TiO₂ sample was synthesized by a simple sol–gel method and was characterized by X-ray diffraction (XRD), Transmission electron microscopy (TEM) and Brunauer–Emmett–Teller (BET) techniques. The XRD result indicated that the obtained product was anatase titanium dioxide with high purity, the TEM image clearly showed that the particle sizes of TiO₂ nanoparticles were in the range of 30–70 nm, and the measured BET surface area of the heated TiO₂ nanoparticles was 147.14 m²/g. In this work, the prepared TiO₂ sample was used as a new adsorbent for the adsorption of radionuclide Co(II) ions from aqueous solutions, and the influence of pH, contact time, ionic strength and temperature in the presence or absence of humic acid/fulvic acid (HA/FA) were also investigated. The experimental results indicated that the adsorption of Co(II) ions onto TiO₂ was strongly pH-dependent. Based on the surface complexation, the presence of HSs enhanced the adsorption of Co(II) ions and the influence of Co(II) adsorption onto FA–TiO₂ hybrids was much stronger than that of HA–TiO₂ at pH values of 2.0–9.0. Adsorption of Co(II) ions onto TiO₂ powder was strongly dependent on ionic strength. The adsorption process mainly occured in the first contact time of 2 h and could be fitted by a pseudo-second-order rate model. The calculated thermodynamic data indicated that the adsorption of Co(II) ions onto TiO₂ was a spontaneous process and favorable at high temperatures.     

Kinetics for the Reaction between Potassium Ferricyanide and Cobalt Chloride in Aqueous Solution and Microemulsion

The kinetics for the reaction between potassium ferricyanide (K₃Fe(CN)₆) and cobalt chloride (CoCl₂) in aqueous solution and water/bis(2-ethylhexyl) sodium sulfosuccianate (AOT)/isooctane microemulsions were studied by three-wavelength spectrophotometry at 298.2 K. The second-order rate constants (k₂) were calculated from the time dependence of the concentration of reactant K₃Fe(CN)₆. The result showed that the reaction rates in water/AOT/isooctane microemulsions were slower than that in the aqueous solution, and k₂ decreased with molar ratio (ω) of water to AOT in microemulsions, which was interpreted by the transition state theory and confirmed that the reaction took place at the interfaces of the microemulsion water pools.     

Rheological Study of Interactions between Anionic Guar and Oppositely Charged Surfactant

We have studied the interactions between anionic carboxymethyl guar (CMG) and oppositely charged surfactant: dodecyltrimethylammonium bromide (DTAB), tetradecyltrimethylammonium bromide (TTAB), cetyltrimethylammonium bromide (CTAB), and gemini surfactants (16-4-16), using rheological measurements. In the present study, two competing forces, electrostatic interaction and hydrophobic interaction, have been identified as important factors. Various types of structure formed on the anionic CMG chains are qualitatively discussed in comparison. For example, C₁₂TAB and gemini surfactant tend to form polymer-bound aggregates, whereas the C₁₆TAB tend to form the polymer-associated architecture. Furthermore, possible mechanisms based on the experimental results to elucidate these interesting phenomena have been proposed and discussed.     

Synthesis and Magnetic Properties of Pt3Co/Fe3O4 Nanocomposites

Bimagnetic Pt₃Co/Fe₃O₄ nanocomposite is synthesized in aqueous solution. The nanoparticles are characterized with TEM, FTIR, and magnetic measurements. The as‐synthesized nanocomposite exhibits ferromagnetic properties at room temperature due to the exchange coupling between Pt₃Co and Fe₃O₄. Magnetic properties of Pt₃Co/Fe₃O₄ nanoparticle can be tuned by varying of the molar ratio of iron to platinum. Pt₃Co/Fe₃O₄ nanoparticles exhibit higher saturation magnetization when the molar ratio of iron to platinum is 1.     

Fusion Dynamics of Aqueous Glutamic Acid/Aminodecane/Ibuprofen Vesicles

Vesicles have been prepared at a constant molar ratio of L-glutamic acid/1-aminodecane/ibuprofen/H₂O. The fusion dynamics of the vesicles have been directly observed and followed by using optical microscopy and freeze fracture replication-electron microscopy technologies. With time increasing up to 25 minutes, the vesicles slowly fuse to form large stable vesicles. A membrane phase transition temperature is detected at 97°C.     

Plutonium-239 sorption and transport on/in unsaturated sediments: comparison of batch and column experiments for determining sorption coefficients

Sorption (distribution) coefficients of plutonium were most often derived by static batch experiments. However, it is not clear how unsaturated flow conditions including moisture content and pore water velocity change the sorption coefficients. Transport experiments of plutonium through the unsaturated sediments packed into the columns were then performed in order to determine the sorption coefficients (column-K _ds). Static batch experiments were also conducted to obtain batch-K _ds and then compare the differences between batch-K _ds and column-K _ds. The results show that unsaturated flow conditions had no significant effect on column-K _ds, and the average column-K _d value was 1.74 ± 0.02 m³/kg. By comparison, batch-K _d values spanned several orders of magnitude, regardless of the specified liquid–solid conditions. Moreover, the batch-K _d (22.7 m³/kg) at the standard L/S (4 mL/g) recommended by ASTM D 4319 was over an order of magnitude larger than the average column-K _d.