Combined X-ray-electron imaging techniques: Limitations on lateral resolution

Capabilities of the imaging techniques, in which X-rays are converted to electrons and then the emitted electrons are registered by means of an electron microscope, are analyzed, the focus being on the factors limiting lateral resolution at the stage of electron emission. Bearing in mind the tendency to use harder synchrotron X-rays for some combined X-ray-electron microscopy methods, calculations were made for two significantly different X-ray energies: E = 1.828 keV (K-edge of Si) and E = 11.923 keV (L₃-edge of Au). By using Monte Carlo simulations of the electron trajectories beneath the surface of the sample we show that the radius of the spot from which photoelectrons are emitted could be as small as 1 nm. However, when proper account is taken of an entire electron cascade associated with the re-building of electron shells after photoelectron emission, spots more than one order of magnitude larger result, limiting the best lateral resolution to 20–30 nm.     

The phase diagram of a single polymer chain: New insights from a new simulation method

We present simulation results for the phase behavior of a single chain for a flexible lattice polymer model using the Wang-Landau sampling idea. Applying this new algorithm to the problem of the homopolymer collapse allows us to investigate not only the high temperature coil–globule transition but also an ensuing crystallization at lower temperature. Performing a finite size scaling analysis on the two transitions, we show that they coincide for our model in the thermodynamic limit corresponding to a direct collapse of the random coil into the crystal without intermediate coil–globule transition. As a consequence, also the many chain phase diagram of this model can be predicted to consist only of gas and crystal phase in the limit of infinite chain length. This behavior is in agreement with findings on the phase behavior of hard-sphere systems with a relatively short-ranged attractive square well. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2542–2555, 2006     

Incubation period in the 2,2,4,4‐tetramethyl‐1‐piperidinyloxy‐mediated thermal autopolymerization of styrene: Kinetics and simulations

Mechanisms and simulations of the induction period and the initial polymerization stages in the nitroxide‐mediated autopolymerization of styrene are discussed. At 120–125 °C and moderate 2,2,4,4‐tetramethyl‐1‐piperidinyloxy (TEMPO) concentrations (0.02–0.08 M), the main source of radicals is the hydrogen abstraction of the Mayo dimer by TEMPO [with the kinetic constant of hydrogen abstraction (k_h)]. At higher TEMPO concentrations ([N?] > 0.1 M), this reaction is still dominant, but radical generation by the direct attack against styrene by TEMPO, with kinetic constant of addition k_ad, also becomes relevant. From previous experimental data and simulations, initial estimates of k_h ≈ 1 and k_ad ≈ 6 × 10^?7 L mol^?1 s^?1 are obtained at 125 °C. From the induction period to the polymerization regime, there is an abrupt change in the dominant mechanism generating radicals because of the sudden decrease in the nitroxide radicals. Under induction‐period conditions, the simulations confirm the validity of the quasi‐steady‐state assumption (QSSA) for the Mayo dimer in this regime; however, after the induction period, the QSSA for the dimer is not valid, and this brings into question the scientific basis of the well‐known expression k_th[M]³ (where [M] is the monomer concentration and k_th is the kinetic constant of autoinitiation) for the autoinitiation rate in styrene polymerization. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 6962‐6979, 2006     

Superdegenerate point in FCC phase diagram: CVM and Monte Carlo investigations

We investigate the topology of the phase diagram of binary alloys on the fee lattice with first-neighbor antiferromagnetic interactions around the superdegenerate point, where the L1₀ and L1₂ phases meet. We treat the system as a hard-constraint lattice gas, following a procedure previously described by Lebowitzet al. We perform cluster variation method calculations in theT0 limit and Monte Carlo simulations directly atT=0 K on the ground states of the superdegenerate point. We find that: (i) there is no disordered phase in the neighborhood of this point; (ii) a phase L for which two of the four cubic sublattices have the same average occupancy and each of the two others are different appears between L1₀ and L1₂; (iii) the transition L/L1₂ is of first order.     

Subtleties in data analysis related to the size of critical region

We comment on the analysis of the critical behavior of a layered driven diffusive system recently done by Achahbar and Marro. We discuss why we believe their method of taking the thermodynamic limit and determining the order-parameter exponent leads to unreliable estimates.     

Electrophoresis simulations using Chebyshev pseudo-spectral method on a moving mesh

We present the implementation and demonstration of the Chebyshev pseudo-spectral method coupled with an adaptive mesh method for performing fast and highly accurate electrophoresis simulations. The Chebyshev pseudo-spectral method offers higher numerical accuracy than all other finite difference methods and is applicable for simulating all electrophoresis techniques in channels with open or closed boundaries. To improve the computational efficiency, we use a novel moving mesh scheme that clusters the grid points in the regions with poor numerical resolution. We demonstrate the application of the Chebyshev pseudo-spectral method on a moving mesh for simulating nonlinear electrophoretic processes through examples of isotachophoresis (ITP), isoelectric focusing (IEF), and electromigration-dispersion in capillary zone electrophoresis (CZE) at current densities as high as 1000 A/m. We also show the efficacy of our moving mesh method over existing methods that cluster the grid points in the regions with large concentration gradients. We have integrated the adaptive Chebyshev pseudo-spectral method in the open-source SPYCE simulator and verified its implementation with other electrophoresis simulators.     

Monte carlo calculations of the conformal charge

The conformal charge is an important quantity which characterizes the nature of the two-dimensional phase transition. We report a first attempt to use a new numerical method to calculate the conformal charge. In this paper, we apply our method to the 2-dimensional, ⁴, continuous-spin Ising model. By varying the parameters in the Hamiltonian, one can change continuously from the known Gaussian limit to the Ising limit. It is well known that the critical points for these two systems are not in the same universality class. We study this behavior for the Gaussian model, the single-well ⁴ model, the border model, and the double-well ⁴ model for a large lattice. Our results, while giving a good general picture, are not so far sufficient to differentiate whether the non-Gaussian cases studied belong to the Ising model universality class or not. Further studies of other lattice sizes should serve to improve greatly our conclusions.     

Three New Acrylic Acid Derivatives from Achillea mellifolium as Potential Inhibitors of Urease from Jack Bean and α-Glucosidase from Saccharomyces cerevisiae

(1) Background: Achillea mellifolium belongs to a highly reputed family of medicinal plants, with plant extract being used as medicine in indigenous system. However, limited data is available regarding the exploitation of the medicinal potential of isolated pure compounds from this family; (2) Methods: A whole plant extract was partitioned into fractions and on the basis of biological activity, an ethyl acetate fraction was selected for isolation of pure compounds. Isolated compounds were characterized using different spectroscopic techniques. The compounds isolated from this study were tested for their medicinal potential using in-vitro enzyme assay, coupled with in-silico studies; (3) Results: Three new acrylic acid derivatives (1–3) have been isolated from the ethyl acetate fraction of Achillea mellifolium. The characterization of these compounds (1–3) was carried out using UV/Vis, FT-IR, 1D and 2D-NMR spectroscopy (¹H-NMR, ¹³C-NMR, HMBC, NOESY) and mass spectrometry. These acrylic acid derivatives were further evaluated for their enzyme inhibition potential against urease from jack bean and α glucosidase from Saccharomyces cerevisiae, using both in-silico and in-vitro approaches. In-vitro studies showed that compound 3 has the highest inhibition against urease enzyme (IC₅₀ =10.46 ± 0.03 μΜ), followed by compound 1 and compound 2 with percent inhibition and IC₅₀ value of 16.87 ± 0.02 c and 13.71 ± 0.07 μΜ, respectively, compared to the standard (thiourea-IC₅₀ = 21.5 ± 0.01 μΜ). The investigated IC₅₀ value of compound 3 against the urease enzyme is two times lower compared to thiourea, suggesting that this compound is twice as active compared to the standard drug. On the other hand, all three compounds (1–3) revealed mild inhibition potential against α-glucosidase. In-silico molecular docking studies, in combination with MD simulations and free energy, calculations were also performed to rationalize their time evolved mode of interaction inside the active pocket. Binding energies were computed using a MMPBSA approach, and the role of individual residues to overall binding of the inhibitors inside the active pockets were also computed; (4) Conclusions: Together, these studies confirm the inhibitory potential of isolated acrylic acid derivatives against both urease and α-glucosidase enzymes; however, their inhibition potential is better for urease enzyme even when compared to the standard.     

Molecular Simulation to Explore the Dissolution Behavior of Sulfur in Carbon Disulfide

Soluble sulfur (S₈) and insoluble sulfur (IS) have different application fields, and molecular dynamics simulation can reveal their differences in solubility in solvents. It is found that in the simulated carbon disulfide (CS₂) solvent, soluble sulfur in the form of clusters mainly promotes the dissolution of clusters through van der Waals interaction between solvent molecules (CS₂) and S₈, and the solubility gradually increases with the increase in temperature. However, the strong interaction between polymer chains of insoluble sulfur in the form of polymer hinders the diffusion of IS into CS₂ solvent, which is not conducive to high-temperature dissolution. The simulated solubility parameter shows that the solubility parameter of soluble sulfur is closer to that of the solvent, which is consistent with the above explanation that soluble sulfur is easy to dissolve.     

Design,Synthesis, Docking,DFT, MD Simulation Studies of a New Nicotinamide-Based Derivative: In Vitro Anticancer and VEGFR-2 Inhibitory Effects

A nicotinamide-based derivative was designed as an antiproliferative VEGFR-2 inhibitor with the key pharmacophoric features needed to interact with the VEGFR-2 catalytic pocket. The ability of the designed congener ((E)-N-(4-(1-(2-(4-benzamidobenzoyl)hydrazono)ethyl)phenyl)nicotinamide), compound 10, to bind with the VEGFR-2 enzyme was demonstrated by molecular docking studies. Furthermore, six various MD simulations studies established the excellent binding of compound 10 with VEGFR-2 over 100 ns, exhibiting optimum dynamics. MM-GBSA confirmed the proper binding with a total exact binding energy of −38.36 Kcal/Mol. MM-GBSA studies also revealed the crucial amino acids in the binding through the free binding energy decomposition and declared the interactions variation of compound 10 inside VEGFR-2 via the Protein–Ligand Interaction Profiler (PLIP). Being new, its molecular structure was optimized by DFT. The DFT studies also confirmed the binding mode of compound 10 with the VEGFR-2. ADMET (in silico) profiling indicated the examined compound’s acceptable range of drug-likeness. The designed compound was synthesized through the condensation of N-(4-(hydrazinecarbonyl)phenyl)benzamide with N-(4-acetylphenyl)nicotinamide, where the carbonyl group has been replaced by an imine group. The in-vitro studies were consonant with the obtained in silico results as compound 10 prohibited VEGFR-2 with an IC₅₀ value of 51 nM. Compound 10 also showed antiproliferative effects against MCF-7 and HCT 116 cancer cell lines with IC₅₀ values of 8.25 and 6.48 μM, revealing magnificent selectivity indexes of 12.89 and 16.41, respectively.