Soft-spring wall based non-periodic boundary conditions for non-equilibrium molecular dynamics of dense fluids

Non-equilibrium molecular dynamics (MD) simulations require imposition of non-periodic boundary conditions (NPBCs) that seamlessly account for the effect of the truncated bulk region on the simulated MD region. Standard implementation of specular boundary conditions in such simulations results in spurious density and force fluctuations near the domain boundary and is therefore inappropriate for coupled atomistic-continuum calculations. In this work, we present a novel NPBC model that relies on boundary atoms attached to a simple cubic lattice with soft springs to account for interactions from particles which would have been present in an untruncated full domain treatment. We show that the proposed model suppresses the unphysical fluctuations in the density to less than 1% of the mean while simultaneously eliminating spurious oscillations in both mean and boundary forces. The model allows for an effective coupling of atomistic and continuum solvers as demonstrated through multiscale simulation of boundary driven singular flow in a cavity. The geometric flexibility of the model enables straightforward extension to nonplanar complex domains without any adverse effects on dynamic properties such as the diffusion coefficient. (c) 2015 AIP Publishing LLC.

Isotopic fractionation in proteins as a measure of hydrogen bond length

If a deuterated molecule containing strong intramolecular hydrogen bonds is placed in a hydrogenated solvent, it may preferentially exchange deuterium for hydrogen. This preference is due to the difference between the vibrational zero-point energy for hydrogen and deuterium. It is found that the associated fractionation factor (I) is correlated with the strength of the intramolecular hydrogen bonds. This correlation has been used to determine the length of the H-bonds (donor-acceptor separation) in a diverse range of enzymes and has been argued to support the existence of short low-barrier H-bonds. Starting with a potential energy surface based on a simple diabatic state model for H-bonds, we calculate (I) as a function of the proton donor-acceptor distance R. For numerical results, we use a parameterization of the model for symmetric 0-H. ``.0 bonds R. H. McKenzie, Chem. Phys. Lett. 535, 196 (2012)]. We consider the relative contributions of the 0-H stretch vibration, O-H bend vibrations (both in plane and out of plane), tunneling splitting effects at finite temperature, and the secondary geometric isotope effect. We compare our total (I) as a function of R with NMR experimental results for enzymes, and in particular with an earlier model parametrization (D(R), used previously to determine bond lengths. (C) 2015 AIP Publishing LLC.

Ag+-induced reverse vesicle to helical fiber transformation in a self-assembly by adjusting the keto-enol equilibrium of a chiral salicylideneaniline

A new chiral amphiphilic salicylideneaniline bearing a terminal pyridine was synthesized. It formed reverse vesicles in toluene. The addition of Ag+, however, reversibly transforms these reverse vesicles into left-handed nanohelices accompanied by spontaneous gel formation at room temperature.

Direct Observation of Thermal Equilibrium of Excited Triplet States of 9,10-Phenanthrenequinone. A Time-Resolved Resonance Raman Study

The photochemistry of aromatic ketones plays a key role in various physicochemical and biological processes, and solvent polarity can be used to tune their triplet state properties. Therefore, a comprehensive analysis of the conformational structure and the solvent polarity induced energy level reordering of the two lowest triplet states of 9,10-phenanthrenequinone (PQ) was carried out using nanosecond-time-resolved absorption (ns-TRA), time-resolved resonance Raman (TR3) spectroscopy, and time dependent-density functional theory (TD-DFT) studies. The ns-TRA of PQ in acetonitrile displays two bands in the visible range, and these two bands decay with similar lifetime at least at longer time scales (mu s). Interestingly, TR3 spectra of these two bands indicate that the kinetics are different at shorter time scales (ns), while at longer time scales they followed the kinetics of ns-TRA spectra. Therefore, we report a real-time observation of the thermal equilibrium between the two lowest triplet excited states of PQ assigned to n pi* and pi pi* of which the pi pi* triplet state is formed first through intersystem crossing. Despite the fact that these two states are energetically close and have a similar conformational structure supported by TD-DFT studies, the slow internal conversion (similar to 2 ns) between the T-2(1(3)n pi*) and T-1(1(3)pi pi*) triplet states indicates a barrier. Insights from the singlet excited states of PQ in protic solvents J. Chem. Phys. 2015, 142, 24305] suggest that the lowest n pi* and pi pi* triplet states should undergo hydrogen bond weakening and strengthening, respectively, relative to the ground state, and these mechanisms are substantiated by TD-DFT calculations. We also hypothesize that the different hydrogen bonding mechanisms exhibited by the two lowest singlet and triplet excited states of PQ could influence its ISC mechanism.

Ag-doped hydroxyapatite as efficient adsorbent for removal of Congo red dye from aqueous solution: Synthesis, kinetic and equilibrium adsorption isotherm analysis

In the present study a versatile and efficient adsorbent with high adsorption capacity for adsorption of Congo red dye in aqueous solution at ambient temperature without adjusting any pH is presented over the Ag modified calcium hydroxyapatite (CaHAp). CaHAp and Ag-doped CaHAp materials were synthesized using facile aqueous precipitation method. The physico-chemical properties of the materials were determined by powder X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy, Transmission electron microscopy (TEM), UV-Visible spectroscopy, N-2 physisorption and acidity was determined by n-butylamine titration and pyridine adsorption methods. XRD analysis confirmed all adsorbents exhibit hexagonal CaHAp structure with P6(3)/m space group. TEM analysis confirms the rod like morphology of the adsorbents and the average length of the rods were in the range of 40-45 nm. Pyridine adsorption results indicate increase in number of Lewis acid sites with Ag doping in CaHAp. Adsorption capacity of CaHAp was found increased with Ag content in the adsorbents. Ag (10): CaHAp adsorbent showed superior adsorption performance among all the adsorbents for various concentrations of Congo red (CR) dye in aqueous solutions. The amount of CR dye adsorbed on Ag (10): CaHAp was found to be 49.89-267.81 mg g(-1) for 50-300 ppm in aqueous solution. A good correlation between adsorption capacity and acidity of the adsorbents was observed. The adsorption kinetic data of adsorbents fitted well with pseudo second-order kinetic model with correlation coefficients ranged from 0.998 to 0.999. The equilibrium adsorption data was found to best fit to the Langmuir adsorption isotherm model. (C) 2015 Elsevier Inc. All rights reserved.

Reconciling results of MOCVD of a CNT composite with equilibrium thermodynamics

Composition and microstructure of the composite films can be tailored by controlling the CVD process parameters if an appropriate model can be suggested for quantitative prediction of growth. This is possible by applying equilibrium thermodynamics. A modification of such standard modeling procedure was required to account for the deposition of a hybrid film comprised of carbon nanotubes (CNTs), metallic iron (Fe), and magnetite (Fe3O4), a composite useful for energy storage. In contrast with such composite nature of the deposits obtained by inert-ambient CVD using Fe(acac)3 as precursor, equilibrium thermodynamic modeling with standard procedure predicts the deposition of only Fe3C and carbon, without any co-deposition of Fe and Fe3O4. A modification of the procedure comprising chemical reasoning is therefore proposed herein, which predicts simultaneous deposition of FeO1-x, Fe3C, Fe3O4 and C. At high temperatures and in a carbon-rich atmosphere, these convert to Fe3O4, Fe and C, in agreement with experimental CVD. Close quantitative agreement between the modified thermodynamic modeling and experiment validates the reliability of the modified procedure. Understanding of the chemical process through thermodynamic modeling provides potential for control of CVD process parameters to achieve desired hybrid growth. (C) 2016 Elsevier B.V. All rights reserved.

SALIENT OBJECT DETECTION VIA OBJECTNESS MEASURE

Salient object detection has become an important task in many image processing applications. The existing approaches exploit background prior and contrast prior to attain state of the art results. In this paper, instead of using background cues, we estimate the foreground regions in an image using objectness proposals and utilize it to obtain smooth and accurate saliency maps. We propose a novel saliency measure called `foreground connectivity' which determines how tightly a pixel or a region is connected to the estimated foreground. We use the values assigned by this measure as foreground weights and integrate these in an optimization framework to obtain the final saliency maps. We extensively evaluate the proposed approach on two benchmark databases and demonstrate that the results obtained are better than the existing state of the art approaches.