Methane and carbon dioxide adsorption on edge-functionalized graphene: a comparative DFT study

With a view towards optimizing gas storage and separation in crystalline and disordered nanoporous carbon-based materials, we use ab initio density functional theory calculations to explore the effect of chemical functionalization on gas binding to exposed edges within model carbon nanostructures. We test the geometry, energetics, and charge distribution of in-plane and out-of-plane binding of CO2 and CH4 to model zigzag graphene nanoribbons edge-functionalized with COOH, OH, NH2, H2PO3, NO2, and CH3. Although different choices for the exchange-correlation functional lead to a spread of values for the binding energy, trends across the functional groups are largely preserved for each choice, as are the final orientations of the adsorbed gas molecules. We find binding of CO2 to exceed that of CH4 by roughly a factor of two. However, the two gases follow very similar trends with changes in the attached functional group, despite different molecular symmetries. Our results indicate that the presence of NH2, H2PO3, NO2, and COOH functional groups can significantly enhance gas binding, making the edges potentially viable binding sites in materials with high concentrations of edge carbons. To first order, in-plane binding strength correlates with the larger permanent and induced dipole moments on these groups. Implications for tailoring carbon structures for increased gas uptake and improved CO2/CH4 selectivity are discussed. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4736568]

Annihilation of vortex dipoles in an oblate Bose-Einstein condensate

We theoretically explore the annihilation of vortex dipoles, generated when an obstacle moves through an oblate Bose-Einstein condensate, and examine the energetics of the annihilation event. We show that the grey soliton, which results from the vortex dipole annihilation, is lower in energy than the vortex dipole. We also investigate the annihilation events numerically and observe that annihilation occurs only when the vortex dipole overtakes the obstacle and comes closer than the coherence length. Furthermore, we find that noise reduces the probability of annihilation events. This may explain the lack of annihilation events in experimental realizations.

Superbubble breakout and galactic winds from disc galaxies

We study the conditions for disc galaxies to produce superbubbles that can break out of the disc and produce a galactic wind. We argue that the threshold surface density of supernovae rate for seeding a wind depends on the ability of superbubble energetics to compensate for radiative cooling. We first adapt Kompaneets formalism for expanding bubbles in a stratified medium to the case of continuous energy injection and include the effects of radiative cooling in the shell. With the help of hydrodynamic simulations, we then study the evolution of superbubbles evolving in stratified discs with typical disc parameters. We identify two crucial energy injection rates that differ in their effects, the corresponding breakout ranging from being gentle to a vigorous one. (a) Superbubbles that break out of the disc with a Mach number of the order of 2-3 correspond to an energy injection rate of the order of 10(-4) erg cm(-2) s(-1), which is relevant for disc galaxies with synchrotron emitting gas in the extra-planar regions. (b) A larger energy injection threshold, of the order of 10(-3) erg cm(-2) s(-1), or equivalently, a star formation surface density of similar to 0.1 M-circle dot yr(-1) kpc(-2), corresponds to superbubbles with a Mach number similar to 5-10. While the milder superbubbles can be produced by large OB associations, the latter kind requires super-starclusters. These derived conditions compare well with observations of disc galaxies with winds and the existence of multiphase halo gas. Furthermore, we find that contrary to the general belief that superbubbles fragment through Rayleigh-Taylor (RT) instability when they reach a vertical height of the order of the scaleheight, the superbubbles are first affected by thermal instability for typical disc parameters and that RT instability takes over when the shells reach a distance of approximately twice the scaleheight.

PLIC: protein-ligand interaction clusters

Most of the biological processes are governed through specific protein-ligand interactions. Discerning different components that contribute toward a favorable protein-ligand interaction could contribute significantly toward better understanding protein function, rationalizing drug design and obtaining design principles for protein engineering. The Protein Data Bank (PDB) currently hosts the structure of similar to 68 000 protein-ligand complexes. Although several databases exist that classify proteins according to sequence and structure, a mere handful of them annotate and classify protein-ligand interactions and provide information on different attributes of molecular recognition. In this study, an exhaustive comparison of all the biologically relevant ligand-binding sites (84 846 sites) has been conducted using PocketMatch: a rapid, parallel, in-house algorithm. PocketMatch quantifies the similarity between binding sites based on structural descriptors and residue attributes. A similarity network was constructed using binding sites whose PocketMatch scores exceeded a high similarity threshold (0.80). The binding site similarity network was clustered into discrete sets of similar sites using the Markov clustering (MCL) algorithm. Furthermore, various computational tools have been used to study different attributes of interactions within the individual clusters. The attributes can be roughly divided into (i) binding site characteristics including pocket shape, nature of residues and interaction profiles with different kinds of atomic probes, (ii) atomic contacts consisting of various types of polar, hydrophobic and aromatic contacts along with binding site water molecules that could play crucial roles in protein-ligand interactions and (iii) binding energetics involved in interactions derived from scoring functions developed for docking. For each ligand-binding site in each protein in the PDB, site similarity information, clusters they belong to and description of site attributes are provided as a relational database-protein-ligand interaction clusters (PLIC).

Switching and Release Time Analysis of Electrostatically Actuated Capacitive RF MEMS Switches

This paper explains the reason behind pull-in time being more than pull-up time of many Radio Frequency Micro-Electro-Mechanical Systems (RF MEMS) switches at actuation voltages comparable to the pull-in voltage. Analytical expressions for pull-in and pull-up time are also presented. Experimental data as well as finite element simulations of electrostatically actuated beams used in RF-MEMS switches show that the pull-in time is generally more than the pull-up time. Pull-in time being more than pull-up time is somewhat counter-intuitive because there is a much larger electrostatic force during pull-in than the restoring mechanical force during the release. We investigated this issue analytically and numerically using a 1D model for various applied voltages and attribute this to energetics, the rate at which the forces change with time, and softening of the overall effective stiffness of the electromechanical system. 3D finite element analysis is also done to support the 1D model-based analyses.

Differential Cocrystallization Behavior of Isomeric Pyridine Carboxamides toward Antitubercular Drug Pyrazinoic Acid

Pyrazinoic acid, the active form of the antitubercular pro-drug Pyrazinamide, is an amphiprotic molecule containing carboxylic acid and pyridine groups and therefore can form both salts and cocrystals with relevant partner molecules. Cocrystallization of pyrazinoic acid with isomeric pyridine carboxamide series resulted in a dimorphic mixed-ionic complex with isonicotinamide and in eutectics with nicotinamide and picolinamide, respectively. It is observed that with alteration of the carboxamide position, steric and electrostatic compatibility issues between molecules of the combination emerge and affect intermolecular interactions and supramolecular growth, thus leading to either cocrystal or eutectic for different pyrazinoic acid-pyridine carboxamide combinations. Intermolecular interaction energy calculations have been performed to understand the role of underlying energetics on the formation of cocrystal/eutectic in different combinations. On the other hand, two molecular salts with piperazine and cytosine and a gallic acid cocrystal of the drug were obtained, and their X-ray crystal structures were also determined in this work.

Effect of ambient on the resistance fluctuations of graphene

In this letter, we present the results of systematic experimental investigations of the effect of different chemical environments on the low frequency resistance fluctuations of single layer graphene field effect transistors. The shape of the power spectral density of noise was found to be determined by the energetics of the adsorption-desorption of molecules from the graphene surface making it the dominant source of noise in these devices. We also demonstrate a method of quantitatively determining the adsorption energies of chemicals on graphene surface based on noise measurements. We find that the magnitude of noise is extremely sensitive to the nature and amount of the chemical species present. We propose that a chemical sensor based on the measurement of low frequency resistance fluctuations of single layer graphene field effect transistor devices will have extremely high sensitivity, very high specificity, high fidelity, and fast response times. (c) 2015 AIP Publishing LLC.

Understanding the Growth of Interfacial Reaction Product Layers between Dissimilar Materials

When one starts to analyze the evolution of the interfacial reaction product layers between dissimilar materials it is often found out that as the number of interacting species grows, the complexity of the analysis increases extremely rapidly. It may even appear that the task is just too difficult to be completed. In this article we present the thermodynamic-kinetic method, which can be used to rationalize the evolution of interfacial reaction layers and bring back the physics to the analyses. The method is conceptually very simple. It combines energetics-what can happen-with kinetics-how fast things take place. Yet the method is flexible enough that it can utilize quantitative and qualitative data starting from the atomistic simulations up to the experiments carried out with bulk materials. Several examples about how to utilize this method in material scientific problems are given.