Alkaline erosion of CR 39 polymer surfaces

We have investigated the mechanism of erosion of CR 39 polymer in alkaline environments. We observed the kinetics of absorption of water and methanol into both unirradiated and γ-irradiated samples. We use a capillary model to interpret our results.We etched our samples in both KOH solutions, and KOH solutions doped with methanol. Etch rate was desensitizing to γ-irradiation when KOH concentration approached saturation, but KOH solutions doped with methanol were not desensitizing, unlike with nuclear tracks. We account for this difference.     

High-sensitivity detection using isotachophoresis with variable cross-section geometry

We present a theoretical and experimental study on increasing the sensitivity of ITP assays by varying channel cross-section. We present a simple, unsteady, diffusion-free model for plateau mode ITP in channels with axially varying cross-section. Our model takes into account detailed chemical equilibrium calculations and handles arbitrary variations in channel cross-section. We have validated our model with numerical simulations of a more comprehensive model of ITP. We show that using strongly convergent channels can lead to a large increase in sensitivity and simultaneous reduction in assay time, compared to uniform cross-section channels. We have validated our theoretical predictions with detailed experiments by varying channel geometry and analyte concentrations. We show the effectiveness of using strongly convergent channels by demonstrating indirect fluorescence detection with a sensitivity of 100 nM. We also present simple analytical relations for dependence of zone length and assay time on geometric parameters of strongly convergent channels. Our theoretical analysis and experimental validations provide useful guidelines on optimizing chip geometry for maximum sensitivity under constraints of required assay time, chip area and power supply.     

CH-stretching overtone spectroscopy of 1,1,1,2-tetrafluoroethane

We have recorded the vibrational absorption spectrum of 1,1,1,2-tetrafluoroethane (HFC-134a) in the fundamental and first five CH-stretching overtone regions with the use of Fourier transform infrared, dispersive long-path, intracavity laser photoacoustic, and cavity ringdown spectroscopies. We compare our measured total oscillator strengths in each region with intensities calculated using an anharmonic oscillator local mode model. We calculate intensities with 1D, 2D, and 3D Hamiltonians, including one or two CH stretches and two CH stretches with the HCH bending mode, respectively. The dipole moment function is calculated ab initio with self-consistent-field Hartree-Fock and density functional theories combined with double- and triple-zeta-quality basis sets. We find that the basis set choice affects the total intensity more than the choice of the Hamiltonian. We achieve agreement between the calculated and measured total intensities of approximately a factor of 2 or better for the fundamental and first five overtones.     

Power-law intermittency of single emitters

We summarize experimental observations of fluorescence intermittency of single semiconductor nanocrystals and single molecules. We review the main models proposed earlier to explain the broad power-law distributions of on- and off-blinking times. We argue that a self-trapping model with a distribution of trapping distances can account for most, if not all, observations to date. We propose possible scenarios for photo-ionization, the switching to states with long on-times and the influence of disorder and surfaces on the trapping dynamics.     

Electrical transport properties of semiconducting lithium molybdate glass nanocomposites

We have reported the formation of lithium molybdate glass nanocomposites embedded with lithium molybdate nanophases from the x-ray diffraction and transmission electron microscopic studies. We have investigated the dc electrical conductivity in a wide temperature range for these glass nanocomposites, which exhibit semiconducting behavior. We have analyzed the dc electrical data in the light of polaronic conduction models of Mott and Schnakenberg. We have also studied ac electrical conductivity of these glass nanocomposites in wide temperature and frequency ranges. The experimental ac results have been analyzed with reference to various theoretical models based on quantum-mechanical tunneling and hopping over the barrier. We have observed that the temperature dependence of the dc conductivity is consistent with the polaronic hopping models, while the temperature and frequency dependence of the ac conductivity is consistent with the polaronic tunneling models.     

DFT Calculations of Vibrational Frequencies of Carbon–Nitrogen Clusters: Raman Spectra of Carbon Nitrides

We have performed the calculation of structures of clusters containing carbon and nitrogen atoms. We determine the bond lengths in each case. We also calculate the vibrational frequencies of all of the clusters. We compare the calculated values of the vibrational frequencies with those measured by the Raman spectra of amorphous carbon nitrides. Some of the calculated frequencies are in agreement with those measured. We identity that linear structures and hence “back bones” are present in the glassy state.     

Electrostatics of DNA complexes with cationic lipid membranes

We present the exact solutions of the linear Poisson-Boltzmann equation for several problems relevant to electrostatics of DNA complexes with cationic lipids. We calculate the electrostatic potential and electrostatic energy for lamellar and inverted hexagonal phases, concentrating on the effects of dielectric boundaries. We compare our results for the complex energy with the known results of numerical solution of the nonlinear Poisson-Boltzmann equation. Using the solution for the lamellar phase, we calculate the compressibility modulus and compare our findings with the experimental data available. Also, we treat charge-charge interactions across, along, and between two low-dielectric membranes. We obtain an estimate for the strength of electrostatic interactions of one-dimensional DNA smectic layers across the lipid membrane. We discuss in the end some aspects of two-dimensional DNA condensation and DNA-DNA attraction in the DNA-lipid lamellar phase in the presence of di- and trivalent cations. We analyze the equilibrium DNA-DNA separations in lamellar complexes using the recently developed theory of electrostatic interactions of DNA helical charge motifs.     

Limit cycles in the presence of convection: a first-order analysis

We consider a diffusion model with limit cycle reaction functions. In an unbounded domain, diffusion spreads pattern outwards from the source. Convection adds instability to the reaction–diffusion system. We see the result of the instability in a readiness to create pattern. In the case of strong convection, we consider that the first-order approximation may be valid for some aspects of the solution behaviour. We employ the method of Riemann invariants and rescaling to transform the reduced system into one invariant under parameter change. We carry out numerical experiments to test our analysis. We find that most aspects of the solution do not comply with this, but we find one significant characteristic which is approximately first order. We consider the correspondence of the Partial Differential Equation with the Ordinary Differential Equation along rays from the initiation point in the transformed system. This yields an understanding of the behaviour.     

Active colloids on fluid interfaces

We review recent work on active colloids at interfaces, including self-propelled colloids that move by generating a propulsive force, and driven colloids that move under external fields. Features unique to fluid interfaces alter the flows generated at interfaces by active colloid motion, and hydrodynamic interactions with these layers. We emphasize recent observations of natural swimmers, like bacteria, and bio-mimetic colloids including self-propelled phoretic and Marangoni swimmers, and magnetically driven colloids. We discuss active colloid interaction with boundaries and with each other. We conclude with a discussion of open issues and opportunities to design active colloids as active surface agents that manipulate interfacial properties and the transport in the vicinity of interfaces.     

Random activation energy model and disordered kinetics, from static to dynamic disorder

We suggest a unified path integral approach for random rate processes with random energy barriers, which includes systems with static and dynamic disorder as particular cases. We assume that the random component of the activation energy barrier can be described by a generalized Zubarev-McLennan nonequilibrum statistical ensemble that can be derived from the maximum information entropy approach by assuming that the time history of the fluctuations of the random components of the energy barrier are known. We show that the average survival function, which is an experimental observable in disorderd kinetics, can be computed exactly in terms of the characteristic functional of this generalized Zubarev-McLennan nonequilibrium statistical ensemble. We investigate different types of disorder described by our approach, ranging from static disorder with infinite memory to random processes with long or short memory, and finally to rapidly fluctuating independent random processes with no memory. We derive expressions of the average survival function for all these types of disorder and discuss their implications in the evaluation of kinetic parameters from experimental data. We illustrate our approach by studying a simple model of dynamic disorder of the renewal type. Finally we discuss briefly the implications of our approach in molecular biology and genetics.     

Elastic and inelastic low-energy electron collisions with pyrazine

We present results of ab-initio scattering calculations for electron collisions with pyrazine using the R-matrix method, carried out at various levels of approximation. We confirm the existing experimental and theoretical understanding of the three well-known π? shape resonances. In addition, we find numerous core-excited resonances (above 4.8 eV) and identify their most likely parent states. We also present differential cross sections, showing high sensitivity to the scattering model chosen at low energies. We make recommendations regarding the selection of models for scattering calculations with this type of targets.     

Kinetic investigation of small systems using different algorithms

We have investigated different algorithms for the simulation of kinetics of small systems. We have simulated the first order reversible reaction with the Gillespie, Gibson and Bruck time simulation as a function of Poisson distribution and compared the results of three algorithms. We have also simulated intracellular viral kinetics for a genome with Gillespie and Poisson distribution algorithms.     

Temperature accelerated Monte Carlo (TAMC): a method for sampling the free energy surface of non-analytical collective variables

We introduce a new method to simulate the physics of rare events. The method, an extension of the Temperature Accelerated Molecular Dynamics, comes in use when the collective variables introduced to characterize the rare events are either non-analytical or so complex that computing their derivative is not practical. We illustrate the functioning of the method by studying the homogeneous crystallization in a sample of Lennard-Jones particles. The process is studied by introducing a new collective variable that we call Effective Nucleus Size N. We have computed the free energy barriers and the size of critical nucleus, which result in agreement with data available in the literature. We have also performed simulations in the liquid domain of the phase diagram. We found a free energy curve monotonically growing with the nucleus size, consistent with the liquid domain.     

Synthesis of N-Pyridylmethylidene-2-aminopyridines and their Methyl-substituted Derivatives in the Presence of Molecular Sieves

We have studied condensation of 2-, 3-, 4-pyridinealdehydes and 6-methylpyridine-2-aldehyde with 2-aminopyridine and its 3-, 4-, and 6-methyl derivatives in benzene in the presence of molecular sieves. The reactions occur even at room temperature to form the corresponding pyridyl-pyridyl azomethines, and also aminals. We have determined the optimal conditions for carrying out the processes with the aim of obtaining both types of products. We consider the characteristics of the mass spectra for the synthesized aldimines. We present the X-ray diffraction results for the two aminals.     

Comparing the density of states of binary Lennard-Jones glasses in bulk and film

We used Wang-Landau density of states Monte Carlo to study a binary Lennard-Jones glass-forming mixture in bulk and films between noninteracting walls. Thermodynamic properties are calculated using two different ensembles and film data are compared with the bulk. Bulk properties are in good agreement with previous simulations. We confirm the formation of a glass using various properties, e.g., energy, heat capacity, and pressure with temperature. We find a change in slope in the energy per particle and pressure as a function of temperature. We do not find any defined crystal structure. A higher glass transition temperature is found for the film.     

First-principle molecular dynamics with ultrasoft pseudopotentials: parallel implementation and application to extended bioinorganic systems

We present a plane-wave ultrasoft pseudopotential implementation of first-principle molecular dynamics, which is well suited to model large molecular systems containing transition metal centers. We describe an efficient strategy for parallelization that includes special features to deal with the augmented charge in the contest of Vanderbilt's ultrasoft pseudopotentials. We also discuss a simple approach to model molecular systems with a net charge and/or large dipole/quadrupole moments. We present test applications to manganese and iron porphyrins representative of a large class of biologically relevant metalorganic systems. Our results show that accurate density-functional theory calculations on systems with several hundred atoms are feasible with access to moderate computational resources.     

Fluctuation-induced interactions between dielectrics in general geometries

We study thermal Casimir and quantum nonretarded Lifshitz interactions between dielectrics in general geometries. We map the calculation of the classical partition function onto a determinant, which we discretize and evaluate with the help of Cholesky factorization. The quantum partition function is treated by path integral quantization of a set of interacting dipoles and reduces to a product of determinants. We compare the approximations of pairwise additivity and proximity force with our numerical methods. We propose a "factorization approximation" that gives rather good numerical results in the geometries that we study.     

Electronic stress tensor analysis of molecules in gas phase of CVD process for gesbte alloy

We analyze the electronic structure of molecules which may exist in gas phase of chemical vapor deposition process for GeSbTe alloy using the electronic stress tensor, with special focus on the chemical bonds between Ge, Sb, and Te atoms. We find that, from the viewpoint of the electronic stress tensor, they have intermediate properties between alkali metals and hydrocarbon molecules. We also study the correlation between the bond order which is defined based on the electronic stress tensor, and energy‐related quantities. We find that the correlation with the bond dissociation energy is not so strong while one with the force constant is very strong. We interpret these results in terms of the energy density on the “Lagrange surface,” which is considered to define the boundary surface of atoms in a molecule in the framework of the electronic stress tensor analysis. © 2015 Wiley Periodicals, Inc.     

Solid-Phase Transformations in Tetraamine and Hexaamine Mixed-Ligand Complexes of Chromium(III) with Cyclic Tetraamines

We have studied solid-phase transformations in mixed-ligand complexes of chromium(III) with cyclic tetraamines. We have established that tetraamine complexes of chromium(III) with 14-membered tetraaza macrocyclic ligands are relatively thermally stable, and do not undergo isomerization in the solid state. We have observed that solid-phase reactions of ammonia substitution in hexaamine complexes with outer-sphere iodide and boron hydride anions may be accompanied by dehydrogenation processes.     

The effect of salt stoichiometry on protein-salt interactions determined by ternary diffusion in aqueous solutions

We report the four diffusion coefficients for the lysozyme-MgCl2-water ternary system at 25 degrees C and pH 4.5. The comparison with previous results for the lysozyme-NaCl-water ternary system is used to examine the effect of salt stoichiometry on the transport properties of lysozyme-salt aqueous mixtures. We find that the two cross-diffusion coefficients are very sensitive to salt stoichiometry. One of the cross-diffusion coefficients is examined in terms of common-ion, excluded-volume, and protein-preferential hydration effects. We use the four ternary diffusion coefficients to extract chemical-potential cross-derivatives and protein-preferential interaction coefficients. These thermodynamic data characterize the protein-salt thermodynamic interactions. We demonstrate the presence of the common-ion effect (Donnan effect) by analyzing the dependence of the preferential-interaction coefficient not only with respect to salt concentration but also with respect to salt stoichiometry. We conclude that the common-ion effect and the protein-preferential hydration are both important for describing the lysozyme-MgCl2 thermodynamic interaction.