Applications of molecular dynamics methods to low energy ion beams and film deposition processes

Abstract

Molecular dynamics methods are used to model the impingement of low energy ions onto crystalline targets, and the effects of these beams on thin film deposition. Simulations of the deposition of silicon films show that the structure of deposits can often be improved by the use of low energy ion beams instead of the conventional thermal beam. We examine the influence of beam energy on the formation of amorphous or crystalline deposits. The influence of ion beams on surface diffusion rates and the interdiffusion between atomic layers near the surface are also considered. Cluster deposition is treated, and the results suggest that cluster beams would be effective for depositing smooth films of materials that do not wet the substrate. We discuss the use of special purpose computers and signal processing boards to extend the time scales of molecular dynamics simulations. Rapid advances in computer hardware, algorithms, and the development of accurate interatomic potentials are dramatically increasing the power of these simulations.     

An experimental survey of a posteriori Courant finite element error control for the Poisson equation

This comparison of some a posteriori error estimators aims at empirical evidence for a ranking of their performance for a Poisson model problem with conforming lowest order finite element discretizations. Modified residual-based error estimates compete with averaging techniques and two estimators based on local problem solving. Multiplicative constants are involved to achieve guaranteed upper and lower energy error bounds up to higher order terms. The optimal strategy combines various estimators.     

A novel methodological approach for δ18O analysis of sugars using gas chromatography-pyrolysis-isotope ratio mass spectrometry

Although the instrumental coupling of gas chromatography-pyrolysis-isotope ratio mass spectrometry (GC-Py-IRMS) for compound-specific δ¹⁸O analysis has been commercially available for more than a decade, this method has been hardly applied so far. Here we present the first GC-Py-IRMS δ¹⁸O results for trimethylsilyl-derivatives of plant sap-relevant sugars and a polyalcohol (glucose, fructose, sucrose, raffinose and pinitol). Particularly, we focus on sucrose, which is assimilated in leaves and which is the most important transport sugar in plants and hence of utmost relevance in plant physiology and paleoclimate studies. Replication measurements of sucrose standards and concentration series indicate that the GC-Py-IRMS δ¹⁸O measurements are not stable over time and that they are amount (area) dependent. We, therefore, suggest running sample batch replication measurements in alternation with standard concentration series of reference material. This allows for carrying out (i) a drift correction, (ii) a calibration against reference material and (iii) an amount (area) correction. Tests with ¹⁸O-enriched water do not provide any evidence for oxygen isotope exchange reactions affecting sucrose and raffinose. We present the first application of GC-Py-IRMS δ¹⁸O analysis for sucrose from needle extract (soluble carbohydrate) samples. The obtained δ¹⁸O_{sucrose/ Vienna Standard Mean Ocean Water (VSMOW)} values are more positive and vary in a wider range (32.1–40.1 ‰) than the δ¹⁸O_{bulk/ VSMOW} values (24.6–27.2 ‰). Furthermore, they are shown to depend on the climate parameters maximum day temperature, relative air humidity and cloud cover. These findings suggest that δ¹⁸O_sucrose of the investigated needles very sensitively reflects the climatically controlled evaporative ¹⁸O enrichment of leaf water and thus highlights the great potential of GC-Py-IRMS δ¹⁸O_sucrose analysis for plant physiology and paleoclimate studies.     

The raspberry model for protein-like particles: Ellipsoids and confinement in cylindrical pores

The study of protein mass transport via atomistic simulation requires time and length scales beyond the computational capabilities of modern computer systems. The raspberry model for colloidal particles in combination with the mesoscopic hydrodynamic method of lattice Boltzmann facilitates coarse-grained simulations that are on the order of microseconds and hundreds of nanometers for the study of diffusive transport of protein-like colloid particles. The raspberry model reproduces linearity in resistance to motion versus particle size and correct enhanced drag within cylindrical pores at off-center coordinates for spherical particles. Owing to the high aspect ratio of many proteins, ellipsoidal raspberry colloid particles were constructed and reproduced the geometric resistance factors of Perrin and of Happel and Brenner in the laboratory-frame and in the moving body-frame. Accurate body-frame rotations during diffusive motion have been captured for the first time using projections of displacements. The spatial discretization of the fluid leads to a renormalization of the hydrodynamic radius, however, the data describes a self-consistent hydrodynamic frame within this renormalized system.     

Phase transitions of nonlinear waves in quadratic waveguide arrays

We study two-color parametric nonlinear modes in waveguide arrays with a quadratic nonlinear response. We predict theoretically and observe experimentally a new type of phase transition manifested in an abrupt power-controlled change of the mode structure from unstaggered to staggered, due to the interplay of localization and synchronization in parametrically driven discrete systems.     

Structure and dynamics of alpha-lactalbumin adsorbed at a charged brush interface

We have studied the adsorption of alpha-lactalbumin at a planar poly(acrylic acid) (PAA) brush using neutron reflectometry (NR) and total internal reflection fluorescence (TIRF) spectroscopy. The PAA brush has been prepared by spin-coating silicon or quartz plates with a hydrophobic poly(styrene) film and by transferring the copolymer poly(styrene)-poly(acrylic acid) onto the modified surface. In the case of NR, the poly(styrene) film and the poly(styrene) chain ends of the copolymer were perdeuterated in order to generate a high contrast to the non-deuterated PAA brush. alpha-Lactalbumin was chosen as the model protein because it is a relatively small globular protein with a negative net charge at neutral pH-values, as chosen in the experiments. Thus, it is interacting with the PAA brush on the 'wrong' side of its isoelectric point. In addition, the effects of temperature on the volume fraction profile and the reorientational mobility of the protein within the PAA brush were determined. From the analysis of the NR data, it has been found that despite of its negative net charge, alpha-lactalbumin is penetrating into the PAA brush. Its volume fraction profile parallels that of the PAA brush, indicating an exclusive interaction between the protein and the PAA. No protein accumulation is found at the inner poly(styrene) or the outer solution interface of the PAA brush. When increasing the temperature from 20 to 40 degrees C, less protein is adsorbed, suggesting the presence of enthalpic interaction contributions. From the analysis of the TIRF data, a high degree of reorientational mobility of alpha-lactalbumin within a PAA brush can be inferred. The reorientational correlation time of alpha-lactalbumin labeled with the Alexa Fluor 488 dye was found to increase from 5.5 to 32 ns upon adsorption, which can well be explained by the higher viscosity inside the PAA brush. Overall, the results of this study quantify for the first time the molecular details of the unique interaction of a protein on the 'wrong' side of its isoelectric point with a planar charged brush interface. It is concluded that the high mobility of alpha-lactalbumin within a PAA brush can partially be understood by the presence of repulsive electrostatic interactions. There is no 'freezing' of the protein dynamics, which is a precondition for biological activity.     

New designer drugs N-(1-phenylcyclohexyl)-2-ethoxyethanamine (PCEEA) and N-(1-phenylcyclohexyl)-2-methoxyethanamine (PCMEA): Studies on their metabolism and toxicological detection in rat urine using gas chromatographic/mass spectrometric techniques

Studies are described on the metabolism and the toxicological detection of the phencyclidine-derived designer drugs N-(1-phenylcyclohexyl)-2-ethoxyethanamine (PCEEA) and N-(1-phenylcyclohexyl)-2-methoxyethanamine (PCMEA) in rat urine using gas chromatographic/mass spectrometric (GC/MS) techniques. The identified metabolites indicated that PCEEA and PCMEA were transformed to the same metabolites by N-dealkylation and O-dealkylation partially followed by oxidation of the resulting alcohol to the respective carboxylic acid and hydroxylation of the cyclohexyl ring at different positions and combinations of those. Finally, aromatic hydroxylation of the O-dealkylated metabolites was partially followed by hydroxylation of the cyclohexyl ring at different positions. All metabolites were partially excreted in conjugated form. The authors' systematic toxicological analysis (STA) procedure using full-scan GC/MS after acid hydrolysis, liquid-liquid extraction and microwave-assisted acetylation allowed the detection of an intake of a common drug users' dose both of PCEEA and PCMEA in rat urine. Assuming similar metabolism in humans, the STA should be suitable for proof of an intake of PCEEA and PCMEA in human urine, although their differentiation is not possible due to common metabolites.