Correlation of chromatographic performance with morphological features of organic polymer monoliths.

Monoliths are considered to be a low pressure alternative to particle packed columns for liquid chromatography (LC). However, the chromatographic performance of organic monoliths, in particular, has still not reached the level of particle packed columns. Since chromatographic performance can be attributed to morphological features of the monoliths, in-situ characterization of the monolith structure in three dimensions would provide valuable information that could be used to help improve performance. In this work, serial sectioning and imaging were performed with a dual-beam scanning electron microscope for reconstruction and quantitative characterization of poly(ethylene glycol) diacrylate (PEGDA) monoliths inside a capillary column. Chord lengths, homogeneity factors, porosities and tortuosities were calculated from three-dimensional (3D) reconstructions of two PEGDA monoliths. Chromatographic efficiency was better for the monolith with smaller mean chord length (i.e., 5.23µm), porosity (i.e., 0.49) and tortuosity (i.e., 1.50) compared to values of 5.90µm, 0.59 and 2.34, respectively, for the other monolithic column. Computational prediction of tortuosity (2.32) was found to be in agreement with the experimentally measured value (2.34) for the same column. The monoliths were found to have significant radial heterogeneity since the homogeneity factor decreased from 5.39 to 4.89 (from center to edge) along the column radius.

A polarizable reactive force field for water to enable molecular dynamics simulations of proton transport.

A new polarizable water model is developed for molecular dynamics (MD) simulations of the proton transport process. The interatomic potential model has three important submodels corresponding to electrostatic interactions, making and breaking of covalent bonds, and treatment of electron exchange and correlation through a van der Waals potential. A polarizable diffuse charge density function was used to describe Coulombic interactions between atoms. Most of the model parameters were obtained from ab initio data for a lone water molecule. Molecules respond realistically to their electrochemical environment by the use of coupled fluctuating charge and fluctuating dipole dynamics, which controlled the charge density. The main purpose of the work is to develop a general model and framework for future studies, though some validation work was performed here. We applied the model to a MD simulation study of bulk properties of liquid water at room temperature and model gave good agreement with thermodynamic and transport properties at the same conditions. The model was then applied to a preliminary study of proton transfer, in which multiple proton transfer events were observed, though the rate of proton transfer was under-predicted by a factor of 5.

Chemical potential perturbation: extension of the method to lattice sum treatment of intermolecular potentials.

The recently developed chemical potential perturbation (CPP) method [S. G. Moore and D. R. Wheeler, J. Chem. Phys. 134, 114514 (2011)] is extended to the lattice (Ewald) sum treatment of intermolecular potentials. The CPP method predicts chemical potentials for a range of composition points using the local (position-dependent) pressure tensor of an inhomogeneous system. When computing the local pressure tensor, one can use the Irving-Kirkwood (IK) or Harasima (H) contours of distributing the pressure. We compare these two contours and show that for a planar interface, the homogeneous pressure and resulting chemical potential can be approximated with the CPP method using either the IK or the H contour, though with the lattice sum method the H contour has much greater computational efficiency. The proposed methods are validated by calculating the chemical potentials of the Lennard-Jones fluid and extended simple point-charge (SPC/E) water, and results show a high level of agreement with respective equations of state.

Intrinsic autotrophic biomass yield and productivity in algae: modeling spectral and mixing-rate dependence.

For non-inhibitory irradiances, the rate of algal biomass synthesis was modeled as the product of the algal autotrophic yield Φ(DW) and the flux of photons absorbed by the culture, as described using Beer-Lambert law. As a contrast to earlier attempts, the use of scatter-corrected extinction coefficients enabled the validation of such approach, which bypasses determination of photosynthesis-irradiance (PI) kinetic parameters. The broad misconception that PI curves, or the equivalent use of specific growth rate expressions independent of the biomass concentration, can be extended to adequately model biomass production under light-limitation is addressed. For inhibitory irradiances, a proposed mechanistic model, based on the photosynthetic units (PSU) concept, allows one to estimate a target speed νT across the photic zone in order to limit the flux of photons per cell to levels averting significant reductions in Φ(DW) . These modeled target speeds, on the order of 5-20 m s(-1) for high outdoor irradiances, call for fundamental changes in reactor design to optimize biomass productivity. The presented analysis enables a straightforward bioreactor parameterization, which, in-turn, guides the establishment of conditions ensuring maximum productivity and complete nutrients consumption. Additionally, solar and fluorescent lighting spectra were used to calculate energy to photon-counts conversion factors.

Chemical potential perturbation: a method to predict chemical potentials in periodic molecular simulations.

A new method, called chemical potential perturbation (CPP), has been developed to predict the chemical potential as a function of density in periodic molecular simulations. The CPP method applies a spatially varying external force field to the simulation, causing the density to depend upon position in the simulation cell. Following equilibration the homogeneous (uniform or bulk) chemical potential as a function of density can be determined relative to some reference state after correcting for the effects of the inhomogeneity of the system. We compare three different methods of approximating this correction. The first method uses the van der Waals density gradient theory to approximate the inhomogeneous Helmholtz free energy density. The second method uses the local pressure tensor to approximate the homogeneous pressure. The third method uses the Triezenberg-Zwanzig definition of surface tension to approximate the inhomogeneous free energy density. If desired, the homogeneous pressure and Helmholtz free energy can also be predicted by the new method, as well as binodal and spinodal densities of a two-phase fluid region. The CPP method is tested using a Lennard-Jones (LJ) fluid at vapor, liquid, two-phase, and supercritical conditions. Satisfactory agreement is found between the CPP method and an LJ equation of state. The efficiency of the CPP method is compared to that for Widom's method under the tested conditions. In particular, the new method works well for dense fluids where Widom's method starts to fail.

Improved implementation of Kirkwood-Buff solution theory in periodic molecular simulations.

Kirkwood-Buff (KB) solution theory is a means to obtain certain thermodynamic derivatives from knowledge of molecular distributions. In actual practice the required integrals over radial distribution functions suffer inaccuracies due to finite-distance truncation effects and their use in closed systems. In this work we discuss how best to minimize these inaccuracies under traditional KB theory. In addition we implement a method for calculating KB quantities in molecular simulations with periodic boundary conditions and particularly within the canonical ensemble. The method is based on a finite-Fourier-series expansion of molecular concentration fluctuations and leads to more reliable results for a given computational effort. The procedure is validated and compared to the original method for a nonideal liquid mixture of Lennard-Jones particles intended to imitate a real system, carbon tetrafluoride, and methane.

MPSA effects on copper electrodeposition investigated by molecular dynamics simulations.

In superconformal filling of copper-chip interconnects, organic additives are used to fill high-aspect-ratio trenches or vias from the bottom up. In this study we report on the development of intermolecular potentials and use molecular dynamics simulations to provide insight into the molecular function of an organic additive (3-mercaptopropanesulfonic acid or MPSA) important in superconformal electrodeposition. We also investigate how the presence of sodium chloride affects the surface adsorption and surface action of MPSA as well as the charge distribution in the system. We find that NaCl addition decreases the adsorption strength of MPSA at a simulated copper surface and attenuates the copper-ion association with MPSA. The model also was used to simulate induced-charge effects and adsorption on a nonplanar electrode surface.

DNA-templated three-branched nanostructures for nanoelectronic devices.

Three-branched DNA molecules have been designed and assembled from oligonucleotide components. These nucleic acid constructs contain double- and single-stranded regions that control the hybridization behavior of the assembly. Specific localization of a single streptavidin molecule at the center of the DNA complex has been investigated as a model system for the directed placement of nanostructures. Highly selective silver and copper metallization of the DNA template has also been characterized. Specific hybridization of these DNA complexes to oligonucleotide-coupled nanostructures followed by metallization should provide a bottom-up self-assembly route for the fabrication and characterization of discrete three-terminal nanodevices.