Gas-Phase Chemistry of Pulsed <Emphasis Type="Italic">n</Emphasis>-Hexane Discharge

Many types of carbon films are being investigated for use in many different applications for their electrical, mechanical, and optical properties. Organic based plasmas are beginning to be used for the production of a wide variety of novel film stacks. The use of these stacks can range from sensor to dielectrics for flexible electronics to biocompatible surfaces. Knowledge of how these films actually grow is largely unknown. In light of this, we have performed Fourier transform infrared (FTIR) spectroscopy to the study of hexane plasmas. We use this diagnostic to identify different plasma-produced daughter species produced from n-hexane. For example, we observe the creation of methane, ethylene, and acetylene. From this we develop a likely dissociation model for the parent gas.     

Examination of the Effect of the Annealing Cation on Higher Order Structures Containing Guanine or Isoguanine Repeats

Isoguanine (2‐oxo‐6‐amino‐guanine), a natural but non‐standard base, exhibits unique self‐association properties compared to its isomer, guanine, and results in formation of different higher order DNA structures. In this work, the higher order structures formed by oligonucleotides containing guanine repeats or isoguanine repeats after annealing in solutions containing various cations are evaluated by electrospray ionization mass spectrometry (ESI‐MS) and circular dichroism (CD) spectroscopy. The guanine‐containing strand (G9) consistently formed quadruplexes upon annealing, whereas the isoguanine strand (Ig9) formed both pentaplexes and quadruplexes depending on the annealing cation. Quadruplex formation with G9 showed some dependence on the identity of the cation present during annealing with high relative quadruplex formation detected with six of ten cations. Analogous annealing experiments with Ig9 resulted in complex formation with all ten cations, and the majority of the resulting complexes were pentaplexes. CD results indicated most of the original complexes survived the desalting process necessary for ESI‐MS analysis. In addition, several complexes, especially the pentaplexes, were found to be capable of cation exchange with ammonium ions. Ab initio calculations were conducted for isoguanine tetrads and pentads coordinated with all ten cations to predict the most energetically stable structures of the complexes in the gas phase. The observed preference of forming quadruplexes versus pentaplexes as a function of the coordinated cation can be interpreted by the calculated reaction energies of both the tetrads and pentads in combination with the distortion energies of tetrads.     

Dynamically polarized target for the g 2 p and G E p experiments at Jefferson Lab

Recently, two experiments were concluded in Hall A at Jefferson Lab which utilized a newly assembled, solid, polarized hydrogen target. The primary components of the target are a new, high cooling power ⁴He evaporation refrigerator, and a re-purposed, superconducting split-coil magnet. It has been used to polarize protons in irradiated NH₃ at a temperature of 1 K and at fields of 2.5 and 5.0 tesla. Maximum polarizations of 55% and 95% were obtained at those fields, respectively. To satisfy the requirements of both experiments, the magnet had to be routinely rotated between angles of 0°, 6°, and 90° with respect to the incident electron beam.     

A biphasic transverse isotropic FEM model for cartilage

Articular cartilage is a viscoelastic, two-phase and fiber-strengthen tissue; it consists of a solid and a fluid phase. We describe this tissue using the Theory of Porous Media (TPM). Some simulation results are shown. (© 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Viability of Human Mesenchymal Stem Cells Seeded on Crosslinked Entropy‐Elastic Gelatin‐Based Hydrogels

Biomimetic polymer network systems with tailorable properties based on biopolymers represent a class of degradable hydrogels that provides sequences for protein adsorption and cell adhesion. Such materials show potential for in vitro MSC proliferation as well as in vivo applications and were obtained by crosslinking different concentrations of gelatin using varying amounts of ethyl lysine diisocyanate in the presence of a surfactant in pH 7.4 PBS solution. Material extracts, which were tested for cytotoxic effects using L929 mouse fibroblasts, were non‐toxic. The hydrogels were seeded with human bone marrow‐derived MSCs and supported viable MSCs for the incubation time of 9 d. Preadsorption of fibronectin on materials improved this biofunctionality.

     

Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations

Molecular dynamics (MD) is one of the most common tools in computational chemistry. Recently, our group has employed accelerated molecular dynamics (aMD) to improve the conformational sampling over conventional molecular dynamics techniques. In the original aMD implementation, sampling is greatly improved by raising energy wells below a predefined energy level. Recently, our group presented an alternative aMD implementation where simulations are accelerated by lowering energy barriers of the potential energy surface. When coupled with thermodynamic integration simulations, this implementation showed very promising results. However, when applied to large systems, such as proteins, the simulation tends to be biased to high energy regions of the potential landscape. The reason for this behavior lies in the boost equation used since the highest energy barriers are dramatically more affected than the lower ones. To address this issue, in this work, we present a new boost equation that prevents oversampling of unfavorable high energy conformational states. The new boost potential provides not only better recovery of statistics throughout the simulation but also enhanced sampling of statistically relevant regions in explicit solvent MD simulations.     

Photocrosslinked co-networks from glycidylmethacrylated gelatin and poly(ethylene glycol) methacrylates

Biopolymer-based systems with adjustable macroscopic properties that can be varied in a wide range using only small changes in chemical composition are promising candidates for biomaterial-induced autoregeneration. Glycidylmethacrylated gelatin is photopolymerized with the addition of PEG mono- or dimethacrylate to form co-networks in pH = 7.4 PBS. The degree of swelling (Q) and water uptake (H) in PBS at 37 °C are tailorable for PEGDMA co-networks (Q ≈ 250-650 vol%), while the storage modulus of swollen networks at 3 °C can be adjusted by the PEG(D)MA content (G' = 0.7-145 kPa). Indirect cytotoxicity tests on ethylene oxide sterilized films show non-toxic responses for the homonetwork and all but one PEGDMA-containing co-networks materials.