Cloud computing in nanoHUB powering education and research

The lack of easy access to powerful simulations and lack of a workforce trained on computer simulations of materials are important factors limiting the adoption of ICME in industry. NSF’s nanoHUB.org is a web-portal that enables users to perform online simulations using simply a web browser. With over 300 simulation tools freely available and high-quality online training and educational material, nanoHUB.org can play an important role making simulation tools widely accessible and training a new generation of engineers familiar with ICME tools. In this presentation, we describe PolymerModeler, a nanoHUB.org tool that offers a free platform for research and education in atomistic polymer simulations. The tool allows users to construct and visualize atomistic models of thermoplastic polymers. The mechanical properties of the resulting systems may be studied using LAMMPS, within the PolymerModeler tool. LAMMPS simulations run on NSF-funded HPC resources, and the results display in the web browser. Users do not need to download or install any software. A first time user guide introduces the tool and common usage scenarios. The polymer builder section of the tool constructs chains by adding successive monomers. Several prebuilt monomers are available, and users can upload any repeated unit, in PDB or XYZ format, making it a very general amorphous builder

A Biochemical Dissection of the RNA Interference Pathway in \u3cem\u3eDrosophila melanogaster\u3c/em\u3e: A Dissertation

In diverse eukaryotic organisms, double-stranded RNA (dsRNA) induces robust silencing of cellular RNA cognate to either strand of the input dsRNA; a phenomenon now known as RNA interference (RNAi). Within the RNAi pathway, small, 21 nucleotide (nt) duplexed RNA, dubbed small interfering RNAs (siRNAs), derived from the longer input dsRNA, guide the RNA induced silencing complex (RISC) to destroy its target RNA. Due to its ability to silence virtually any gene, whether endogenous or exogenous, in a variety of model organisms and systems, RNAi has become a valuable laboratory tool, and is even being heralded as a potential therapy for an array of human diseases. In order to understand this complex and unique pathway, we have undertaken the biochemical characterization of RNAi in the model insect, Drosophila melanogaster. To begin, we investigated the role of ATP in the RNAi pathway. Our data reveal several ATP-dependent steps and suggest that the RNAi reaction comprises as least five sequential stages: ATP-dependent processing of double-stranded RNA into siRNAs, ATP-independent incorporation of siRNAs into an inactive ~360 kDa protein/RNA complex, ATP-dependent unwinding of the siRNA duplex to generate an active complex, ATP-dependent activation of RISC following siRNA unwinding, and ATP-independent recognition and cleavage of the RNA target. In addition, ATP is used to maintain 5´ phosphates on siRNAs, and only siRNAs with these characteristic 5´ phosphates gain entry into the RNAi pathway. Next, we determined that RISC programmed exogenously with an siRNA, like that programmed endogenously with microRNAs (miRNAs), is an enzyme. However, while RISC behaves like a classical Michaelis-Menten enzyme in the presence of ATP, without ATP, multiple rounds of catalysis are limited by release of RISC-produced cleavage products. Kinetic analysis of RISC suggests that different regions of the siRNA play distinct roles in the cycle of target recognition, cleavage and product release. Bases near the siRNA 5´ end disproportionately contribute to target RNA-binding energy, whereas base pairs formed by the central and 3´ region of the siRNA provide helical geometry required for catalysis. Lastly, the position of the scissile phosphate is determined during RISC assembly, before the siRNA encounters its RNA target. In the course of performing the kinetic assessment of RISC, we observed that when siRNAs are designed with regard to \u27functional asymmetry\u27 (by unpairing the 5´ terminal nucleotide of the siRNA\u27s guide strand, i.e. the strand anti-sense to the target RNA), not all of the RISC formed was active for target cleavage. We observed, somewhat paradoxically, that increased siRNA unwinding and subsequent accumulation of single-stranded RNA into RISC led to reduced levels of active RISC formation. This inactive RISC did not act as a competitor for the active fraction. In order to characterize this non-cleaving complex, we performed a series of protein-siRNA photo-crosslinking assays. From these assays we found that thermodynamic stability and termini structure plays a role in determining which proteins an siRNA will associate with, and how association occurs. Furthermore, we have found, by means of the photo-crosslinking assays, that siRNAs commingle with components of the miRNA pathway, particularly Ago1, suggesting overlapping functions or crosstalk for factors thought to be involved in separate, distinct pathways

Vacancy assisted arsenic diffusion and time dependent clustering effects in silicon

We present results of kinetic lattice Monte Carlo (KLMC) simulations of substitutional arsenic diffusion in silicon mediated by lattice vacancies. Large systems are considered, with 1000 dopant atoms and long range \textit{ab initio} interactions, to the 18th nearest lattice neighbor, and the diffusivity of each defect species over time is calculated. The concentration of vacancies is greater than equilibrium concentrations in order to simulate conditions shortly after ion implantation. A previously unreported time dependence in the applicability of the pair diffusion model, even at low temperatures, is demonstrated. Additionally, long range interactions are shown to be of critical importance in KLMC simulations; when shorter interaction ranges are considered only clusters composed entirely of vacancies form. An increase in arsenic diffusivity for arsenic concentrations up to $10^{19} \text{cm}^{-3}$ is observed, along with a decrease in arsenic diffusivity for higher arsenic concentrations, due to the formation of arsenic dominated clusters. Finally, the effect of vacancy concentration on diffusivity and clustering is studied, and increasing vacancy concentration is found to lead to a greater number of clusters, more defects per cluster, and a greater vacancy fraction within the clusters.Comment: 22 pages, 16 figure

Vacancy clustering and diffusion in silicon: Kinetic lattice Monte Carlo simulations

Diffusion and clustering of lattice vacancies in silicon as a function of temperature, concentration, and interaction range are investigated by Kinetic Lattice Monte Carlo simulations. It is found that higher temperatures lead to larger clusters with shorter lifetimes on average, which grow by attracting free vacancies, while clusters at lower temperatures grow by aggregation of smaller clusters. Long interaction ranges produce enhanced diffusivity and fewer clusters. Greater vacancy concentrations lead to more clusters, with fewer free vacancies, but the size of the clusters is largely independent of concentration. Vacancy diffusivity is shown to obey power law behavior over time, and the exponent of this law is shown to increase with concentration, at fixed temperature, and decrease with temperature, at fixed concentration.Comment: 14 pages, 12 figures. To appear in Physical Review

Development of Electron Microscopy Analysis and Simulation tools for nanoHUB

Electron microscopy has a crucial role in the field of materials science and structural biology. Although electron microscopy gives lots of important results and findings, some additional simulations and image processing/reconstruction is required to get more information from the data that are collected from the experiments. For this purpose, researchers are using IMOD1 and QSTEM2 for electron microscopy analysis and simulation. IMOD is a set of programs used for tomographic reconstruction and 3D visualization and QSTEM is used for quantitative simulations of TEM and STEM images. However, IMOD and QSTEM are hard to install or use for beginners who are not familiar with computational skills. To overcome this issue, we have developed “Online IMOD and STEM tools” to allow users to perform microscopy analysis and simulation with ease. We applied several ways to launch or combine tools. Based on the original source codes of the software, we used the graphical interface builder Rappture to build a new interface to launch several tools. Also, we used the nanowhim window manager to combine and organize tools. The online version of IMOD and QSTEM will enable researchers from all over the world to use IMOD and QSTEM programs directly and easily on the nanoHUB website

Building for Beyond: Designing Courses to Empower Longer-Term Student Projects

Panel session on using Historiography and other intermediate prerequisites as launch courses toward longer-term late-collegiate, graduate-level, and preprofessional skill-, resource-, and contact-building

Thermal and Mechanical Properties of Polymers using Molecular Dynamics

Polymer systems have gained attention during the past years because of their technological and industrial applications. Simulations, particularly molecular dynamics, are very useful for exploring properties of amorphous polymers, without using experiments. Our goal is to create a readily-available tool that will perform MD simulations in order to get thermal and mechanical properties (Glass transition temperature, Young Modulus) of the polymers. The work that has been done will be part of a tool to help people to learn about polymer properties including Glass Transition Temperature. We model some polymers at a scale of 10,000 atoms. The tool uses LAMMPS to perform MD simulations, with the DREIDING force field. The polymer structures were obtained using Polymer Modeler and the post processing is done using a created Python code. Thus far the problems in modeling the glass transition temperature have been many, but we have been able to model it to a relatively good degree. This tool is intended to be open for general use on NanoHUB. In the future, this tool will likely be expanded to cover further physical properties of further polymers

Does the Cage Position in Transforaminal Lumbar Interbody Fusion Determine Unilateral versus Bilateral Screw Placement?: A Review of the Literature

This literature review examines the relative placement of the interbody cage with respect to the unilateral screw construct to address the need for bilateral screw placement versus unilateral screw placement. Transforaminal lumbar interbody fusion (TLIF) has become a widely used technique for correcting lumbar intervertebral pathologies. This review addresses the necessity for further study on the effects of the relative position of intervertebral cage placement on the outcome of lumbar spine surgery after TLIF with unilateral pedicle screw fixation. Previous studies have addressed various factors, including posterior screw fixation, cage size, cage shape, and number of levels fused, that impact the biomechanics of the lumbar spine following TLIF. A simple survey of the literature was conducted. A search of the English literature was conducted using the keywords ‘TLIF,’ ‘transforaminal lumbar interbody fusion,’ ‘graft placement,’ ‘graft position,’ ‘cage position,’ ‘cage placement,’ ‘unilateral pedicle screw,’ ‘unilateral TLIF cage placement,’ ‘lumbar biomechanics,’ ‘lumbar stability,’ ‘lumbar fusion,’ and ‘lumbar intervertebral cage’ with various combinations of the operators ‘AND’ and ‘OR’ and no date restrictions. Seventeen articles in the English literature that were most relevant to this research question were identified. To the best of our knowledge, there are no published data addressing the effects of cage placement relative to the unilateral screw on lumbar stability in TLIF with unilateral pedicle screw fixation. Investigation of the effects of cage placement is, thus, warranted to achieve optimal clinical outcomes in patients undergoing TLIF with unilateral pedicle screw fixation

Micro-optical Tandem Luminescent Solar Concentrators

Traditional concentrating photovoltaic (CPV) systems utilize multijunction cells to minimize thermalization losses, but cannot efficiently capture diffuse sunlight, which contributes to a high levelized cost of energy (LCOE) and limits their use to geographical regions with high direct sunlight insolation. Luminescent solar concentrators (LSCs) harness light generated by luminophores embedded in a light-trapping waveguide to concentrate light onto smaller cells. LSCs can absorb both direct and diffuse sunlight, and thus can operate as flat plate receivers at a fixed tilt and with a conventional module form factor. However, current LSCs experience significant power loss through parasitic luminophore absorption and incomplete light trapping by the optical waveguide. Here we introduce a tandem LSC device architecture that overcomes both of these limitations, consisting of a PLMA polymer layer with embedded CdSe/CdS quantum dot (QD) luminophores and InGaP micro-cells, which serve as a high bandgap absorber on top of a conventional Si photovoltaic. We experimentally synthesize CdSe/CdS QDs with exceptionally high quantum-yield (99%) and ultra-narrowband emission optimally matched to fabricated III-V InGaP micro-cells. Using a Monte Carlo ray-tracing model, we show the radiative limit power conversion efficiency for a module with these components to be 30.8% diffuse sunlight conditions. These results indicate that a tandem LSC-on-Si architecture could significantly improve upon the efficiency of a conventional Si photovoltaic module with simple and straightforward alterations of the module lamination steps of a Si photovoltaic manufacturing process, with promise for widespread module deployment across diverse geographical regions and energy markets