SUG Meeting Minutes and Agendas

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SUG Meeting Agendas

SUG Meeting Minutes

Statewide Users Group Agenda - Dec 4, 2014

Wednesday, Dec. 3th

4:00  Allocations Committee Meeting

Thursday, Dec. 4th

10:30 - 11:30

Software Committee Meeting

Hardware Committee Meeting

Face:Face OSCHelp

11:30 - 12:30 Lunch
12:30 - 1:15

Keynote Address
NSF support for High Performance Computing and Cyberinfrastructure
Dr. Evelyn M. Goldfield
Program Director, Chemistry Division, NSF

1:15 - 1:45

Invited Talk
Total Sim USA and the Ohio Supercomputer Center
Ray Leto
President of Total Sim USA

1:45 - 2:00 Break
2:00 - 3:00 OSC Perspective
3:00 - 4:00 Flash Talk Contest
4:00 - 6:00

Poster Contest

Interface Lab Open House

6:00 Social Outing at Hofbräuhaus

Flash Talks

  • Jonathan Brown
  • Ginevra Cochran
  • Frank King
  • Matthew McMahon
  • Youngmi Seo
  • Joy-El Talbot
  • Mahendra Thapa

Posters

Poster Map

  • Ayse Arslanargin
  • Nikolas Antolin
  • Molly Ball
  • Katharine Cahill
  • Ginevra Cochran
  • Sukirth Ganesan
  • Michael Gibbons
  • Mark Hornak
  • Frank King
  • Matthew McMahon
  • Travis P. Pollard
  • August Powers
  • Rodney Richardson
  • David Riegner
  • Janani Sampath
  • Youngmi Seo
  • Anne Shim
  • Joy-El Talbot
  • Mahendra Thapa
  • Travis Withrow
  • Xing Zhang

Flash Talk and Poster Topics

Modeling ion solvation in ethylene carbonate and propylene carbonate
Ayse Arslanargin, University of Cincinnati

Non-aqueous solvents are widely used as liquid electrolytes in lithium-ion batteries. Understanding the solvent structure is essential for battery performance enhancements. This work investigates the thermodynamics of ion solvation in ethylene carbonate and propylene carbonate. Free energy and enthalpy of solvation calculations have been conducted employing different force fields. Simulated annealing calculations have been performed to alter non-bonded energy parameters. The new parameters result in good agreement with the experimental free energy of solvation values, while the enthalpy of solvation results show deviations from the experimental data. These results suggest that classical models often do not accurately predict basic interactions in ion-solvent systems.

Phonon induced magnetism in diamagnetic materials
Nikolas Antolin, The Ohio State University

Thermoelectric phenomena in magnetic materials create exciting possibilities in future  spin caloritronicdevices by manipulating spin information using heat. An accurate understanding of spin-lattice interactions, i.e. coupling between magnetic excitations (magnons) and phonons (lattice vibrations), holds the key to unraveling their underlying physics. Here we present ab-initio frozen-phonon calculations of CsI and InSb that result in non-zero magnetization when degeneracy between spin-up and spin-down electronic density of states is lifted for certain phonon displacements. We discuss mechanisms of this previously unobserved effect as well as present data collected by collaborating OSU researchers measuring the magnitude of this response in InSb.

First principles study of the origin of Strain-tunable extraordinary magnetocrystalline anisotropy in Sr2CrReO6 epitaxial films
Molly Ball, The Ohio State University

We report the discovery of extraordinarily large, strain-tunable magnetocrystalline anisotropy (MCA) in Sr2CrReO6 epitaxial films. These films grown on several different substrates undergo dramatic changes in MCA shown by a shift in easy-axis from in-plane to out-of plane. We determine the strain-induced structural distortions by performing density functional theory (DFT) calculations using VASP. The change in easy-axis under strain can be examined through the energy differences for magnetic orientation along crystalline axes known as the magnetic anisotropy energy (MAE). We are able to establish the origin of this large strain-tunable MCA by directly relating the MAE to the orbital moments.

Co-Authors:  M. R. Ball, J. M. Lucy, OD. Restrepo, A. J. Hauser, J. R. Soliz, J. W. Freeland, P. M. Woodward, W. Windl, and F. Y. Yang

Phase Behavior of Tapered Diblock Copolymers from Self-Consistent Field Theory
Jonathan Brown, The Ohio State University

Tapered block copolymers are similar to AB diblock copolymers, but with a statistical A-to-B (normal) or B-to-A (inverse) gradient “taper” between the A and B blocks. Depending on the sequence of monomers along the chain and the segregation strength χN, the A and B monomers microphase separate to form various ordered morphologies. We map the phase diagrams of model tapered polymers using self-consistent field theory (SCFT). The normal tapered systems are similar to diblocks, but show a wider region of network structures. In inverse tapered systems, the polymer can fold across the interface and new ordered structures are found.

Co-Authors:  Jonathan Brown, Scott W. Sides, Lisa M. Hall

Molecular docking study of Organophosphorus pesticides with G3C9 and its variants
Katharine Cahill, The Ohio State University

Organophosphorus (OP) compounds are highly toxic chemicals capable of inhibiting the hydrolysis of the neurotransmitter acetylcholine by acetylcholinesterase. Catalytic hydrolysis of OPs with enzymatic bio-scavengers, such as paraoxonase (PON1), is an active avenue of investigation towards the treatment of OP exposure. G3C9 is a recombinant PON1 enzyme which was developed for its improved solubility and has some activity against OP pesticides. In this study, molecular docking simulations were performed on G3C9 and several of its variants. Docking analysis shows that, the V346A mutation significantly improves OP binding to the active site compared to G3C9. Several OP compounds with bulky leaving groups, including paraoxon and diazoxon, were studied to understand both the efficiency of binding as well as the orientation of the guest in the active site.

Co-Authors:  Katharine J. Cahill, Kiran Doddapaneni, Shameema Oottikkal, Thomas J. Magliery and Christopher M. Hadad

Convergence criteria for PIC simulations of electrons in an ultraintense laser field
Ginevra Cochran, The Ohio State University

We present a study of particle-in-cell (PIC) simulation error in modeling an electron in an ultraintense laser field. We find an unexpectedly small timestep is required to resolve the electron motion, decreasing with increasing laser intensity. We consider several sources of PIC error, and find that the error from the particle velocity and position advance is dominant. We derive the timestep constraint and find that it decreases with laser intensity. We find the particle advance error accumulates when the electron is at rest and the laser fields are strong, and present a sub-cycled particle advance which reduces error.

Co-Authors:  Alexey V. Arefiev, Douglass W. Schumacher, A.P.L. Robinson

What’s In A Cigarette? Nicotine, Not Metals, Affects Biofilm Transcription
Sukirth Ganesan, The Ohio State University

Dysbiotic oral microbial communities underlie the etiology of cancer, caries and periodontitis. Since smoking is a primary risk factor for these bacterially-driven diseases, a metatranscriptomic approach was used to examine the effect of smoke on gene transcription within oral biofilms. Polymicrobial biofilms were generated in smoke-free, smoke-rich, nicotine-conditioned and heavy-metal-depleted environments. Enriched mRNA was sequenced and analyzed using the computational tools incorporated within the MG-RAST pipeline. The pipeline was offloaded to the Oakley Cluster at OSC, allowing for expedited processing of immense datasets. Smoke significantly modulates transcription in oral biofilms with a majority of the effects attributable to nicotine.

Co-Authors: SM Dabdoub, W. Tang,  J. Bischof, F. Meyer, PS Kumar

FFT modeling of deformation behavior in bulk metallic glass composites
Michael Gibbons, The Ohio State University

Bulk metallic glass composites (BMGCs), consisting of an amorphous matrix and a homogeneous distribution of crystalline dendrites, offer a promising solution to the low fracture toughness and brittleness of pure bulk metallic glasses. To date, the interaction between the crystalline and amorphous phase during deformation is not well understood and will be examined here with fast Fourier transform (FFT) based continuum modeling. Given appropriate computational resources, the efficiency of this FFT approach allows us to study the mesoscale deformation behavior of these composites in 3D, using spatial and time resolutions high enough to obtain meaningful insight.

Determining Point Defect Energetics and Optics in Sapphire from First Principles
Mark Hornak, The Ohio State University

Single crystal α-Al2O3 (sapphire) is a potential candidate for optical fibers and sensors in extreme high-temperature radiation environments.  Transmission of light under such conditions can be impeded by the generation of defects within the material.  In order to validate sapphire, we determine the stable point defects, and their charge states, in stoichiometric sapphire.  The increase in attenuation due to individual point defects was calculated using density functional theory and hybrid functional mixing.  We find that oxygen and aluminum vacancies are dominant, and attenuate light in the 200-300nm range.  Oxygen divacancies also show significant attenuation in the 100-200nm and 300-450nm ranges.

Simulations of High Intensity Short Pulse Lasers Incident on Reduced Mass Targets Using LSP
Frank King, The Ohio State University

We present the results of a series of fully kinetic 2D and 3D simulations using the Particle-In-Cell code LSP for the study of the heating and deformation of micron scale targets.  These simulations model an experimental laser pulse incident on a realistic several micron thick copper target as a function of intensity, spot size, pre-plasma, and target lateral extent and thickness.  We observe that the target deformation and heating has a strong dependence on intensity of the laser pulse and creation of a shock in the target.

Co-Authors: Chris Orban, Kramer U. Akli, Douglass Schumacher

First PIC simulations modeling the interaction of ultra-intense lasers with sub-micron, liquid crystal targets
Matthew McMahon, The Ohio State University

We recently introduced liquid crystal films as on-demand, variable thickness (50 – 5000 nanometers), inexpensive targets for intense laser experiments. Here we present the first particle-in-cell (PIC) simulations of short pulse laser excitation of liquid crystal targets using the PIC code LSP. In order to accurately model the target evolution, a low starting temperature and field ionization model are employed. This is essential as large starting temperatures lead to expansion of the target causing significant reduction of the target density before the laser pulse can interact. We also present an investigation of the modification of laser pulses by very thin targets

The thermodynamics of proton hydration and the electrochemical surface potential
Travis P. Pollard, University of Cincinnati

A major roadblock in refining our understanding of the role of ions in chemistry and biology is the inability of experiment to resolve single-ion contributions to the hydration thermodynamics of salts. Numerous methods have been proposed to decompose the whole into a sum of its parts. These methods agree on the thermodynamics of various salts but not on individual ion quantities which appear systematically shifted from one another by a charge-dependent amount (q*x). The poster highlights our recent work, which concludes that a solvent-specific surface potential (x) of -11.6 to -9 kcal/mol-e may account for the observed differences.

Co-Author: Thomas L. Beck

Investigating Classical Models of Non-Aqueous Ion Solvation
August Powers, University of Cincinnati

Modeling energy storage systems is an important avenue in the optimization and advance of these technologies. This work investigates the classical models used in describing ion solvation in non-aqueous systems relevant to lithium-ion batteries and supercapacitors. Quantum mechanical data was used to try improving the van der Waals parameters for ions solvating in ethylene carbonate; improvements (relative to experimental data) were seen for the solvation free energies, but not for the solvation enthalpies. Additional symmetry-adapted perturbation theory results suggest the discrepancies may lie in the description of the non-electrostatic interactions within the ions' first solvation shells.

Co-Authors: Ayse Arslanargin, Thomas Beck

A comparative study of ITS2 metabarcoding and traditional microscopic palynology as methods of identifying taxonomic origins of bee collected pollen
Rodney Richardson, The Ohio State University

Honey bees, Apis mellifera, display high floral fidelity as they collect pollen from across large geographical areas.  Honey bees pack pollen into corbicular pellets for transport back to the colony. Identifying the flowers used by bees is important for understanding both bee and plant biology. Traditionally, microscopic palynology has been employed to identify floral sources. We developed a novel, molecular strategy for determining the floral sources of bee collected pollen, which involves amplifying the ITS2 locus using universal primers (Chen et al., 2010), followed by amplicon sequencing on the Illumina MiSeq platform

Co-Authors: Chia-Hua Lin, Juan QuijiaPillajo, Douglas B. Sponsler, Karen Goodell and Reed Johnson

Molecular Dynamics Simulations of Al-La Glass and Liquid
David Riegner, The Ohio State University

Metallic glass, a metal without an ordered atomic structure, may represent the next generation of engineering material. Design and application of these materials is hampered by long-standing challenges in fabrication and characterization. Molecular dynamics simulations can probe properties of undercooled (below their melting temperature) metallic liquids as they transition from liquid to glass. Characteristics and mechanisms at work during this transition, some attainable only through computer simulations, will narrow future experiments to target only systems and compositions that most readily assume a glassy state.

Effect of Aggregation on the Mechanical Properties of Ionomers From Molecular Dynamics Simulations
Janani Sampath, The Ohio State University

Ionomers are polymers with a small fraction of charged monomers that have a wide range of applications. We consider dense melts of ionomers and counterions with no solvent; an important aspect of their performance is the aggregation of ions, which holds polymer chains together like temporary cross-links. Because of the size scales involved, it is difficult to obtain a complete 3D microscopic picture of polymer aggregation. By performing MD simulations of ionomers of various architectures, we will show aggregate morphology and scattering profiles. Connecting these results with observed mechanical features will suggest how to design new ionomers with improved properties.

Co-Author: Lisa M. Hall

Molecular Dynamics Simulations of Microphase Separating Tapered Diblock Copolymers
Youngmi Seo, The Ohio State University

Tapered AB copolymers consist of pure A and B blocks separated by a midblock whose composition is a statistical gradient from A to B (B to A for an inverse taper); they can microphase-separate into various ordered phases. Taper length can be used as a tuning parameter to control microphase separation, but better physical understanding is needed for experimentalists to use this new parameter effectively. Using coarse-grained molecular dynamics simulations, we study structure and dynamics of these materials. Among other results, we show that inversely tapered polymers fold across the microphase interface, leading to significantly shorter domain spacing than diblocks.

Co-Authors: Jonathan R. Brown and Lisa M. Hall

Micellular encapsulation of nanoparticles from dissipative particle dynamics simulations
Anne Shim, The Ohio State University

Polymer-protected nanoparticles are of interest for drug delivery and medical imaging. Experimentalists need to generate uniform size micelles containing a predetermined number of particles for the particles to be useful commercially. We aim show on a molecular scale how the polymer micellization around hard nanoparticles occurs and thus can be controlled experimentally. We perform dissipative particle dynamics simulations of polymers and nanoparticles in solution. The solvent interaction strength varies over time to account for changing solvent concentration, which allows the micelles to form. We observed how changing polymer concentration, polymer length, and particle size affect the system.

Co-Authors: Jonathan Brown and Lisa Hall

RNA polymerase IV affects nascent transcription in maize
Joy-El Talbot, UC-Berkeley and The Ohio State University

Three RNA polymerases transcribe eukaryotic genomes into RNA. The roles of additional plant RNA polymerases like Pol IV remain unclear, although transcriptional silencing of transposons and normal maize development require Pol IV. Seedling nascent transcriptomes identify a novel role for Pol IV: regulating transcription at gene boundaries. While most transposons remain untranscribed in Pol IV mutants, specific near-genic transposons may promote transcription. To test this hypothesis, I will collapse multi-mapping nascent transcriptome data (500Gb/library) into locus- and read-specific SQLite databases on OSC systems. The maize genome is >85% repetitive, therefore including multi-mapping reads will increase understanding of Pol IV.

Co-Authors: Karl F. Erhard, Jr. and Jay B. Hollick

Comparison of Side-chain Motion of the Protein Calbindin D9k in its Four Calcium Binding States using Molecular Dynamics Simulations
Mahendra Thapa, University of Cincinnati

Molecular Dynamics (MD) simulation of a protein helps to study motion and its development with time which may not be studied experimentally. The side chains of a protein play important role in folding ,ligand binding and interactions. We used AMBER 12.0 software suit on GPU to simulate a protein Calbindin D9k (CAB), which is involved in the uptake and transport of the calcium, on its four calcium binding states: a doubly-loaded state, two singly-loaded states and an apo state. Force field ff12SB and water model TIP3P at NVT condition were chosen in the simulation. Experimental and computational studies on the dynamics of backbone atoms of the protein confirmed that calcium binding occur in a positive cooperative fashion. Studies of the doubly loaded state of the protein by molecular dynamics simulation and NMR experiment further enhance the point. To further investigate by computation, MD approach has been used to study the side chain dynamics of all these states of the protein.

Co-Author: Dr. Mark Rance

Atomistic Simulation for a Better Atom Probe Algorithm
Travis Withrow, The Ohio State University

Atom probe tomography holds a lot of promise as a technique allowing materials engineers to examine a structure in an atom-by-atom basis but is hampered by a simplistic reconstruction algorithm that overly relies on instrumentalist interpretation and fails to take into account much of the physics of sample behavior in the machine. Supercomputer simulations of the atomistic behavior of samples under measurement conditions will allow us to improve the current reconstruction algorithm, remove much of the human error and allow for true error propagation based on the physics of atomic interactions within the device.

Simulations of Energy Transfer in a Self-Assembling Organic Nanotube
Zhi-Qiang You, The Ohio State University

Recent experimental work at Ohio State has led to the synthesis and atomic-resolution structural model for a self-assembling organic nanotube consisting of several hundred naphthalenediimide chromophore units.  Experimentally, this system exhibits rapid (sub-ps) fluorescence depolarization,

with rapid excited-state energy transfer dynamics, and the atomic detail of the structural model facilitates detailed electronic structure calculations that are presented here.  Calculated energy-transfer rates are consistent with experimental estimates, and significant excited-state delocalization is predicted.

Co-Authors: Jon Parquette, Christopher P. Jaroniec, John M. Herbert

Analytic Derivative Couplings for Spin-Flip TDDFT:  An Inexpensive and Topologically-Correct Approach to Simulating Photochemistry
Xing Zhang, The Ohio State University

We have derived, implemented, and tested analytic derivative couplings for the “spin-flip” variant of time-depdendent density functional theory (TDDFT), within the Q-Chem electronic structure code.  Unlike traditional TDDFT, the spin-flip version exhibits correct topology in the vicinity of conical intersections and can therefore correctly describe the “conical funnels” that are responsible for photochemistry and photophysics, but at DFT cost. This should facilitate both non-adiabatic molecular dynamics simulations and the mapping of excited-state reaction pathways in large molecules.  Preliminary applications will be presented.

Co-Author: John M. Herbert

 

Statewide Users Group Agenda - June 4, 2015

Wednesday, June. 3th

4:00

Allocations Committee Meeting

Thursday, June. 4th

10:30 - 11:30

Software Committee Meeting

Hardware Committee Meeting

Face:Face OSCHelp

11:30 - 12:30

Lunch

12:30 - 1:15

Keynote Address

AFRL DSRC - not just a DoD Supercomputing Resource Center

Jeff Graham (Director of AFRL's HPC facility at WPAFB)

1:15 - 1:45

Keynote Address

Exploring the Dark Side with Simulations

Annika Peter (Assistant Professor, Department of Physics at OSU)

1:45 - 2:00

Break

2:00 - 3:00

Flash Talk Contest

3:00 - 4:00

OSC Presentation

4:00 - 6:00

Poster Contest

Interface Lab Open House

Social Networking

5.45

Talk and Poster Winner Announcement

Flash Talks

  • Jim Giuliani
  • Joseph Owino
  • Xiang Chen
  • Jason Brown
  • Andrew Paluch
  • Janani Sampath
  • Shameema Oottikkal

Posters

Poster Map

  • David Riegner
  • Nikolas Antolin
  • Jason Brown
  • Daqing Gao
  • Bryan Esser (2)
  • Fenglin Han
  • Elizabeth O'Loughlin
  • Ryan Ley
  • Jeremy Phifer
  • Travis Blanton
  • Tingting Liu
  • Rodney Richardson
  • Travis Withrow
  • Minkyu Kim
  • Gabriel Goncalves Nogueira
  • Mark Hornak

Flash Talk and Poster Topics

Simulations of nanometer-scale inclusion-matrix interactions in shape memory alloys
Xiang Chen, The Ohio State University

This flash talk presents two projects in materials science which utilized the HPC resources at OSC. The first project investigates the transformation-induced dislocation effect in single crystal nickel-titanium shape memory alloy. The driving force profile on different dislocation slip systems are solved through micromechanics, utilizing the large memory node on OSC’s Oakley cluster. The results correlate well with the electron microscope observations. The second project investigates the phase evolution in nano-precipitated Ni-Ti-Hf shape memory alloy through finite-element simulation. The large scale multi-precipitate simulations shed lights on the physical basis underlying the microstructures observed in high-resolution electron microscopy.

MetaBase: Structural and Metabolic analysis of microbial communities
Joseph Owino, Bowling State University

Metagenomics is based on the genome analysis of microbial DNA extracted directly from environmental samples. The analysis provides information on the structure and metabolic activities within microbial communities. We intend to use publicly available metagenomics data to construct an easily accessible and highly informative database describing the structural and metabolic relationships within microbial communities, following a five step process; data acquisition, data analysis, prediction of microbial community population, database management and implementation. This database will aid our current and future research and also be made available to the public.

Effect of Aggregation on the Mechanical Properties of Ionomers From Molecular Dynamics Simulations
Janani Sampath, The Ohio State University

Ionomers are polymers with a small fraction of charged monomers that have a wide range of applications. We consider dense melts of ionomers and counterions with no solvent; an important aspect of their performance is the aggregation of ions, which holds polymer chains together like temporary cross-links. Because of the size scales involved, it is difficult to obtain a complete 3D microscopic picture of polymer aggregation. By performing MD simulations of ionomers of various architectures, we will show aggregate morphology and scattering profiles. We also obtain stress-strain curves and will discuss effects of degree of neutralization of the ionomers. Connecting these results with observed mechanical features will suggest how to design new ionomers with improved properties.

A Computational Study of Organophosphonate Encapsulation in Functionalized Molecular Baskets
Jason Brown, The Ohio State University

Organophosphorus nerve agents (OPs) are a toxic class of compounds that have been used as pesticides and chemical warfare agents, and compounds for which there is a great need of effective therapeutics. Gated molecular baskets conjugated to aliphatic amino acid functionalities have been examined for the binding and hydrolysis of the toxic nerve agent upon entering the bloodstream. A computational protocol was developed for the molecular baskets including a Monte Carlo conformational search, Molecular Dynamics simulations, and docking calculations. The results of the computational studies of the baskets and the critical features for encapsulation of OPs will be presented.

Using Molecular Simulation and Electronic Structure Methods to Develop Chemical Engineering Design Tools
Andrew Paluch, Miami University

For the design of commercial separation processes, accurate analytic models to predict the underlying phase-behavior is essential. The chemical engineering community has risen to the challenge by developing several such models. However, design engineers are often confronted with the challenge of designing processes for novel compounds, for which model parameters do not exist. In this flash talk I will highlight the efforts of undergraduate students in my research group to use molecular simulation and electronic structure methods to develop predictive analytic models for non-electrolyte solids in solution suitable for chemical engineering design.

Compressor Response to Boundary Layer Ingesting (BLI) Inlet Distortions
Jim Giuliani, The Ohio State University

Many future civil transport designs incorporate engine inlets integrated into the body of the aircraft. Increased engine efficiency can be obtained if the inlet ingests lower momentum boundary layer flow that develops along the body of the aircraft. Engines that employ Boundary Layer Ingesting (BLI) inlets are very sensitive to the magnitude of fan and inlet duct losses. This talk presents a detailed analysis of the fan response to the distorted flowfield. Several stall cells are identified and examined. The stall occurs at a point of rapid incidence angle oscillation and shows similar characteristics to dynamic stall.

Exploring Molecular Interactions of AChE enzyme with substrates through GPU accelerated MD methods
Shameema Oottikkal, The Ohio State University

Acetylcholinesterase enzyme plays important roles during the signal transmission at cholinergic synapses. Dysfunctions of AChE are involved in the inhalation of extremely poisonous nerve agents and in several human diseases. As a result, AChE has become an important target for rational drug design. The AChE-substrate interactions are modeled with various computational software available at Ohio Super computer center like AMBER, GAUSSIAN, SCHRODINGER, R etc. Our methodologies involve, molecular docking, molecular dynamics, accelerated MD, steered MD, QM/MM methods, statistical data analysis etc. We have used GPU computing extensively to increase the simulation time and probe the molecular interactions extensively and efficiently.

Co-Authors: Christopher M. Hadad

Molecular Dynamics Simulation of Metallic Glass Formation
David Riegner, The Ohio State University

Metallic glass, a metal without an ordered atomic structure, may represent the next generation of engineering material. Despite having properties not accessible with current alloys, applications are limited by long-standing challenges in design and fabrication. Using the LAMMPS package, molecular dynamics simulations can probe properties of undercooled metallic liquids as they become glass. Some characteristics of this transition are attainable only through computer simulation, providing new insights for the deliberate design of new alloys that readily form glass. Experimentalists can apply this information to new alloy design by targeting promising systems and compositions that behave like the simulations.

DFT Modeling of Solute Segregation at Stacking Faults Informed by Atomic-Resolution EDS
Nikolas Antolin, The Ohio State University

Developing improved deformation models for polycrystalline Ni-based superalloys requires a deeper understanding of the rate controlling processes at higher temperatures. Compression creep tests on specially prepared single crystals of an exploratory Ni-base superalloy were conducted at 760°C in the [001] orientation in order to promote precipitate shearing by stacking faults. Scanning transmission electron microscopy imaging using high angle annular dark field imaging was coupled with state-of-the-art energy dispersive x-ray spectroscopy (EDS) to reveal for the first time to an ordered compositional variation along the extrinsic faults inside the Ni3Al precipitates. The local structure and chemistry is consistent with the eta phase, a D024 hexagonal structure. Density Functional Theory (DFT) computations are used to assess the energetics of this segregation and discuss implications of eta phase formation on deformation mechanisms.

A Computational Study of Organophosphonate Encapsulation in Functionalized Molecular Baskets
Jason Brown, The Ohio State University

Organophosphorus nerve agents (OPs) are a toxic class of compounds that have been used as pesticides and chemical warfare agents, and compounds for which there is a great need of effective therapeutics. Gated molecular baskets conjugated to aliphatic amino acid functionalities have been examined for the binding and hydrolysis of the toxic nerve agent upon entering the bloodstream. A computational protocol was developed for the molecular baskets including a Monte Carlo conformational search, Molecular Dynamics simulations, and docking calculations. The results of the computational studies of the baskets and the critical features for encapsulation of OPs will be presented.

Binding Studies of Hydrogen-Bonded Complexes in Solution
Daqing Gao, Central State University

Hydrogen bonding plays an important role in structural biology and supramolecular chemistry. We have obtained the free energies of association of nearly 50 hydrogen bonded complexes which belong to medium and large size both in the gas phase and solution at the M06-2X/cc-pvdz and SMD/M06-2X/cc-pvdz level of theory. This represents the first comprehensive solution phase evaluation of free energies of association of H-bonded complexes covering all the H-bonding interaction patterns of doubly and triply H-bonded complexes. We have justified that our computational protocol can give reliable binding free energies of hydrogen bonded complexes in organic solvent chloroform and dichloromethane.

Acknowledgement: Gratitude is expressed to Central State University, NSF and Ohio Supercomputer Center for support of this work

Understanding Dislocation Core Contrast using Atomic Resolution Electron Microscopy Image Simulation
Bryan Esser, The Ohio State University

Atomic resolution scanning transmission electron microscopy (STEM) is often used to analyze deformation mechanisms and properties. Strong contrast has been observed around dislocation cores using medium-angle annular dark field STEM, but not in high-angle conditions. Atomic resolution image simulations using μSTEM have been employed with atomistic simulations on model FCC alloys to explain the nature of the contrast variation as a function of scattering angles for these HEAs in thin foil geometries necessary for high resolution imaging. Only through the use of HPC, especially with GPU acceleration, can such large systems be reasonably studied.

Marked Improvements in Sample Thickness Estimations Using GPU Accelerated Diffraction Simulations
Bryan Esser, The Ohio State University

In high-resolution electron microscopy and spectroscopy, quantification of sample thickness is very important for interpretation of results. Until recently there were very few reliable experimental techniques for measuring sample thickness. Position average convergent beam electron diffraction (PACBED) has been shown to be very sensitive to sample thickness, giving thickness values to within 10%; however, experimental PACBED patterns are only useful when compared with simulation. Initial attempts at simulating PACBED were computationally expensive, until GPU acceleration and creative code writing allowed the average experimentalist to run complete simulations in a matter of minutes with little to no help from theorists.

Studying the Suitability of Ionic Liquids for Pharmaceutical Separation Processes
Fenglin Han, Miami University

Ionic liquids (ILs) are a unique class of highly tunable solvents. The IL cation and anion may virtually be altered to change their physical and chemical properties, allowing a near infinite number of IL candidates for particular tasks. However, exploring such a massive chemical compound space using experimentation is highly challenging. Given this situation, atomistic molecular simulation is a promising design tool to help understand the structure-property relationships governing the phase-behavior of solutes in ILs. In this work we studied the phase-behavior of acetaminophen in 21 ILs, and observed solubility enhancement on the order of million times that in water.

Predicting the Equilibrium Solubility of Nonelectrolyte Solids Using MOSCED and Molecular Simulation
Elizabeth O'Loughlin, Miami University

Accurate and efficient models to predict the phase-behavior of nonelectrolyte solids in a wide range of solvents are central to the design of novel separation processes. A promising design tool is the MOSCED limiting activity coefficient model which is parameterized for 133 solvents. However, before predictions may be made for a solute of interest, solute MOSCED parameters are required. For novel compounds of interest, the necessary MOSCED parameters are unavailable and sufficient data is likely unavailable to regress the necessary parameters. In this study we explore the use of molecular simulation to generate the necessary reference data.

Calculating the Fugacity of Pure, Low Volatile Liquids via Molecular Simulation
Ryan Ley, Miami University

A simple, molecular simulation framework to compute the pure liquid fugacity of low volatile liquids is presented and compared to reference Monte Carlo simulations. The method involves calculation of the residual chemical potential and the molar volume of the liquid at the conditions of interest. For substances that are solid at the conditions of interest, simulations may be performed at elevated temperatures and extrapolated to sub-cooled conditions because direct calculations at sub-cooled conditions provide erroneous results. Knowledge of the pure liquid fugacity is essential to compute activity coefficients defined with respect to a Lewis-Randall standard state for thermodynamic property modeling.

Developing a Predictive form of MOSCED for Nonelectrolyte Solids using QChem
Jeremy Phifer, Miami University

MOSCED is a promising model to predict the limiting activity coefficient of nonelectrolyte solids in solution. However, before it may used for a new solute, a limited set of reference data is needed to obtain the necessary solute MOSCED parameters. In this study we explore the use of electronic structure calculations to generate the reference data necessary to obtain solute MOSCED parameters. Specifically, we use the popular software package QChem which employs the SM8 solvation model. The method is applied to acetaminophen, acetanilide, phenacetin, anthracene, phenanthrene, naphthalene, pyrene and dibenzothiophene.

Mechanistic Insights into the Alkylation Reactions of Quino ne Methide Precursors: Studies Towards the Realkylation of Aged Acetylcholinesterase
Travis Blanton, The Ohio State University

Acetylcholinesterase(AChE) is an essential enzyme in the human body, which hydrolyzes the neurotransmitter acetylcholine(ACh) at neurosynaptic junctions. Organophosphorus(OP) nerve agents such as Sarin and Tabun are covalent inhibitors of AChE. Following exposure to OPs, AChE is inhibited and undergoes a subsequent irreversible aging process in which the OP-AChE adduct is de-alkylated, destroying AChE’s ability to hydrolyze ACh. No known therapeutic is effective on aged AChE. Our research focuses on re-activation of the aged AChE using Quinone methides(QM), using computational methods to perform molecular dynamics on QMs and aged AChE.

Co-Authors: Ryan McCauslin

Water Adsorption on Olivine(010) surface
Tingting Liu, The Ohio State University

Olivine minerals ([Mg,Fe]2SiO4) in the deep earth could promote the generation of abiotic hydrocarbons. As a first step towards understanding CO2 surface chemistry at the aqueous surfaces in a Fisher-Tropsch Type (FTT) reaction, we examined the energetics of water adsorption on olivine(010) surface using density functional theory (DFT) calculations. Severals effects have been identified that lead to the different favorabilities of water adsorption with different metal dopants, including the common alkaline earth (AE) elements and transition metals (TM) seen in natural olivine. Our work provides a detailed picture of water interaction with olivines at molecular level.

Rank-based inference of pollen type abundance using a multi-locus metabarcoding approach
Rodney Richardson, The Ohio State University

Pollen analysis, or palynology, is useful for determining preferred pollinator forage, authenticating apicultural products and monitoring allergenic pollen dispersal. Metabarcoding could make palynology more tractable, however, comparative studies are needed to test the strengths and weaknesses of metabarcoding approaches. We applied metabarcoding, targeting the ITS2, matK and rbcL loci, alongside traditional microscopic palynology to characterize six samples of bee-collected pollen. We found significant rank-based associations between the relative abundance of pollen types within our samples as inferred by the two methods. Results suggest metabarcoding data from plastid loci, as opposed to ribosomal loci, are more reliable for quantitative palynology.

An Ab Initio Method for Improving Atom Probe Tomography Reconstructions
Travis Withrow, The Ohio State University

Atom Probe tomography can theoretically provide 3D, atom-by-atom characterization of samples. Having this capability would allow materials researchers to more easily link material properties to micro structure which has the potential to accelerate materials development. Unfortunately, a lack of understanding of the instrument process undermines current reconstruction algorithms, leading to the artifacts prevalent in current literature. We use supercomputer resources to examine atomic evaporation using density functional theory and develop a model for this process. Our models will be used in higher level simulations as part of developing a new, iterative reconstruction algorithm for atom probe data.

Kinetic Monte Carlo simulation for thermal reduction of PdO(101) surface
Minkyu Kim, The Ohio State University

In this work, thermal reduction of PdO(101) surface is closely investigated. To do this study, the Density Functional Theory calculation (DFT) and kinetic Monte Carlo (kMC) simulation are used. From the DFT calculation, reaction mechanism of O2 on the surface is investigated and energetic data, including diffusion energy barrier, reaction energy barrier and desorption energy barrier, are obtained. Further, by conducting the kMC simulation with the energetic data from the DFT calculation, connection between energetic data and overall kinetic behavior on the surface is elucidated. The results make us understand the mechanism of thermal reduction of PdO(101) surface.

Predicting the Phase Behavior of Naphthalene, Anthracene, Phenanthrene, Pyrene and Dibenzothiophene Using Molecular Simulation
Gabriel Goncalves Nogueira, Miami University

Accurate and efficient models to predict the phase-behavior of nonelectrolyte solids in a wide range of solvents are central to the design of novel separation processes. A promising design tool is the MOSCED limiting activity coefficient model which is parameterized for 133 solvents. However, before predictions may be made for a solute of interest, solute parameters are required. For novel compounds of interest, the necessary parameters are unavailable and sufficient reference data is likely unavailable. Here we explore the use of molecular simulation to generate the reference data necessary to obtain MOSCED parameters for naphthalene, anthracene, phenanthrene, pyrene and dibenzothiophene.

Co-Authors: Larissa Ferreira da Silva, Ana Karolyne Pereira Barbosa

First Principles Study of Point Defects in Sapphire
Mark Hornak, The Ohio State University

Single crystal α-Al2O3 (sapphire) is a potential candidate for optical fibers and sensors in extreme high-temperature radiation environments. Transmission of light under such conditions can be impeded by the generation of defects within the material. In order to validate sapphire, we determine the stable point defects, and their charge states, in stoichiometric sapphire. The increase in attenuation due to individual point defects was calculated using density functional theory and hybrid functional mixing. We find that oxygen and aluminum vacancies are dominant, and attenuate light in the 200-300nm range. Oxygen divacancies also show significant attenuation in the 100-200nm and 300-450nm ranges.

Statewide Users Group Agenda - June 5th, 2014

June 5th, 2014

10:00 a.m.: Coffee and Tea (BALE Conference)

10:15 a.m.: Committee Meetings

    Hardware and Operations (BALE Conference)
    Allocations (BALE Theatre (TBD))
    Software and Activities (Stutz/Buckeye Conference)

11:45 a.m.: Lunch (BALE Conference)

12:30 p.m.: Welcome—Aravind Asthagiri, Chair

12:30 p.m.: Guest Speaker, Barry Dunietz, Assistant Professor, Chemistry and Biochemistry, Kent State University. ("Two tales on computational modeling of charge transfer processes that revise understanding of measured spectra.")

1:00 p.m.: SUG Officer Election Results

1:05 p.m.: OSC Policy Change Announcements

1:10 p.m.: OSC Roadmap (hardware and services) - Dave Hudak

1:40 p.m.: Roadmap open discussion

2:00 p.m.: Lightning talks

     "Social Interactions under Incomplete Information with Heterogeneous Expectations", Chao Yang, Ph.D. Candidate, Department of Economics, Ohio State Universidy 
     "Theoretical Characterization of Urea Electrolysis on Nickel Electrodes: Effect of crystal structure”, Damilola A. Daramola, Ph.D., Ohio University
     “Fast & Accurate Quantum Chemistry Calculations for Non-Covalent Interactions”, John Herbert, Ph.D., Ohio State University
     "Exploring the influence of time and spatial resolution on the prediction of latent heat fluxes”, Renato Frasson, Ph.D., Ohio State University
     "Light-induced Protein Actions through Computer Glasses”, Hoi Ling (Calvin) Luk, Bowling Green State University
     "CAPS' CCBL: An Experiment In Collaboration”, Jeffery Campbell, Ohio State University
     "Science on the edge: Structural and dynamical studies of interfaces”, Sherwin Singer, Ph.D., Ohio State University
     "Adapting Particle-In-Cell simulations to the study of short pulse laser damage”, Robert Mitchell, Ohio State University
     "MIRG: Multiphysics Interactions Research Group”, Jack McNamara, Ph.D., Ohio State University

3:00 p.m.: Poster session & reception

4:00 p.m.: Breakout group: December SUG meeting planning

NB: Committee reports to be made available online. 

A live stream of the meeting will be available via WebEx.

Statewide Users Group Agenda, August 8, 2013

Statewide Users Group Agenda
August 8, 2013 

10:00 a.m.: Coffee and Tea (BALE Conference)

10:15 a.m.: Committee Meetings

    Hardware and Operations (BALE Conference)
    Allocations (BALE Theater)
    Software and Activities (Stutz/Buckeye Conference)

11:45 a.m.: Lunch (BALE Conference)

12:30 p.m.: Welcome--Aravind Asthagiri, Chair

12:30 p.m.: Guest Speaker, Lisa M. Hall, Assistant Professor, HC Slip Slider Professorship, Chemical and Biomolecular Engineering, The Ohio State University, "Coarse-Grained Modeling of Ionomers and Salt-Doped Block Copolymers"

1:00 p.m.: OH-Tech/OARnet and OSC Update--Pankaj Shah, Executive Director

1:20 p.m.: Allocations Committee Update--Christopher Hadad

1:30 p.m.: Supercomputing Update--Doug Johnson

1:40 p.m.: IntelSim Launch--Alan Chalker

1:50 p.m.: Research Update--Dave Hudak

2:000 p.m.: User Support, Education, and Training Update--Brian Guilfoos

2:10 p.m.: Approval of Minutes and Remarks; election results--Aravind Asthagiri

2:20 p.m.: Software Committee Report--Rick Prairie

2:30 p.m.: Hardware Committee Report--John Heimaster

Statewide Users Group Agenda, November 8, 2013

Statewide Users Group Agenda
November 8, 2013

10:00 a.m.: Coffee and Tea (BALE Conference)

10:15 a.m.: Committee Meetings

    Hardware and Operations (BALE Conference)
   *****Allocations--will take place on Thursday, December 12*****
    Software and Activities (Stutz/Buckeye Conference)

11:45 a.m.: Lunch (BALE Conference)

12:30 p.m.: Welcome--John Herbert, Vice-chair

12:30 p.m.: Guest Speaker, Daniel Lacks, Professor, Chemical Engineering, Case Western Reserve University, "Molecular simulation of interfacial properties"

1:00 p.m.: OH-Tech/OARnet and OSC Update--Pankaj Shah, Executive Director

1:15 p.m.: Allocations Committee Update--Christopher Hadad

1:25 p.m.: Industrial Update--Alan Chalker

1:35 p.m.: Research Update--Dave Hudak

1:45 p.m.: Supercomputing Update--Doug Johnson

1:55 p.m.: User Support, Education, and Training Update--Brian Guilfoos

2:05 p.m.: XSEDE Update--Karen Tomko

2:15 p.m.: Approval of Minutes and Remarks--John Herbert

2:25 p.m.: Software Committee Report--Rick Prairie

2:35 p.m.: Hardware Committee Report--John Heimaster

Statewide Users Group Minutes, April 11, 2013

Statewide Users Group Minutes, April 11, 2013

Celebrating The Ohio Supercomputer Center's 25th Anniversary, at the University Plaza Hotel

Attending: Aravind Asthagiri, Judy Gardiner, Jim Giuliani, Brian Guilfoos, John Heimaster, Anthony Johnson, Doug Johnson, Robert Marcus, Diane Milholland, Rick Prairie, Jarri Prince, Tim Prince, Sid Samsi, Sarah Sed, Keith Stewart, Kevin Wohlever,  Christa Yandrich, Yuan Zhang

 

 

Please see the slide show presentation.

 

Notes from the Hardware Committee report, John Heimaster

Discussion of downtime extension

Discussion of the question of future file structures, future storage, and integrating amodel in which customers provide financial support, while others do not, for such resources as storage. Must view the problems of computational power vis-a-vis storage. It's a fairly new situation in which experimental sciences produce significant amounts of data that must be retained for extended periods.

Older hardware must soon be retired, and these changes provide an opportunity to restructure storage.

We have a range of options. But we must give our users guidance. What incentives do we provide users to move in a particular direction. We must make decisions.

Hardware options have changed. We have to allow our users to retrieve their data, which means that data placement is key.

 

 

Documentation Attachment: 

Statewide Users Group Minutes, November 8, 2013

Statewide Users Group Minutes, November 8, 2013

 

Attending: Mike Drapcho, Jim Giuliani, Christopher Hadad, John Heimaster, Dan Lacks, Robert Marcus, Rich Markham, Russ Pitzer, Rick Prairie, Keith Stewart

 

Agenda:

Statewide Users Group Agenda
November 8, 2013  

10:00 a.m.: Coffee and Tea (BALE Conference)

10:15 a.m.: Committee Meetings

    Hardware and Operations (BALE Conference)
   *****Allocations--will take place on Thursday, December 12*****
    Software and Activities (Stutz/Buckeye Conference)

11:45 a.m.: Lunch (BALE Conference)

12:30 p.m.: Welcome--John Herbert, Vice-chair

12:30 p.m.: Guest Speaker, Daniel Lacks, Professor, Chemical Engineering, Case Western Reserve University, "Molecular simulation of interfacial properties"

1:00 p.m.: OH-Tech/OARnet and OSC Update--Pankaj Shah, Executive Director

1:15 p.m.: Allocations Committee Update--Christopher Hadad

1:25 p.m.: Industrial Update--Alan Chalker

1:35 p.m.: Research Update--Dave Hudak

1:45 p.m.: Supercomputing Update--Doug Johnson

1:55 p.m.: User Support, Education, and Training Update--Brian Guilfoos

2:05 p.m.: XSEDE Update--Karen Tomko

2:15 p.m.: Approval of Minutes and Remarks--John Herbert

2:25 p.m.: Software Committee Report--Rick Prairie

2:35 p.m.: Hardware Committee Report--John Heimaster

 

Guest Speaker: Daniel Lacks, Professor Chemical Engineering, Case Western Reserve University, "Molecular simulation of interfacial properties"

see attachment

Slides from meeting

see attachment