Time | Session |
---|---|
9:30 a.m. - 10:00 a.m. |
Hardware Committee Meeting (led by John Heimaster) |
10:00 a.m. - 10:05 a.m. |
Welcome |
10:05 a.m. - 10:35 a.m. |
Flash Talks
|
10:35 a.m. - 11:20 a.m. |
Keynote Address |
11:20 a.m. - 12:00 p.m. |
Ab Initio Study of Proton Transport in Protic Ionic Liquids, Research done using OSC's resources |
12:00 p.m. - 1:00 p.m. |
Lunch (in person only) Posters:
|
1:00 p.m. - 1:45 p.m. | OSC Updates |
1:45 p.m. - 3:00 p.m. |
Afternoon Presentations
|
3:00 p.m. |
Adjourn |
Time | Session |
---|---|
9:30 a.m - 10:00 a.m. |
Hardware Committee Meeting (led by John Heimaster) |
10:00 a.m. - 11:00 a.m. |
Breakouts
|
11:00 a.m. - 11:15 a.m. | Break |
11:15 a.m. - 12:15 p.m. |
Keynote Address Program Officer, Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) Program Director, Research Coordination Networks: Fostering and Nurturing a Diverse Community of CI Professionals (RCN:CIP) |
12:15 p.m. - 1:15 p.m. |
Lunch (in person only) Networking |
1:15 p.m. - 2:15 p.m. | OSC Welcome & Presentation |
2:15 p.m. - 3:15 p.m. | Flash Talks |
3:15 p.m. - 3:30 p.m. |
Flash Talks Winner Announced |
A very special thank you to our Flash Talk competition participants:
Winner: Pranav Jois, The Ohio State University
"Coarse-grained modeling of side-chain liquid crystal polymers: effect of the architectural properties on phase behavior"
Daniyal Khan, Youngstown State University
"Missing Data Imputation using Graph Representation Learning"
Net Zhang, The Ohio State University
"Franklin County Opioid Activity Level"
Yuan Xue, Oberlin College & Conservatory
"A DFT Study of the Gas Reaction MOVPE Growth of InN"
Time | Session |
---|---|
10:00 a.m - 12 p.m. |
Keynote Address: OSC Update |
12 - 12:30 p.m. | Break |
12:30 - 2:30 p.m. | Flash Talks + Poster Session |
Thanks to the generosity of Intel, all attendees can order lunch to be delivered. Sometime between 10:00 and 10:30 a.m., log in to the Zoom link you were emailed to receive the voucher.
Jeff McVeigh's career has focused on enriching lives through the magic of Intel technologies and products, starting with the earliest days of Internet video (late 90's) and culminating today in bringing Intel's high-performance computing and visual cloud product lines to life. He has worked with the brightest minds to create industry-shaping technologies and products including multiple generations of Intel integrated graphics, Intel's first server GPU, OpenVINO inference engine, and oneAPI programming model and toolkits.
In his current role, he is responsible for Intel's Super Compute Group, which encompasses Intel's HPC and datacenter GPU business and products with a software-first approach to enable developers to realize the value of Intel's Xeon and Xe GPU architectures.
Jeff was recently named one of HPCwire's People to Watch 2022
Andrew Paluch, Miami University (Poster): Predicting octanol/water partition coefficients using molecular simulation for the SAMPL7 challenge: comparing the use of neat a
Eric Hantz, The Ohio State University (Poster): Actives-Based Receptor Selection Strongly Increases Success Rate in Structure-Based Drug Design
Time | Session |
---|---|
10:30 a.m - 11:15 a.m. |
OSC Presentation |
11:15 a.m. - 12 p.m. | Keynote provided by Dell Technologies: Fast Computers, Big Data, and Lots of Little Devices: How We Will Make Better, Faster Discoveries & Decisions |
12 - 12:30 p.m. | Break |
12:30 - 2:30 p.m. | Flash Talks + Poster Session |
Thanks to the generosity of Dell, all attendees can visit Uber Eats before lunch and order lunch to be delivered. Login to the zoom link you were emailed sometime between 10:00 and 10:30AM to receive the Uber Eats voucher (you will need to have a Uber account or sign up for one).
Kamalnath Kadirvel, The Ohio State University (flash talk): Texture Evolution in Metal Additive Manufacturing
Louis Christensen, The Ohio State University (flash talk): Investigating Heat Transfer in a Straight Cooling Passage Using Transient Infrared Temperature Data and URANS Conjugate Heat Transfer
Alina Lazar, Youngstown State University (flash talk): Accelerating the Inference Time of Machine Learning-based Track Finding Pipeline
Himanshu Singh, Ohio University (flash talk): Predicting the Equilibrium Adsorption Morphologies of Surfactant Molecules on Metal Surfaces via Advanced MD Simulations
Anna Schuler, The Ohio State University (poster): Effects of graft density on entanglement number and type in model polymer-grafted nanoparticle monolayers
Aurelia Moses, Youngstown State University (poster): The Mechanism of Charge Transfer in Imidazole-Solvated Protic Ionic Liquid Systems
Theresia Yazbeck, The Ohio State University (poster): Modeling Fluxes, Fate And Transport Of Ammonia Emission From Egg Production And Manure Management Facilities
Time | Session |
---|---|
10:30 a.m - 11:15 a.m. |
OSC Presentation |
11:15 a.m. - 12 p.m. | Keynote provided by Dell Technologies: Fast Computers, Big Data, and Lots of Little Devices: How We Will Make Better, Faster Discoveries & Decisions |
12 - 12:30 p.m. | Break |
12:30 - 2:30 p.m. | Flash Talks + Poster Session |
Kamalnath Kadirvel, The Ohio State University (flash talk): Texture Evolution in Metal Additive Manufacturing
Louis Christensen, The Ohio State University (flash talk): Investigating Heat Transfer in a Straight Cooling Passage Using Transient Infrared Temperature Data and URANS Conjugate Heat Transfer
Alina Lazar, Youngstown State University (flash talk): Accelerating the Inference Time of Machine Learning-based Track Finding Pipeline
Himanshu Singh, Ohio University (flash talk): Predicting the Equilibrium Adsorption Morphologies of Surfactant Molecules on Metal Surfaces via Advanced MD Simulations
Anna Schuler, The Ohio State University (poster): Effects of graft density on entanglement number and type in model polymer-grafted nanoparticle monolayers
Aurelia Moses, Youngstown State University (poster): The Mechanism of Charge Transfer in Imidazole-Solvated Protic Ionic Liquid Systems
Theresia Yazbeck, The Ohio State University (poster): Modeling Fluxes, Fate And Transport Of Ammonia Emission From Egg Production And Manure Management Facilities
First place:
Theresia Yazbeck, The Ohio State University
"Modeling Fluxes, Fate And Transport Of Ammonia Emission From Egg Production And Manure Management Facilities"
Second place (tie):
Alina Lazar, Youngstown State University
"Accelerating the Inference Time of Machine Learning-based Track Finding Pipeline"
Himanshu Singh, Ohio University
"Predicting the Equilibrium Adsorption Morphologies of Surfactant Molecules on Metal Surfaces via Advanced MD Simulations"
Congratulations to our winners and thank you to everyone who presented.
Calls to action
We encourage you to remain engaged with OSC in between SUG conferences. Discover how you can make use of available services, learn about OSC’s impact, help shape future plans and find ways to engage with OSC
Thursday, April 5th
9:00 - 10:00 am |
Hardware and Operations Committee Meeting (non-members welcome) Software Committee Meeting (non-members welcome) |
|
10:00 - 11:00 am
|
Breakout Sessions (selected at registration) 1. OnDemand and App Development 2. Big Data 4. SOCC Tour |
|
11:00 - 11:45 am |
Keynote Address: |
|
11:45 am - 12:00 pm |
Lunch Pick-up |
|
12:00 - 12:55 pm |
OSC: Welcome and Presentation |
|
12:55 - 1:00 pm |
Break |
|
1:00 - 1:50 pm |
Flash Talks: Session 1 |
|
1:50 – 2:00 pm |
Break |
|
2:00 - 2:50 pm |
Flash Talks: Session 2 |
|
2:50 - 3:00 pm | Break | |
3:00 - 4:45 pm |
Poster Session Networking and Hors D'oeuvres |
|
4:45 pm |
Poster and Flash Talk Winner Announcement |
|
|
Flash Talk Session 1
Flash Talk Session 2
Poster Session
4:00 - 5:00 pm |
Software Committee Meeting (non-members welcome) |
6:00 - 7:30 pm |
SUG Executive Meeting (members only) |
8:15 - 9:00 am 9:00 - 10:00 am
11:45 am - 12:00 pm
4:45 pm
4:45 - 5:30 pm
5:30 pm |
SOCC Tour (closed access)
Breakout Sessions (determined by which you signed up for)
Keynote Address: NVIDIA
Flash Talks: Session 2
Poster Session Networking and Hors D'oeuvres OSC Help: Available
Poster and Flash Talk Winner Announcement
SOCC Tour: Closed Access
Social Hour (not sponsored by OSC): |
|
Jonathan Bentz is a Senior Solutions Architect with NVIDIA, focusing on Higher Education and Research customers. In this role he works as a technical resource to support and enable the use of GPU computing. Jonathan has a background in computational chemistry and software engineering and frequently conducts hands-on programming sessions for CUDA, OpenACC and GPU-accelerated deep learning. With OSC’s recent GPU adoption, Jonathan will discuss current advances in GPU hardware and software which directly impact accelerated applications in HPC and have been a catalyst in the rapid advancement of deep learning technologies.
Please see our detailed agenda.
Statewide Users Group Conference Agenda - April 9, 2020
4:00 - 6:00 pm |
Allocations Committee Meeting (members only) |
6:00 - 7:30 pm |
SUG Executive Meeting (members only) |
All Day
9:00 - 10:00 am
12:00 - 12:15 pm
12:15 - 1:05 pm
1:05 - 1:15 pm
1:15 - 2:15 pm
2:15 - 3:15 pm
4:45 pm |
OSC Help will have a booth set up
Breakfast Assortment Software Committee Meeting (non-members welcome)
Breakout Sessions (determined by which you signed up for) 4. Birds of a Feather: SIMCenter: Utilizing Online Classroom Space Outside the Traditional Class
Flash Talks: Session 2 Networking and Hors D'oeuvres
Poster and Flash Talk Winner Announcement |
|
Anthony Dina serves as the North America Director of Data Analytics at Dell EMC. He leads a team of solutions architects that synthesize the tsunami of new datatypes (machine, application, person-driven) with traditional systems of record. Their expertise in big data, data warehouse modernization and analytic modeling, artificial intelligence helps customers succeed in the era of Digital Transformation. This work not only involves intellectual property from Dell EMC but also from partners like Cloudera, HortonWorks, Splunk, Intel, NVIDIA and SAP. Prior to this, he served as Executive Director of Strategy and Director of Solutions Marketing. He has earned a Masters of Business Administration from the University of St. Thomas and a Masters of Fine Art from Cranbrook Academy of Art.
Flash Talk Session 1
Flash Talk Session 2
Poster Session
Statewide Users Group Conference Agenda - October 17, 2019
4:00 - 6:00 pm |
Allocations Committee Meeting (members only) |
6:00 - 7:30 pm |
SUG Executive Meeting (members only) |
9:00 - 10:00 am
10:00 - 11:00 am
12:00 - 12:15 pm
3:15 - 4:45 pm
4:45 pm |
Breakfast Assortment Software Committee Meeting (non-members welcome)
4. Tour of the SOCC Keynote Address: Raj Krishnamurthy Flash Talks: Session 2 Networking and Hors D'oeuvres OSC Help: Available
Poster and Flash Talk Winner Announcement |
|
Raj Krishnamurthy, an IBM STSM (Senior Technical Staff Member), IBM Master Inventor and Elected Member of the IBM Academy of Technology, designs and develops system stacks consisting of software and hardware elements for emerging and contemporary AI workloads. He has been a technical staff member in the Systems division at IBM since 2006. His work has impacted several platforms, software products, and roadmaps in IBM—both on mainframes and Power Systems. Raj holds 100+ patents and has written a number of external peer-reviewed publications. He has received best paper awards, Best of IBM award, Outstanding Technical Achievement Awards and an IBM Corporate Award. Raj holds a PhD in computer science and an MS/BS degree in electrical engineering. Raj evangelizes the benefits of Enterprise AI at various conferences, meetups and on twitter using the hash-tag #AIMeansBusiness and #BornOnPower.
Flash Talk Session 1
Youssef Golestani
Kent State
Surfaces Formed by Liquid Crystal Elastomer Coating
Flash Talk Session 2
Poster Session
4:00 - 6:00 pm |
Allocations Committee (members only) |
6:00 - 7:30 pm |
SUG Executive Meeting (members only) |
9:00 - 10:00 am
10:00 - 11:00 am
2:00 - 2:50 pm
3:00 - 4:45 pm
4:45 pm |
Breakfast Assortment Hardware and Operations Committee Meeting (non-members welcome) Software and Activities Committee Meeting (non-members welcome)
2. OSC Campus Champions 3. Data Analytics 4. Client Portal
Break
Flash Talks: Session 2
Break
Poster Session Networking and Hors D'oeuvres
Poster and Flash Talk Winner Announcement |
|
Russ Fromkin is the Americas HPC and HPDA Sales Director for the Intel
Corporation. Russ and his team are responsible for helping technical computing
and data analytics customers implement cutting edge technologies developed
by Intel Corporation. Russ joined Intel Corporation in 1999 as part of an
acquisition of Dialogic Corporation. Previous to his current role, Russ helped
lead Information Assurance, HPC and Cloud Computing activities for the Intel
Federal team. Prior to the acquisition, Russ developed and managed the ISV
program for Dialogic. Russ holds a BA from The Johns Hopkins University.
Wednesday, September 27th
2:00 - 5:00 pm |
SUG Executive Meeting (members only) |
5:30 - 8:30 pm |
OSC/OARnet 30th Anniversary Celebration |
Thursday, September 28th
8:15 - 9:00 am |
SOCC Tour (invitation only) |
|
9:00 - 10:00 am
|
Hardware and Operations Committee Meeting (non-members welcome) Software Committee Meeting (non-members welcome) |
|
10:00 - 11:00 am |
Breakout Sessions (determined by which you signed up for) |
|
11:00 - 11:45 am |
Keynote Address: Bryan C. Carstens |
|
11:45 am - 12:00 pm |
Lunch Pick-up |
|
12:00 - 12:05 pm |
OSC: Welcome and Presentation |
|
12:55 - 1:00 pm |
Break |
|
1:00 - 1:50 pm |
Flash Talks: Session 1 |
|
1:50 – 2:00 pm |
Break |
|
2:00 - 3:00 pm |
Flash Talks: Session 2 |
|
3:15 - 4:45 pm |
Poster Session Networking and Hors D'oeuvres |
|
4:45 pm |
Poster and Flash Talk Winner Announcement |
|
5:00 pm |
Social Hour (not sponsored by OSC): |
|
Flash Talks
Poster Sessions
Thursday, April 18th
9:00 - 10:00 am |
Breakfast Assortment Hardware and Operations Committee Meeting (non-members welcomed) Software Committee Meeting (non-members welcomed) |
|
10:00 - 11:00 am
|
Breakfast Assortment Breakout Sessions (selected at registration)
|
|
11:00 - 11:45 am |
|
|
11:45 am - 12:00 pm |
Lunch Pick-up |
|
12:00 - 12:55 pm |
Keynote Address |
|
12:55 - 1:00 pm |
Break |
|
1:00 - 1:50 pm |
|
|
1:50 – 2:00 pm |
Break |
|
2:00 - 2:50 pm |
|
|
2:50 - 3:00 pm | Break | |
3:00 - 4:45 pm |
Networking Hors D'oeuvres |
|
4:45 pm |
|
|
|
Santosh Rao is responsible for NetApp’s AI and data engineering products and solutions business. He works closely with the AI solution ecosystem across GPU, compute, software, consulting and channel partners as well as customers worldwide. He is a regular speaker at various events and writes a blog on the data pipeline for AI.
He has held a number of roles within NetApp and led the original ground-up development of Clustered ONTAP SAN for enterprise workloads. Over the years, he has led to market a number of follow-on products for NetApp involving data migration, virtualization, distributed systems, management by SLO, application integration and most recently, all flash SAN technologies, NoSQL and big data solutions.
Prior to joining NetApp, Santosh was a Master Technologist for HP and led the development of a number of storage and operating system technologies for HP including the development of their first generation products for a variety of storage and OS technologies over the years.
Software and Activities Committee
Hardware and Operations Committee
Arif Hossain, Graduate Research Associate at The Ohio State University
"Sweeping Jet Film Cooling and Impingement Cooling for Gas Turbine Heat Transfer Application"
Due to the increased freedom in additive manufacturing, the complex internal and external geometries of the turbine blade can be leveraged to utilize innovative cooling designs to address some of the shortcomings of current cooling technologies. The sweeping jet film cooling has shown some promise to be an effective method of cooling where the coolant can be brought very close to the blade surface due to its sweeping nature. A series of experiments and numerical calculations were performed using a fluidic oscillator that can generate an oscillating jet without any moving parts. Adiabatic cooling effectiveness, convective heat transfer coefficient, thermal field, and discharge coefficient were estimated over a range of blowing ratios and freestream turbulence using computational fluid dynamics (CFD). Results were compared with a conventionally shaped hole (777-hole) and the sweeping jet hole shows improved cooling performance in the lateral direction. Large Eddy Simulation (LES) and Unsteady RANS (URAN) calculations confirmed that the sweeping jet creates two alternating vorticies that do not have mutual interaction in time. When the jet sweeps to one side of the hole exit, it acts as a vortex generator as it interacts with the mainstream flow. This prevents the formation of the counter-rotating vortex pair (CRVP) and allows the coolant to spread in the lateral direction. The results obtained from the CFD were utilized to design the sweeping jet film cooling hole for more representative turbine vane geometry. Experiments were performed in a low-speed linear cascade and a high-speed transonic cascade facility. Results showed that the sweeping jet hole has higher cooling effectiveness in the near hole region compared to the shaped hole at high blowing ratios.
Spatial uniformity is identified as a major issue for impingement cooling at the leading edge of the turbine blade which can be significantly improved by sweeping jet impingement cooling. A series of numerical simulations were also performed with a fluidic oscillator for impingement cooling on a flat surface and a curved surface. URANS simulations were adopted to investigate the unsteady sweeping jet impingement cooling in a faired cylinder leading edge model at an engine-relevant Biot number (Bi). Heat transfer performance was studied at varying coolant mass flow rates, jet-to-wall spacing (H/D), jet pitch (P/D), and freestream turbulence. The effect of varying aspect ratio (AR) of the sweeping jet geometries was also studied. Numerical simulations were performed to understand the internal fluid dynamics of the impinging sweeping jet, the effect of surface curvature and exit fan angle of the device. Results show that the peak heat transfer for an impinging sweeping jet is lower than the steady jet. The sweeping action of the jet augments local turbulence in the jet shear layer and heats up the core flow as it interacts with the target wall, resulting in a drop in local Nusselt number (Nu). However, the overall cooling uniformity improves due to the sweeping motion of the jet which could be instrumental for gas turbine cooling application where uniform surface temperature is desirable.
Alexandria Volkening, Post Doctoral Fellow at The Ohio State University
"Forecasting Elections with Mathematical Models of Contagion Spread"
Election forecasting involves polling likely voters, making assumptions about voter turnout, and accounting for features such as state demographics and voting history. While U.S. elections are decided at the state level, errors in forecasting are correlated between states. Here we develop a data-driven framework for forecasting elections from the perspective of dynamical systems. By borrowing ideas from epidemiology and using OSC resources to fit model parameters, we combine a compartmental model of contagion spread with polling data to forecast gubernatorial, senatorial, and presidential elections as accurately as popular pollsters.
Zhiping Zhong, Post Doctoral Fellow at The Ohio State University
"Viruses Potentially Enhance Hosts Cold- and Salt-Tolerance"
Viruses in polar cryopeg and sea ice were largely ignored. Here we characterized, for the first time, the viral communities in such extreme environments with large metagenomic dataset analyzed using OSC supercomputers. Most (88.3%) viruses were novel. Viral communities varied between environments and across sea ice depths, and significantly correlated with microbial profiles. Viruses likely infected dominant cold- and salt-tolerant microbes and contributed to their hosts’ responses to cold and salt stresses through modulating microbial metabolisms. This study extends the exploration of the virosphere deep into ancient cryopeg and reveals viral impacts on microbial functions in cold and salt environments.
Harper McMinn-Sauder, Graduate Research Associate at The Ohio State University
"Measuring Honey Bee Utilization of Conservation Reserve Program (CRP) Pollinator Plantings Using DNA Metabarcoding"
Since its introduction in the 1980s to help improve soil quality on agricultural land, the Conservation Reserve Program (CRP) has had a number of positive ecological effects, including reduced habitat fragmentation and increased natural forage for pollinators. One present goal of CRP management is to increase pollinator abundance and diversity by planting native seed mixes that promote foraging. This high-quality habitat provides an excellent opportunity to study honey bee nutrition and identify if floral resources from CRP plantings are being collected by honey bees. This study aims to highlight the primary sources of honey bee forage on CRP land in the northern Midwest. Using citizen science methods, we received pollen trapped samples from beekeepers in Ohio, South Dakota, Indiana, Illinois, and Michigan. Pollen homogenization and metabarcoding methods were used to analyze and quantify pollen collected at different points throughout the season. Results indicate that honey bees located near CRP properties are utilizing diverse genera of pollen floral resources, suggesting that CRP may provide resources comparable to what bees would experience in an undisturbed habitat. In addition, pollen from seven genera in 2016 and eight genera in 2017 was identified from the CRP pollinator seed mix, indicating that honey bees are utilizing this resource. These results have implications regarding colony management as well as land management for foraging honey bees.
Please see our press release and separate OSC Facebook album for additional photos.
Wednesday, April 4th
4:00 - 6:00 pm |
Allocations Committee (members only) |
|
6:00 - 7:30 pm |
SUG Executive Committee (members only) |
9:00 - 10:00 am |
Hardware and Operations Committee Meeting (non-members welcomed) Software Committee Meeting (non-members welcomed) |
|
10:00 - 11:00 am
|
Breakout Sessions (selected at registration) 1. OnDemand and App Development 2. Big Data 4. SOCC Tour |
|
11:00 - 11:45 am |
Keynote Address: |
|
11:45 am - 12:00 pm |
Lunch Pick-up |
|
12:00 - 12:55 pm |
|
|
12:55 - 1:00 pm |
Break |
|
1:00 - 1:50 pm |
|
|
1:50 – 2:00 pm |
Break |
|
2:00 - 2:50 pm |
|
|
2:50 - 3:00 pm | Break |
|
3:00 - 4:45 pm |
Networking and Hors D'oeuvres |
|
4:45 pm |
Poster and Flash Talk Winner Announcement |
|
|
Andrew Siegel is a senior scientist at Argonne National Laboratory, with appointments in both the Mathematics/Computer Science and Nuclear Engineering divisions. For the past decade, he has led Argonne's program in advanced reactor modeling and simulation. His research has focused on developing improved methods to model the physics of advanced reactors, including mixing, neutron/fluid coupling, and innovative computational approaches to stochastic methods for neutron transport.
Andrew has taught more than 60 courses at the University of Chicago over the past 20 years, including high-performance computing, numerical methods, stochastic simulation, and computer architecture. He holds an undergraduate degree from the University of Chicago and a Ph.D. in astrophysics from the University of Colorado Boulder. For the past 9 years, Andrew has also held the position of Resident Dean of Burton-Judson at the University of Chicago.
Flash Talk Session Winner:
Lifeng Jin, Graduate Student at The Ohio State University
"Unsupervised Depth-bounded Grammar Induction Model for PCFG with Inside-sampling"
Grammar acquisition or grammar induction for natural languages has been of interest to linguists and cognitive scientists for decades. Unfortunately, previous attempts converged to weak modes of a very multimodal distribution of grammars. Depth-bounding a grammar has been a popular technique for applying cognitively motivated restrictions to grammar induction to limit the search space of grammars. This work introduces a Bayesian depth-bounded grammar induction model with inside-sampling (DIMI) from raw text. Several analyses are performed in this work showing that depth-bounding is indeed effective in limiting the search space of the inducer. Results are also presented for successful unbounded PCFG induction as well as bounded induction on three different languages showing that our model is able to produce parse trees better than or competitive with state-of-the-art constituency grammar induction models in terms of parsing accuracy.
Flash Talk Session Runner-Up:
Jorge Torres, Graduate Student at The Ohio State University
"The role of HPC in the radio-detection of astrophysical neutrinos"
The radio-detection of neutrinos opens a window to unravel mysteries of the most energetic particles that arrive to Earth from space: astrophysical neutrinos, which can help us to answer open questions in fundamental physics, astrophysics and cosmology. Understanding the physics behind radio detection, designing experiments and analyzing experimental data often relies on the use of high-performance computing (HPC). In this talk, we will present how HPC has helped us, and will continue to play an important role, in our main goal: the detection of astrophysical neutrinos.
Poster Session Winner:
Adriaan Riet, Graduate Student at Case Western Reserve University
"Enhanced Diffusion in an MgO Grain Boundary Through Molecular Dynamics Simulations "
Grain boundary diffusion could be the driving mechanism by which metals in the core mix within the mantle. Understanding the magnitude and limits of diffusion can yield insight into the composition of the core mantle boundary, but the conditions present in the inner earth are difficult to achieve experimentally. We report the self-diffusion constant of magnesium in a magnesium oxide grain boundary as a function of temperature and pressure, obtained through molecular dynamics simulations.
Poster Session Runner-Ups:
Masood Delfarah, Graduate Student at The Ohio State University
"Recurrent Neural Networks for Cochannel Speech Separation in Reverberant Environments "
Speech separation is a fundamental problem in speech and signal processing. A particular challenge is monaural separation of cochannel speech, or a two-talker mixture, in a reverberant environment. In this paper, we study recurrent neural networks (RNNs) with long short-term memory (LSTM) in separating and enhancing speech signals in reverberant cochannel mixtures. Our investigation shows that RNNs are effective in separating reverberant speech signals. In addition, RNNs significantly outperform deep feedforward networks based on objective speech intelligibility and quality measures. We also find that the best performance is achieved when the ideal ratio mask (IRM) is used as the training target in comparison with alternative training targets. While trained using reverberant signals generated by simulated room impulse responses (RIRs), our model generalizes well to conditions where the signals are generated by recorded RIRs.
Rosario Distefano, Postdoctorate at The Ohio State University
"miREpiC: miRNA Editing Profiling in Cancer "
RNA editing is emerging as a new player in cancer biology (PubmedID:26439496;26440895). Specifically, editing in microRNAs, established gene regulators, could aid in cancer prognosis and therapy (28411194). Expanding on our previous works (23044546;27298257), we leveraged on the NIH TCGA dataset (phs000178.v9.p8, comprising ~11K samples over 33 cancer types) and carried out a computational analysis to characterize and compare profiles of edited microRNAs, dysregulated across different cancer types. Our goal is to elucidate the potential of the RNA modification phenomena as potential marker for the classification of cancer subtypes as well as provide functional characterization of the shifted gene targetome.
Please see our press release and separate OSC Facebook album for additional photos.
4:00 - 5:00 pm |
Software Committee Meeting (non-members welcome) |
6:00 - 7:30 pm |
SUG Executive Meeting (members only) |
8:15 - 9:00 am 9:00 - 10:00 am
10:00 - 11:00 am
11:45 am - 12:00 pm
4:45 pm
5:30 pm |
SOCC Tour (closed access)
Breakout Sessions (determined by which you signed up for)
Keynote Address: NVIDIA
Networking and Hors D'oeuvres OSC Help: Available
Poster and Flash Talk Winner Announcement
SOCC Tour: Closed Access
Social Hour (not sponsored by OSC): |
|
Jonathan Bentz is a Senior Solutions Architect with NVIDIA, focusing on Higher Education and Research customers. In this role he works as a technical resource to support and enable the use of GPU computing. Jonathan has a background in computational chemistry and software engineering and frequently conducts hands-on programming sessions for CUDA, OpenACC and GPU-accelerated deep learning. With OSC’s recent GPU adoption, Jonathan will discuss current advances in GPU hardware and software which directly impact accelerated applications in HPC and have been a catalyst in the rapid advancement of deep learning technologies.
Please see our detailed agenda.
Flash Talk Session Winner:
Sandip Mazumder, Associate Professor at The Ohio State University
"Phonon Boltzmann Transport Equation Based Modeling of Time Domain Thermo-Reflectance Experiments"
Time Domain Thermo-Reflectance (TDTR) experiments have been recently identified as a viable pathway toward extracting the phonon mean free path spectrum of semiconductor materials. However, this requires an intervening model. It is now widely believed that the frequency and polarization dependent phonon Boltzmann Transport Equation (BTE) is the most suitable model for this purpose. In this study, TDTR experiments are simulated using large-scale parallel computations of the phonon BTE in a two-dimensional computational domain. Silicon is used as the candidate substrate material. Simulations are performed for multiple pulse and modulation cycles of the TDTR pump laser. This requires resolution of a picosecond laser pulse within a computational timeframe that spans several hundreds of nanoseconds. The metallic transducer layer on top of the substrate is modeled using the Fourier law and coupled to the BTE within the silicon substrate. Studies are conducted for four different laser spot sizes and two different modulation frequencies. The BTE results are fitted to the Fourier law, and effective thermal conductivities are extracted. It is demonstrated that the time delay of the probe laser could have a significant effect on the fitted (extracted) thermal conductivity value. The modulation frequency is found to have negligible effect on the thermal conductivity, while the spot size variation exhibits significant impact. Both trends are found to be in agreement with experimental observations. The thermal conductivity accumulation function is also computed, and the effect of the mean free path spectrum on the thermal conductivity suppression is delineated.
Flash Talk Session Runner-Up:
Gregory Wheeler, Graduate Student at The Ohio State University
"Identification of Carnivory in Plants via Genomic Functional Annotation"
The purpose of this project was to identify evidence of carnivory in plants using functional gene annotation. Illumina sequence reads of a carnivorous pitcher plant Sarracenia alata were processed and assembled with Velvet, with contigs assigned function via Blast2GO. These data, along with annotations from other carnivorous and non-carnivorous plants, were scored by representation of functions previously identified as related to carnivory. Carnivorous plants were found to have an overabundance of certain enzymes relative to most non-carnivorous plants; however, the non-carnivorous close relatives of these plants also showed overrepresentation, indicating that phylogenetic effects may play a role as well.
Poster Session Winner:
Ryan Lundgreen, Postodctorate at The Ohio State University
"Heat Transfer and Deposition in Gas Turbine Engines"
This poster highlighted some of the major research efforts of the Turbine Aerothermodynamics Laboratory. These research efforts include novel cooling technologies such as reverse cooling holes, sweeping jet film cooling and impingement heat transfer, and particle deposition modeling with mesh morphing.
Poster Session Runner-Up:
Melanie Aprahamian, Graduate Student at The Ohio State University
"Incorporation of Mass Spectrometry Covalent Labeling Data into Rosetta Protein Structure Prediction"
The Rosetta Commons software suite is used for modeling and prediction of protein structures. Prediction of protein structure is done in an ab initio fashion and is based upon the primary amino acid sequence of a protein where a score is given to each predicted structure. Currently, Rosetta is only accurate for proteins with fewer than 150 amino acids. In order to improve the accuracy of protein structures predicted using Rosetta, a new score term is being incorporated that takes into account specific amino acid solvent exposure based upon covalent labeling mass spectrometry data.
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4:00 - 6:00 pm |
Allocations Committee (members only) |
6:00 - 7:30 pm |
SUG Executive Meeting (members only) |
9:00 - 10:00 am
11:00 - 11:45 am
2:00 - 2:50 pm
2:50 - 3:00 pm
3:00 - 4:45 pm
4:45 pm |
Breakfast Assortment Hardware and Operations Committee Meeting (non-members welcome) Software and Activities Committee Meeting (non-members welcome)
2. OSC Campus Champions 3. Data Analytics 4. Client Portal
Break
Networking and Hors D'oeuvres
Poster and Flash Talk Winner Announcement |
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Dylan Wood, Graduate Research Associate at The Ohio State University
"Modeling of Failure Mechanisms for Flood Control Systems in a Hydrodynamic Storm Surge Model"Risk-informed decision making plays a critical role in mitigation of loss of life and assets during a catastrophic event such as the land fall of a hurricane or tropical cyclone. In this case, many factors, such as proximity to coastline and resilience of structures, influence the probable degree of risk posed to coastal regions by storm surge, though perhaps the most relevant and poorly understood factor is the ability of flood control systems to withstand forces attributed to storm surge and to protect coastal regions from inundation. We present on the development and application of techniques for resolving and assessing the risk of failure for flood defense structures within a large scale hydrodynamic storm surge model for forecasting risks posed by tropical cyclone impacts.
Megan Smith, Graduate Fellow at The Ohio State University
"Disentangling the Process of Speciation Using Machine Learning"
Historically, investigations into the processes driving speciation have largely been isolated from systematic investigations into species limits. Recent advances in sequencing technology have led to a rapid increase in the availability of genomic data, and this, in turn, has led to the introduction of many novel methods for species delimitation. However, these methods have been limited to divergence-only scenarios and have not attempted to evaluate complex modes of speciation, such as those that include gene flow during early stages of divergence (sympatric speciation) or population size changes (founder effect speciation). This shortcoming is primarily the result of the computational demands of evaluating such models. To address this, we introduce delimitR, an R-package that enables biologists to infer species boundaries and evaluate the demographic processes that may have led to speciation. delimitR uses the binned multidimensional Site Frequency Spectrum and a machine-learning algorithm (Random Forests) to compare speciation models while minimizing the computational resources required. We use simulations to evaluate the accuracy of delimitR. When comparing models that include lineage divergence and gene flow for three populations, error rates are near zero with recent divergence times (<100,000 generations) and a modest number of Single Nucleotide Polymorphisms (SNPs; 1,500). When applied to a more complex model set (including divergence, gene flow, and population size changes), error rates are moderate (~0.15 with 10,000 SNPs), and misclassifications are generally between highly similar models.
Changlong Zou, Graduate Research Associate at The Ohio State University
"Computational Studies of Zeolite Nanosheets as Pervaporation Membranes for Ethanol Extraction"
Pervaporation is a promising approach for anhydrous ethanol extraction from dilute biomass fermentation broth. Using siliceous zeolite membranes can offer outstanding separation factors but relatively low fluxes. Zeolite nanosheets, synthesized with a thickness of a few nanometers, may overcome this limitation because of their intrinsically short diffusion paths. However, the potential of zeolite nanosheets as pervaporation membranes for ethanol extraction remains unknown. In this study, by employing molecular dynamics techniques, we demonstrated the outstanding performance of zeolite nanosheets for ethanol extraction. The ethanol flux of zeolite nanosheets was found to be orders of magnitude higher than currently available membranes reported in the literature, while a high separation factor can be still achieved. We have also discovered the critical role of nanosheet surfaces in the separation performance. The outcomes of this work are anticipated to be instrumental to the future development of zeolite nanosheet membranes.
Heather Hansen, Graduate Teaching Associate at The Ohio State University
"Using the Ohio Supercomputer Cluster to Measure Developmental Changes in Connectivity between the Amygdala Subnuclei and Occipit"Previous work in macaques has shown that connectivity from the lateral and basal amygdalar subnuclei to the occipitotemporal cortex decreases on a gradient from anterior to posterior, and refines across development. Can we delineate this connectivity in humans, and determine what functional regions might be driving it? Using Diffusion Weighted Imaging data, we ran probabilistic tractography with FSL between the amygdala subnuclei as seeds and the occipitotemporal cortical parcellations as targets. Given that connectivity between 170 parcellations was computed for each of 45 subjects, the use of parallel computing through the Ohio Supercomputer Center was essential. Results showed that the development of human amygdalar connectivity to the occipitotemporal cortex resembles that of macaques, and is especially driven by functional parcels such as PPA, PFS, LO, and OFA.
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If you couldn't make it to the SUG Mini Meeting or would like to review specific sections of the updates, you can access the recorded presentations below.
OSC is working to re-envision the way we interact with our clients through our community events. Your input is valuable in guiding this process. If you have not already, please take a moment to complete the survey provided below.
Wednesday, September 27th
2:00 - 5:00 pm |
SUG Executive Meeting (members only) |
5:30 - 8:30 pm |
OSC/OARnet 30th Anniversary Celebration |
Thursday, September 28th
8:15 - 9:00 am |
SOCC Tour (invitation only) |
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9:00 - 10:00 am
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Hardware and Operations Committee Meeting Software Committee Meeting |
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10:00 - 11:00 am |
Breakout Sessions: |
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11:00 - 11:45 am |
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11:45 am - 12:00 pm |
Lunch Pick-up |
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12:00 - 12:05 pm |
OSC: Welcome and Presentation |
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12:55 - 1:00 pm |
Break |
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1:00 - 1:50 pm |
Flash Talks: Session 1 |
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1:50 – 2:00 pm |
Break |
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2:00 - 3:00 pm |
Flash Talks: Session 2 |
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3:15 - 4:45 pm |
Poster Session Networking and Hors D'oeuvres |
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4:45 pm |
Poster and Flash Talk Winner Announcement Second Place Posters First Place Flash Talk Second Place Flash Talk |
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5:00 pm |
Social Hour (not sponsored by OSC): |
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Carstens is a longtime client of OSC. His keynote discussion presented his research into the protection of biodiversity. His presentation discussed his thesis that publicly accessible databases contain millions of data points that are relevant to the discovery and protection of biodiversity, but are currently underutilized.
“Despite millions of data points, few large-scale global analyses have been attempted because the synthesis of results across the thousands of research studies that collected these data, each using different methods and forms of analysis, is a daunting and time-consuming task,” Carstens said. “My lab proceeds by repurposing existing data using automated data analysis on processor nodes hosted by the Ohio Supercomputer Center.”
Using software that has largely been developed by lab postdoctoral researcher Tara Pelletier, Carstens presented results from several pilot studies. In terms of the number of species and the taxonomic breadth of these species, the analyses presented by Carstens are some of the largest of their kind to date. They suggest that information contained within existing biodiversity data can be extracted via parallel analyses and predictive machine learning approaches.
Flash Talks
Poster Session
Statewide Users Group Meeting 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
4:00 | Allocations Committee Meeting |
10:30 - 11:30 |
Software Committee Meeting Hardware Committee Meeting Face:Face OSCHelp |
11:30 - 12:30 | Lunch |
12:30 - 1:15 |
Keynote Address |
1:15 - 1:45 |
Invited Talk |
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 |
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.
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.
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
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
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
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
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
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.
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.
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
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
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
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
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
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.
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
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
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
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
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
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.
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
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
3:00 - 5:00 pm |
Allocations Committee Meeting |
6:00 - 7:30 pm |
SUG Executive Meeting |
10:00 - 11:00 am |
Software Committee Meeting Hardware Committee Meeting Face-to-Face with OSCHelp |
11:00 - 11:45 am |
Flash Talk Session 1 |
11:45 - 12:15 pm |
Lunch |
12:15 - 1:00 pm |
OSC Organizational Update |
1:00 - 1:40 pm |
Keynote Address Suzy Tichenor |
1:40 - 2:20 pm |
Keynote Address Dr. Daniel Lacks |
2:20 - 2:30 pm |
Break |
2:30 - 3:15 pm |
Flash Talk Session 2 |
3:15 - 5:30 pm |
Poster Session Social Networking |
5:30 pm |
Talk and Poster Winner Announcement |
In today’s highly competitive world, companies are using modeling and simulation with high performance computing to gain important competitive advantages. Yet many firms have computational problems that exceed their internal computing capabilities. The Oak Ridge Leadership Computing Facility at Oak Ridge National Laboratory has an industrial partnerships program that helps companies access its Titan supercomputer, the nation’s most powerful HPC system for open research. This talk will provide an overview of this program, and how companies are using Titan to make progress on their seemingly intractable computational challenges and advance in their use of large scale HPC systems.
We all know that surfactants partition to the surface of water, because one part of the surfactant molecule is "hydrophilic" and wants to be in the water, while the other part of the molecule is "hydrophobic" and wants to be out of the water. Perhaps the simplest example of a surfactant consists of a carboxylic acid, which is hydrophilic, connected to an alkane chain, which is hydrophobic. But what happens when the solvent is not just water, but a water-alcohol mixture? The alkane chain, which is hydrophobic, may not be "solvophobic" with this water-alcohol solvent. What molecular segments will be solvophobic, and can we determine the particular characteristics of the molecule that make it solvophobic? We describe in this talk our combined experimental-simulation investigation to address these questions.
4:00 |
Allocations Committee Meeting |
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 |
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.
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.
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.
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.
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.
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.
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
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.
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.
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.
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
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.
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.
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.
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.
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.
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.
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
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.
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.
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.
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.
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
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.
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 Meeting 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
3:00 - 5:00 pm |
Allocations Committee Meeting (members only) |
6:00 - 7:30 pm |
SUG Executive Meeting (members only) |
9:00 - 10:00 am
10:00 - 11:00 am
11:15 - 12:00 pm
12:15 - 1:15 pm
1:15 pm - 2:00 pm
3:15 - 5:00 pm
5:00 |
Q&A with OSC Help
Software Committee Meeting (non-members welcome) Hardware Committee Meeting (non-members welcome) OSC Help: Open
Keynote Address: Duane Detwiler, Chief Engineer Honda R&D Americas, Inc.
Lunch Pick-up
OSC: Welcome and Presentation (food welcome)
Keynote Address: Alexey Zayak, Assistant Professor Bowling Green State University, Department of Physics and Astronomy
Flash Talk Sessions 1) Chemistry Flash Talks 2) Non-Chem Flash Talks
Poster Session Social Networking OSC Help: Open
Poster and Flash Talk Winner Announcement Networking: TBD |
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Duane Detwiler, Chief Engineer and Manager of Vehicle Structures Reliability Department, Honda R&D
"CAE for Lightweight Vehicle Development"
The automotive industry shares the goal to develop advanced vehicle structures which are light weight yet perform well for a variety of performance criteria without incurring significant penalties to manufacturing costs or efficiency. In order to further improve the efficiency of our development process and the quality of our products Honda has increased our ability to predict performance for a given vehicle design using Computer Aided Engineering. This presentation will highlight current CAE methods used for virtual validation of vehicle designs and consider computational challenges for future greater application of lightweight materials and technologies.
Alexey Zayak, Assistant Professor of Physics and Astronomy, Bowling Green State University
“Computational angle to vibrational spectroscopy of heterogeneous chemical interfaces”
Heterogeneous chemical interfaces play increasingly important role in the nano-technology. We are in a great need for better methods that could study surfaces and atomic-scale interfaces, able to reveal physical and chemical properties that vary on the scale of a few chemical bonds. Raman spectroscopy promises exciting opportunities, being able to report not only about a particular chemical species, but also about its interaction with the immediate chemical environment. It utilizes interactions of light with atomic vibrations, and provides unique “fingerprints” of any chemical species. While the conventional Raman spectroscopy cannot be used at the nano-scale due to its extremely small scattering cross section and the far-field diffraction limit of light, the Surface Enhanced Raman Spectroscopy (SERS) has emerged to overcome these weaknesses.
In this talk, I will give a brief overview of SERS and focus on the chemical aspect of this phenomenon, to demonstrate how Raman interactions can reveal local chemical interactions, visualizing the role of the interfacial electron-phonon coupling. Our computationally - intensive results obtained using Oakley demonstrate unique capabilities of the Raman scattering for studying interfacial properties, especially focusing on the aspect of the interfacial charge transfer. As a particular example, I will present Raman analysis of molecule-surface interactions tuned by external electric bias.
Please see our detailed agenda.
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.
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
3:00 - 5:00 pm |
Allocations Committee Meeting (members only) |
6:00 - 7:30 pm |
SUG Executive Meeting (members only) |
9:00 - 10:00 am
10:00 - 11:00 am
11:15 - 12:00 pm
2:15 - 3:00 pm
5:00 |
Q&A with OSC Help
Software Committee Meeting (non-members welcome) Hardware Committee Meeting (non-members welcome) OSC Help: Open
Keynote Address: Duane Detwiler, Chief Engineer Honda R&D Americas, Inc.
Lunch Pick-up
OSC: Welcome and Presentation (food welcome)
Keynote Address: Alexey Zayak, Assistant Professor Bowling Green State University, Department of Physics and Astronomy
Flash Talk Sessions 1) Chemistry Flash Talks 2) Non-Chem Flash Talks
Poster Session Social Networking OSC Help: Open
Poster and Flash Talk Winner Announcement 1st Place Chemistry Flash Talk:
Sean Marguet - Graduate Student, The Ohio State University |
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Please see our webpage.
Please see our Facebook page.
Duane Detwiler, Chief Engineer and Manager of Vehicle Structures Reliability Department, Honda R&D
"CAE for Lightweight Vehicle Development"
The automotive industry shares the goal to develop advanced vehicle structures which are light weight yet perform well for a variety of performance criteria without incurring significant penalties to manufacturing costs or efficiency. In order to further improve the efficiency of our development process and the quality of our products Honda has increased our ability to predict performance for a given vehicle design using Computer Aided Engineering. This presentation will highlight current CAE methods used for virtual validation of vehicle designs and consider computational challenges for future greater application of lightweight materials and technologies.
Alexey Zayak, Assistant Professor of Physics and Astronomy, Bowling Green State University
“Computational angle to vibrational spectroscopy of heterogeneous chemical interfaces”
Heterogeneous chemical interfaces play increasingly important role in the nano-technology. We are in a great need for better methods that could study surfaces and atomic-scale interfaces, able to reveal physical and chemical properties that vary on the scale of a few chemical bonds. Raman spectroscopy promises exciting opportunities, being able to report not only about a particular chemical species, but also about its interaction with the immediate chemical environment. It utilizes interactions of light with atomic vibrations, and provides unique “fingerprints” of any chemical species. While the conventional Raman spectroscopy cannot be used at the nano-scale due to its extremely small scattering cross section and the far-field diffraction limit of light, the Surface Enhanced Raman Spectroscopy (SERS) has emerged to overcome these weaknesses.
In this talk, I will give a brief overview of SERS and focus on the chemical aspect of this phenomenon, to demonstrate how Raman interactions can reveal local chemical interactions, visualizing the role of the interfacial electron-phonon coupling. Our computationally - intensive results obtained using Oakley demonstrate unique capabilities of the Raman scattering for studying interfacial properties, especially focusing on the aspect of the interfacial charge transfer. As a particular example, I will present Raman analysis of molecule-surface interactions tuned by external electric bias.
Please see our detailed agenda.
Non-Chemistry Flash Talk Session Winner:
Aaron Wilson, Byrd Polar & Climate Research Center at The Ohio State University
“Pushing the Next-Generation Arctic System Reanalysis to the Human Scale”
The Ohio Supercomputer Center (OSC) has long supported the development of the Arctic System Reanalysis (ASR), led by the Polar Meteorology Group (PMG) of the Byrd Polar & Climate Research Center. ASR is a high-resolution regional assimilation of model output, observations, and satellite data across the mid- and high latitudes of the Northern Hemisphere. This dataset has proven instrumental in understanding key mesoscale processes in the Arctic including topographically-induced wind flows, representing a skillful tool for analyzing Arctic climate change. ASR was recently refined from 30 km to 15 km horizontal resolution and shown to add substantial value over contemporary reanalyses. With greater supercomputing resources made available through OSC’s Owens Cluster, it is the goal of the PMG to make ASR directly useable by Arctic decision makers by resolving the fine-scale features of Arctic weather and climate.
Chemistry Flash Talk Session Winner:
Tomas Rojas Solorzano, Physics and Astronomy, Graduate Student at Ohio University
“Strain fields and electronic structure of CrN”
Chromium nitride (CrN) has a promising future for its resistance to corrosion and hardness, and fascinating magnetic and electronic properties. CrN presents a phase transition in which the crystal structure, magnetic ordering, and electronic properties change at a (Neel) temperature ~280K. Thin films from different labs exhibit different conductance behavior at low temperature. We performed ab initio calculations using the LSDA+U method, and estimate the interaction between the Cr-3d and N-2p orbitals, by analyzing the band structure. We also calculate effective masses and investigate the effect of strain fields in the electronic structure to understand the electronic behavior near the phase transition.
Poster Winners:
Stephanie Kim, Biophysics, Graduate Student at The Ohio State University
“Novel Binding Site of Cyclin A2 and Potential Inhibitors”
A novel binding site of cyclin A2, a protein that functions as a potential early sensor for DNA damage, has been discovered via 100 ns molecular dynamic simulations. We have confirmed that cyclin A2 opens up and allows the embedded binding pocket to interact with the environment through MD simulations. We incorporated relaxed complex scheme for receptor flexibility to identify probable binding conformations of cyclin A2, and applied structure-based computational ligand docking to find potential ligands that activate cyclin A2 to stimulate DNA repair process. We are collecting in-vitro biochemical data to confirm the functionality of the selected 40 compounds.
Sean Marguet, Chemistry and Biochemistry, Graduate Student at The Ohio State University
“Computationally Guided Resonance Raman Spectroscopy of Nickel-Substituted Rubredoxin, A Model Hydrogenase Enzyme”
In the search for sustainable energy storage and conversion, hydrogen has emerged as a leading alternative to carbon-based fuels. Towards this end, catalytic hydrogen generation and oxidation are increasingly important, yet fundamentally challenging, chemical reactions. Nature has delicately optimized this reaction through the use of metalloenzymes called hydrogenases, which utilize a multimetallic active site for the reversible interconversion of hydrogen gas, protons, and electrons. Due to the complexity of the active site and presence of multiple accessory cofactors, the mechanism of catalysis of this enzyme remains poorly understood, which thwarts efforts to develop mimics of this system for synthetic use. Nickel-substituted rubredoxin (NiRd) has been developed by our group as a functional enzyme mimic of hydrogenase, and NiRd has been shown to be capable of both electrocatalytic and solution-phase hydrogen generation with a modest overpotential. We are interested in characterizing the catalytic mechanism of hydrogen evolution by NiRd. Quantum chemical calculations using density functional theory (DFT) have been performed on an active site cluster model of NiRd in conjunction with multi-wavelength resonance Raman experiments to probe the electronic and geometric structures of the resting state. Excellent agreement between experiment and theory is observed, allowing the assignment of vibrational normal modes on the basis of both frequency and resonance Raman intensities. Differential enhancement of metal-ligand and ligand-centered vibrations are observed across distinct electronic transitions, which provides high-resolution information on the structure of the active site, the hydrogen bonding network, and the effects of the secondary coordination sphere. The oxidized NiIIIRd state has also been characterized both computationally and experimentally. This work, which develops and validates a tractable active-site cluster model of NiRd, establishes a foundation for using computationally guided resonance Raman spectroscopy in a predictive fashion.