" Please join us for a distinguished lecture on April 13, 2017 by Dr. Moshe Y. Vardi on Humans, Machines and the Work of Future"

(Where:) Lecture: Chem-Phys building room: 1st floor, no: 153, Reception: Boone Center

(When:) Thursday, April 13th 2017 Lecutre: 4 pm and Reception: 5-6pm

The Center for Computational Sciences, College of Engineering, Department of Computer Science and the Institute for Biomedical Informatics presents a distinguished lecture by Dr. Moshe Y. Vardi, Rice University on "Humans, Machines and The Work Of Future"

Automation, driven by technological progress, has been increasing inexorably for the past several decades. Two schools of economic thinking have for many years been engaged in a debate about the potential effects of automation on jobs: will new technology spawn mass unemployment, as the robots take jobs away from humans? Or will the jobs robots take over create demand for new human jobs?
I will present data that demonstrate that the concerns about automation are valid. In fact, technology has been hurting working Americans for the past 40 years. The discussion about humans, machines and work tends to be a discussion about some undetermined point in the far future. But it is time to face reality. The future is now. Please read more ...

"CCS hands-on Workshop (Oct 6, 13 and 20) on using Google Drive for Research Data Storage "

If you are looking for cost-effective space to store your data, this hands-on tutorial may be for you. Google Drive currently provides unlimited free storage to UK faculty, staff, and students who have a google education account through the UK account manager. Although many users have used Google Drive in the past, making effective use of Google Drive's unlimited storage service to store/archive large (research) data sets can be challenging.

To help UK users make effective use of Google Drive storage services, the Center for Computational Sciences (CCS) will provide a hands-on workshop and tutorial describing how to setup a UK a Google Drive account with unlimited storage. It will also show users how to setup, configure, and use free open source software such as rclone http://www.rclone.org to transfer large amounts of data quickly and efficiently between UK and Google Drive, particularly for transfers between the DLX supercomputer and Google Drive.

Workshops are currently scheduled for October 6, 13, and 20. Note that each session is limited to 15 participants.


Depending on demand, additional dates may be added.

Register here

** Attendees are asked to bring their laptop on the day of the workshop. **

"Paul Hime, UK Biology Grad Student Wins Prestigious Blue Waters Fellowship and he credits CCS department"

The NCSA's Blue Waters Fellowship will give Hime access to one of the most powerful supercomputers in the world the Blue Waters supercomputer. He will also receive a $38,000 stipend, up to $12,000 in tuition allowance, an allocation of up to 50,000 node-hours on the computing system, and funds for travel to a Blue Waters-sponsored symposium to present research progress and results.

Hime credits Weisrock and others in the Department of Biology and Center for Computational Sciences as being instrumental to his research and scholarship thus far.

Read more.....

"Dr. Menon has been awarded short Term Innovative Research grant from the U.S. Army Research Office"

The grant will fund Menon's work to synthesize the new 2D material he predicted using theoretical simulations. In February, he predicted that a new one atom-thick flat material made up of silicon, boron and nitrogen could upstage the wonder material graphene and advance digital technology.

Read more.....

"CPE, UK partnership provides link to high-speed Internet2 network"

The upgrade allows universities that are part of KyRON to transmit very large databases, conduct complex scientific research, and access remote computing systems.
"Research and healthcare are increasingly relying on supercomputers and very high speed networks,??? said Vince Kellen, senior vice provost, analytics and technologies at the University of Kentucky." The University of Kentucky now joins the leading universities in the country in this area of technology. Our researchers will be able to collaborate with the best and brightest both on campus and across other leading universities.

Read more.....

"Paul Hime, UK Biology PhD student, has been selected to receive prestigious "Blue Waters Graduate Fellowships" for 2016-2017."

Ten PhD Students Selected as Blue Waters Graduate Fellows

The awards are made to outstanding PhD graduate students who have decided to incorporate high performance computing and data analysis into their research.

Paul Hime, University of Kentucky, will investigate the deep branches in the tree of life. Collecting DNA sequence data is no longer a rate-limiting step in molecular phylogenetic. Yet for all its promise, genome-scale phylogenetic is currently limited to unrealistically simple evolutionary models due to computational constraints. Hime's work will leverage the massive CPU/GPU resources on Blue Waters and newly developed statistical models to explore codon-based Bayesian methods for resolving deep (inter-ordinal) branches in the amphibian phylogeny with hundreds of genes. This research stands to make significant and impactful contributions to our understanding of tetrapod relationships. But more broadly, the methods proposed here have the potential to fundamentally change the ways that phylogeneticists analyze multi-gene data sets.

Paul Hime was also awarded a National Science Foundation Graduate Research Fellowship..Read More..

"James Griffioen Named Director of UK Center for Computational Sciences"

James Griffioen has been appointed as director of the Center for Computational Sciences (CCS)

"New material discovered by Dr. Madhu Menon that could upstage graphene"

University of Kentucky Physicist Discovers New 2D Material that could Upstage Graphene

Dr. Madhu Menon, physicist from Center For Computational Sciences, University Of Kentucky discovers New 2D Material that could Upstage Graphene.

"University Of Kentucky Top 10 User on NERSC/DOE System"

NERSC Report

"SBOI Systems Biology and Omics Integration Journal Club and Seminar Series"

March 23, 2015    Intergenerational epigenetic inheritance
June 25, 2014    Noncoding RNA-mediated regulation in innate and adaptive immunity
May 7th, 2014    (Long) Non-Coding RNAs

"Novel Approach to the Study of a New Alloy for Energy Applications" - July 1, 2014 - June 30, 2015

July 1, 2014

Madhu Menon from CCS has been awarded a grant from the Kentucky Science and Technology Corporation (KSEF) for a computational study of new alloys for solar energy applications. The total project award is $30,000 for a duration of one year. He is proposing to study Gallium Phosphide (GaP) based ternary alloys for band gap engineering for the purposes of Photoelectrochemical (PEC) water splitting using first principles theoretical methods. GaP is a promising material since it has a band gap of 2.26 eV and its band edges straddle the water oxidation and reduction reactions. The work will focus on the use of alloying to achieve a indirect to direct band gap transition through an isovalent low concentration doping by antimony.

VOEIS - Virtual Observatory And Ecological Informatics System

The Virtual Observatory and Ecological Informatics System (VOEIS ?????????????????? “voice”) is a collaborative project between the EPSCoR jurisdictions of Montana and Kentucky with partners from industry and the public sector and is funded by the National Science Foundation.

VOEIS is a collaboration of 5 universities in KY and 2 universities in Montana. The project's goal is to build a high tech system for gathering, centralizing and sharing data important to the study of water systems.  With the assistance of environmental sensors, deployed in the field, real time data is archived and streams to the laboratories

The VOEIS Kentucky Lake Project posters were featured at the 17th Annual KY EPSCOR Conference, May 17, 2012, see them on the KY NSF EPSCoR Facebook Page  https://www.facebook.com/.

Find out more about the VOEIS initiative and the research, watch the video by the Center for Visualization and Virtual Environments, University of Kentucky.

CCS researcher wins a prestigious grant from National Science Foundation

October 29, 2012

Alan Dozier, senior scientist at the Center for Computational Sciences, has recently been awarded a $300,000 NSF grant, "SI2-SSI Collaborative Research: A Computational Materials Data and Design Environment." Dozier is the University of Kentucky principal investigator with collaborator Raphael Finkel. This grant is part of a larger grant that also involves Dane Morgan, University of Wisconsin; Kristin Persson, Laurence Berkeley National Laboratory; and Gerbrand Ceder,Massachusetts Institute of Technology.

This grant will enable UK researchers to participate in developing the cyber-infrastructure of the Materials Project at the University of Kentucky. Cyber-infrastructure refers to software automation, middleware, portal, database interface, and data conversion. This project will allow researchers to create customized computational solutions to material and chemical problems and thereby explore material or chemical property spaces.

In addition to developing the cyber-infrastructure, the grant will focus on developing new algorithms for computing properties of materials, such as diffusion, defects, and surface charge. These algorithms will support the State of Kentucky battery-research initiatives, important for economic development. The researchers will make their applications and computation results available to the world through a website at the University of Kentucky. In time, UK researchers will be able to adapt this technology for their own research and form collaborations with other UK groups. The cyber-infrastructure will be partially based on the PyMatGen middleware (being developed at MIT as a generalized toolset for integrating scientific codes), and the website will serve as a portal to the applications and database. Some benefits of this grant are already being realized through programming projects, tutoring, and Master's program integration with Kentucky State University.

UK Research Brings "Spintronics" Closer To Reality

May 14, 2012

Please click here for more information

UK Research Brings Quantum Computing Closer to Reality

May 4, 2012


LEXINGTON, Ky. (May 4, 2012) ??????????????????? A team of theoretical physicists from the University of Kentucky and University of South Florida has taken a big step toward the development of practical "spintronics" based on graphene, which promises to make electronic devices smaller and much faster than today's silicon-based technology.

The research, funded by the U.S. Department of Energy, was led by Professor Madhu Menon at the UK Center for Computational Sciences and Sergey Lisenkov at the University of South Florida. Their findings were published today in Physical Review Letters.

Spin is a quantum mechanical property that has a binary directional value, either "up" or "down." This is analogous to the "on/off" property that enables binary digital coding in modern computers. A key advantage to potential spintronics devices is that once the direction of the spin is set, no energy is required to keep it that way. Thus, data stored using spintronics will not disappear when the electric current stops.

An important step toward fabrication of spintronics ("the Holy Grail," Menon says) is finding a semiconductor that has a net "spin" at room temperature. The biggest challenge is in finding a suitable material and figuring out how to set the spin. The UK-USF team showed that a flat sheet of pure carbon only one atom thick, called graphene, can be suitably engineered and used for this purpose when combined with atoms of the metallic element cobalt.

"Control over the directionality of spin is critical for practical spintronics applications," Menon said. "Hopefully, our findings will open new venues for industrial applications of graphene."

Using state-of-the-art theoretical computations, the UK-USF team demonstrated that by placing cobalt atoms in graphene "holes," created by removing one or two nearby carbon atoms, it is possible to set the spin states of the carbon atoms in a controlled way, which the researchers say is key to practical spintronics application for graphene.

Despite its single-atom thickness, graphene is a relatively tangible material. In fact, anyone can make a small quantity of graphene by "peeling" ordinary graphite (the substance that makes up the "lead" in an ordinary pencil) with clear plastic tape.

Graphene is one of the toughest materials ever tested, with a breaking strength 200 times greater than steel. Of particular interest to the electronics and data-storage industries, graphene is also highly conductive, allowing electric currents to pass through it about 100 times faster than silicon.

MEDIA CONTACT: Keith Hautala, (859) 323-2396; keith.hautala@uky.edu

Researchers have discovered that graphene, a sheet of carbon atoms (green), can be modified with the addition of cobalt atoms (red), as a potential material for the development of practical spintronics applications.

CCS researchers win a prestigious grant from National Science Foundation

April 4, 2012

Center for Computational Sciences researchers Madhu Menon and R. Michael Sheetz teamed up with UofL researchers Mahendra Sunkara and Jacek Jasinski of UofL Conn Center and Somnath Datta from UofL Department of Biostatistics & Bioinformatics and Krishna Rajan of Iowa State University??????????????????s Institute of Combinatorial Discovery to win a $1.1M grant from National Science Foundation entitled ????????????????SOLAR: New Materials Search for Solar Energy Conversion to Fuels?????????????????.

The search for suitable, durable inorganic semiconductors that can convert solar energy to fuels is a grand challenge in the fields of chemistry, renewable energy, and materials science. There is no material available currently that meets all the criteria required for spontaneous water splitting with solar light for hydrogen production at appreciable efficiency and durability. Despite rapid advances with computing, the first principles-based techniques for predicting properties of materials are time consuming. In many cases, the search process itself requires some direction. One approach has been to utilize a combinatorial, high throughput sample creation from different elements as a means of screening materials; however, the search space that has been explored is relatively small. This research project seeks to develop a fundamentally transformative strategy by using an informatics-guided computational and experimental approach for proposing and testing new materials. The team extracts design rules to systematically identify critical structure-property relationships in a quantitative fashion to determine the exact role of specific combinations of materials descriptors that govern a given property of interest. Statistical inference methods are used to identify and experimentally validate new materials with new properties. This information is then linked to a targeted first principles modeling step to provide a physical interpretation of mechanisms controlling opto-electronic properties. The predictions will be validated using electronic and photoelectrochemical properties of synthesized semiconductor alloys.

This project brings together investigators from physics (Menon, Sheetz, Jasinski), chemical engineering (Sunkara), mathematical sciences and informatics methods (Datta and Rajan), and materials science & engineering (Rajan) from the University of Kentucky, University of Louisville, and Iowa State University. This SOLAR project will: (a) develop materials informatics-guided modeling for predicting band gaps and work functions for creating a new materials database that links structure with properties as a guide for both experimentalists and computational materials scientist/physicists; (b) advance new non-linear manifold learning methods in promoting informatics as a predictive tool for materials discovery; (c) utilize accurate first principles modeling techniques as a second step for refined prediction of physical and electronic properties of the new alloys; and (d) perform materials synthesis toward experimental validation of properties of promising materials systems and for validation of theoretical predictions and associated errors.

This SOLAR team's PIs leverage this effort through existing collaborations on energy materials and informatics with scientists from several countries such as Slovenia, Greece, Poland, Germany, and the UK by hosting a number of visiting scientists and students from these countries. The team will also involve a large number of high school and undergraduate students and will expose them to solar energy and materials research. "This grant is a recognition of the prominent role researchers in Kentucky are playing in the field of renewable energy," says Menon.

Novel alloy could produce hydrogen fuel from sunlight

August 31, 2011

Using advanced theoretical computations, a team of Kentucky scientists has derived a means to "tweak" an inexpensive semiconductor to function as photoelectrochemical catalyst.

Scientists from the University of Kentucky and the University of Louisville have determined that an inexpensive semiconductor material can be "tweaked" to generate hydrogen from water using sunlight.

The research, funded by the U.S. Department of Energy, was led by Professors Madhu Menon and R. Michael Sheetz at the UK Center for Computational Sciences, and Professor Mahendra Sunkara and graduate student Chandrashekhar Pendyala at the UofL Conn Center for Renewable Energy Research. Their findings were published Aug. 1 in the Physical Review Journal (Phys Rev B 84, 075304).

The researchers say their findings are a triumph for computational sciences, one that could potentially have profound implications for the future of solar energy

Using state-of-the-art theoretical computations, the UK-UofL team demonstrated that an alloy formed by a 2 percent substitution of antimony (Sb) in gallium nitride (GaN) has the right electrical properties to enable solar light energy to split water molecules into hydrogen and oxygen, a process known as photoelectrochemical (PEC) water splitting. When the alloy is immersed in water and exposed to sunlight, the chemical bond between the hydrogen and oxygen molecules in water is broken. The hydrogen can then be collected.

"Previous research on PEC has focused on complex materials," Menon said. "We decided to go against the conventional wisdom and start with some easy-to-produce materials, even if they lacked the right arrangement of electrons to meet PEC criteria. Our goal was to see if a minimal 'tweaking' of the electronic arrangement in these materials would accomplish the desired results."

Gallium nitride is a semiconductor that has been in widespread use to make bright-light LEDs since the 1990s. Antimony is a metalloid element that has been in increased demand in recent years for applications in microelectronics. The GaN-Sb alloy is the first simple, easy-to-produce material to be considered a candidate for PEC water splitting. The alloy functions as a catalyst in the PEC reaction, meaning that it is not consumed and may be reused indefinitely. UofL and UK researchers are currently working toward producing the alloy and testing its ability to convert solar energy to hydrogen.

Hydrogen has long been touted as a likely key component in the transition to cleaner energy sources. It can be used in fuel cells to generate electricity, burned to produce heat, and utilized in internal-combustion engines to power vehicles. When combusted, hydrogen combines with oxygen to form water vapor as its only waste product. Hydrogen also has wide-ranging applications in science and industry.

Because pure hydrogen gas is not found in free abundance on Earth, it must be manufactured by unlocking it from other compounds. Thus, hydrogen is not considered an energy source, but rather an "energy carrier." Currently, it takes a large amount of electricity to generate hydrogen by water splitting. As a consequence, most of the hydrogen manufactured today is derived from non-renewable sources such as coal and natural gas.

Sunkara says the GaN-Sb alloy has the potential to convert solar energy into an economical, carbon-free source for hydrogen.

"Hydrogen production now involves a large amount of CO2 emissions," Sunkara said. "Once this alloy material is widely available, it could conceivably be used to make zero-emissions fuel for powering homes and cars and to heat homes."

Menon says the research should attract the interest of other scientists across a variety of disciplines.

"Photocatalysis is currently one of the hottest topics in science," Menon said. "We expect the present work to have a wide appeal in the community spanning chemistry, physics and engineering."

For more information, please contact Keith Hautala at the University of Kentucky at (859) 323-2396 or keith.hautala@uky.edu. At the University of Louisville, please contact Judy Hughes at (502) 852-6171 or judy.hughes@louisville.edu.

Visible-light absorption and large band-gap bowing of GaN1-x Sbx from first principles

August 1, 2011

Please click here for more information

"Spin Doctors????????????????? Look to Revolutionize Information Storage and Electronic Devices

May 6, 2011
by Jeff Mossey???????????????, Vinayak Bhat???????????????, R. Michael Sheetz???????????????, Lance De Long??????????????? Photo by Brian Connors Manke (brian.manke@uky.edu)

????????????????Spin Doctors????????????????? Look to Revolutionize Information Storage and Electronic Devices


A Kentucky-Montana Consortium: A collaborative project between Kentucky and Montana, and partners from industry and the public sector, that will develop integrated water quality sensors and an ecological informatics system by creating an updated cyberinfrastructure* has been funded by the National Science Foundation. Links


The Center for Computational Science has received funding for the development of ParamChem. ParamChem is a NSF sponsored initiative to develop an integrated cyber environment to address the simulation needs of molecular sciences. The proposed infrastructure will provide reference data organizers and generators as well as workflows for automatic parameterization of Molecular Mechanics (MM) Force Fields as well as Semi-Empirical (SE) methods.

Cyber-infrastructure Strategic Plan

John Connolly, director of CCS has recently submitted a Strategic development plan for cyber-infrastructure in the state of Kentucky to state government agencies. This plan will guide future investment and development of state cyber-resources for several years to come.
Link: KYCI Plan

New Supercomputer Puts UK in Top 10

LEXINGTON, Ky. (Sept. 20, 2010)

A new high-performance supercomputer that will help power the University of Kentucky's research mission has already put the school in the top 10 public universities for computing power. The Dell supercomputer, named the Lipscomb High-Performance Supercomputing Cluster after UK alumnus and Nobel Laureate William N. Lipscomb, is three times more powerful than UK's old machine.

???????????????????????????????????The University of Kentucky likes being ranked in the top ten,?????????????????????????????????? said UK President Lee T. Todd, Jr. ???????????????????????????????????And this new piece of equipment will do that for UK in the world of supercomputing. More exciting than that, however, is what this cluster will mean to our researchers. This supercomputer will allow our world-class researchers to discover new solutions to the complex problems facing the Commonwealth, the nation, and the world.??????????????????????????????????

UK recently purchased and installed a supercomputing cluster based on the new Dell PowerEdge C6100 High Performance Computing (HPC) server chassis. The PowerEdge C6100 was chosen for its high density, shared infrastructure and efficient power and cooling features. The installation of the cluster began in July. After weeks of work by Dell Inc., the UK HPC team, and the UK Center for Computational Sciences, the new supercomputer cluster went live August 25. The team completed the transition from the old supercomputer to the new cluster with minimum research interruption and in a much shorter amount of time than the last supercomputer transition in 2007.

The Lipscomb High-Performance Supercomputing Cluster is important for UK research projects, including the design of new materials for magnetic applications, understanding biological chemical processes, investigations of the origins of the universe and subatomic particles, development of new types of batteries, improvements in automobile manufacture, and design of improved pharmaceuticals.

"A first-class research university must have first-class research facilities," said John Connolly, director of UK's Center for Computational Sciences. "Computation is becoming a more and more important component of modern research. The new UK supercomputer will provide high-speed access for our faculty and students so they can be competitive with anyone in the country, and will help UK achieve its goal of Top 20 status."

Matthew Beck, an assistant professor and researcher in the College of Engineering, said the computer, known as the DLX cluster, will allow researchers to run calculations of increasingly realistic and complex systems.

"Metal-oxide nanoparticles, one of the things we??????????????????????????????????????re using DLX to study now, are a great example," said Beck. "They're exciting because they have shown both the potential to protect against oxidative stress-related diseases like Alzheimer??????????????????????????????????????s and as high-performance catalysts for the production of molecular hydrogen and oxygen for fuel cells. But nobody really understands how these nanoparticles work. Ultimately, unless we can calculate properties of whole nanoparticles, we don??????????????????????????????????????t really know if what we??????????????????????????????????????re calculating is what really happens. DLX allows us to do exactly that. Suddenly the line between traditional experiment - which is about the real things that you can hold in your hand, and computation - which is supposed to be just theory, goes away."

Just before going live, the cluster was measured at speeds of over 40 teraflops. A teraflop is a trillion calculations, known as floating point operations, per second. This would rank UK 162 on the current list of the top 500 supercomputers in the world, and eighth among higher education sites not funded by government grants. (Though the rankings have not been updated since UK's new high-performance computer went live, its speed would currently place it at these levels among other supercomputers.) The previous supercomputer measured speeds under 13 teraflops, making the new machine more than three times faster.

The DLX cluster offers 376 Basic Nodes, each powered by two 2.66 GHz Intel Xeon X5650 (Westmere) CPUs (4,512 processor cores total) and 36 GB of RAM (more than 13 TB RAM total). For comparison, a high-end desktop computer, like the Dell Studio XPS 8100, uses a processor similar to the two in each of UK's compute nodes, but the cluster has 752 of these connected together by a high speed "fabric". DLX also has eight Hi-Mem Nodes, each powered by four 2.66 GHz Intel Xeon X7560 CPUs (256 processor cores total) and 512 GB of RAM (4 TB total). This equates to about 2,800 times the computing power of the average personal laptop, such as the Intel i3-350M laptop processor available in laptops such as the Dell Studio 15 and 17.

The compute nodes are networked with a Mellanox quad data rate Infiniband switch. The high-performance Panasas cluster file system contains about 200 TB of usable disk storage (for home and scratch directories). The cluster includes a dedicated backup node running IBM's Tivoli Storage Manager (TSM) and Hierarchical Storage Manager (HSM) with a 10 gigabit link to the rest of UK's central backup system. This will cut cluster backup times by an order of magnitude and drastically improve access to UK's near-line tape storage system, which is heavily used by UK's supercomputing researchers. The new cluster provides approximately a three-fold increase in processing power and a five-fold increase in data storage, while reducing overall power consumption. Additional hardware information is available at: http://hpc.uky.edu/Hardware/Dell_cluster.html

For more details on High Performance Computing at UK, visit http://hpc.uky.edu/. Questions and assistance with High Performance Computing should be directed to the Help HPC List at help-hpc@@uky.edu.

Lipscomb High-Performance Computing Cluster Facts: https://www.ccs.uky.edu/UserSupport/Resources/Dell/Facts/

The Oxford Handbook of Nanoscience and Technology

Dr. Menon along with Dr. Andriotis, E. Richter and R.M. Sheetz published a chapter titled “Structural, electronic, magnetic, and transport properties of carbon-fullerene-based polymers” in the book “The Oxford Handbook of Nanoscience and Technology.”
The link to the book: http://www.oup.com/us/catalog/general/subject/Chemistry/?view=usa&ci=9780199533053

The book cover and the first page in the chapter have been illustrated below.

First page of chapter 21

UK to acquire New Supercomputer

The University of Kentucky has approved the replacement of the current aging IBM supercomputer, whose lease is running out. The new supercomputer is anticipated to substantially increase the computing capabilities of University researchers. This will open new vistas in many research areas including Energy and Medicine. The IT department and Center for Computational Science are currently hosting vendor seminars prior to the issuance of the RFP which is expected by the end of February. So far IBM, HP, Dell, and SGI have participated. It is planned the new system will be up and running by mid-year 2010.

Cyber-infrastructure to be Highlighted at UK

Provost Subbaswamy, Vice President for Research, Jim Tracy and the Center for Computational Sciences are jointly sponsoring a Cyberinfrastructure Days Workshop at the University of Kentucky on February 22-23, 2010. The workshop is part of a national series of workshops sponsored by a consortium of federal agencies and national organizations. In addition, IBM has contributed their support to the UK CI Days. For more details visit website: http://www.ccs.uky.edu/CIDays