Category: Computational Nanoscience

During the 2012-2013 year, under suspended status, the activities of the IFN Computational Nanoscience Group (CNG) were funded by the UPR. Three postdoctoral scholars and one system administrator were hired with institutional funds to work on computational nanoscience, principally supporting the IRGs 2, 3, and 4. IFN researchers also continued work on EPSCoR RII Track 2 award entitled “Collaborative Research: Adaptive Cyberinfrastructure for Computational Nanoscience for Energy Research” in collaboration with Nebraska Jurisdiction.

 The IFN strategic plan includes a mechanism to provide synergy between the EPSCoR Track-1 and Track-2 projects to develop the cyberinfrastructure of the Jurisdiction. By the end of the five-year plan, the number of nanocomputational scientists in the Jurisdiction should have increased to eleven members and the cyberinfrastructure will be expanded to provide access to the IFN researchers to the Open Science Grid (OSG) and XSEDE, the successor to TeraGrid. 

 As part of the synergy, Track 1 and Track 2 in Puerto Rico and the Track 2 in Nebraska held a joint workshop to strengthen collaboration, November 7-8, 2011 in San Juan, Puerto Rico.  As a result of the workshop, proposals for exchanges of faculty, post-docs, and students were solicited, and 14 projects were selected for funding in January 2012.  Fifteen participants from Puerto Rico were funded from UPR funds for stays of 2 weeks up to 2 months duration in Nebraska.  The IRG’s reported the activity of these exchanges.

 The CNG currently consists of Drs. Ortiz-Zuazaga, Ishikawa (recently retired), Velev, Koutis and Cheng from UPR-RRP, Drs. Cordova, Curet-Arana, and Lu from UPR-RUM, and Dr. Zimbovskaya from UPR-CUH. Since the summer of 2012, these researchers have produced 25 publications.

 Dr. Velev’s group works on multiple projects, including work on organic ferroelectrics for spintronics applications. Their theoretical work predicts that these effects are highly tunable.  Theoretical calculations on zwitterions indicate the possibility of organic semimetals.  The lab also developed a novel computational model for non-equilibrium electron transport which should allow novel materials to be studied theoretically, including the effects of disorder in the crystal structure.

Dr. Alan Kalitsov continued as an IFN postdoctoral fellow under the mentorship of Dr. Julian Velev.  He works on the IRG2 subproject entitled "Logic and Memory Devices" directed by Dr. Ram Katiyar, working on simulation of electronic transport properties and especially in spin transport and spin torque. He developed a new code for a single-band tight-binding model for computing charge, spin currents and spin-transfer torque in multiferroic tunnel junctions.

Dr. Dmitry Skachkov continued to work as a postdoc on IRG3: Nanotechnology Based Remediation thrust. This IRG is directed by Dr. Arturo Hernandez. Dr. Skachkov’s research work is focused on the theoretical study of hydrogen and ammonia oxidation reaction on low-index Pt single crystals by use of a combined direct molecular dynamics/density-functional theory simulation under the supervision of Dr. Yasuyuki Ishikawa and in collaboration with Dr. Carlos Cabrera. This year Ishikawa retired, and Skachkov transferred to the Track 2 project, where he continues work with Velev.


Aimed at achieving graphene-based materials with ideal band gaps for solar energy harvesting, Dr. Chen carefully examined graphene nanoribbons in different configurations. Yafei Li has continues as a postdoctoral fellow in IRG4 under the supervision of Dr. Z. Chen.  Using his expertise in computational nanoscience and its application to novel light harvesting materials, Dr. Li is working on the theoretical modeling to develop novel graphene- and inorganic graphene- based materials for light harvesting, the central theme of IRG 4.  Under the supervision of Dr. Zhongfang Chen searches for small band gap semiconductor materials for e-h separation, and models the polar semiconductor/graphene interface and its behavior under electric fields. These efforts provide guidance to IRG4 experimental efforts.  Drs. Li and Chen have published 4 papers this year together.

Dr. Junqiang Lu and his group study electronic transport property of a graphene monolayer covered by another layer with infinite or finite size. They demonstrate that electronic transport property of a graphene monolayer can be changed considerably if the other layer is a nanoribbon with finite width; while the change is more insignificant if the other layer is infinite or even semi-infinite large.  They show that the different effects from infinite and finite coverage are attributed to the interlayer interference between the wavefunctions.

Dr. Ioannis Koutis is a new recruit to the IFN. He is faculty in the Department of Computer Science, UPR-RRP. He was awarded an IFN startup grant to develop novel algorithms for extracting 3D models of neurons from electron microscopy images. Unmyelinated axons and dendritic spines in mammals are of the order of 50-100 nm in width, requiring nanoscopy to fully resolve their 3D structure. Dr Koutis group has developed novel theoretical frameworks for image segmentation, and implemented them to study neurons in EM images. Their affinity-graph based techniques are nearly optimal, allowing the study of much larger datasets than previously possible. Dr. Koutis work is crucial for the development of the Testbed led by Dr. Eduardo Rosa-Molinar.  Dr. Koutis is a IFN startup recipient, but has not been able to purchase the equipment described in his award because of the suspended status.

HPCf Logo

Because of the suspended status of the award, the IFN was unable to purchase a 320 core Linux cluster and 10 GB Ethernet networking equipment to be housed in the UPR HPCf to complement cyberinfrastructure investments by the Track 2. These purchases would have doubled the computational capacity available to IFN participants.

In partnership with Nebraska’s Holland Computing Center (HCC), the UPR HPCf has established condor job flocking between Nebraska and Puerto Rico. With the help of Nebraska staff, the IFN has established the first island-wide cyberinfrastructure with computers in Mayaguez, the HPCf and the Rio Piedras campus. Over 1.8 million jobs were run on this combined infrastructure. Researchers have also been able to run on Nebraska clusters, and have applied to XSEDE for computing accounts.