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MSI Principal Investigator Richard Isaacson (Veterinary and Biomedical Sciences) is using MSI resources as part of his investigations into antibiotics that are used as growth promoters in livestock. Antibiotics have been used in this way for decades, but we don’t know the mechanism by which they promote growth. It is possible that this result is from the control of bacterial growth in the animals’ intestines, or because the antibiotics control specific bacterial populations in the intestinal tract. Recently, there are concerns that the use of these antibiotics may be eliminated or reduced in the future.
These researchers are using a molecular epidemiology approach to see if eliminating the use of these antibiotic growth promoters affects, for better or worse, the health of swine. Another goal is to see whether antibiotic growth promoters mediate their effects by alteration of microflora. They use software available through MSI to generate the data and then to analyze it. Besides various software packages, the group makes use of the Galaxy analytical framework.
Professor Isaacson and members of his research group, including fellow MSI Principal Investigator Srinand Sreevatsan (Veterinary Population Medicine) published a paper concerning this work in the Proceedings of the National Academy of Science in Fall 2012: “Microbial Shifts in the Swine Distal Gut in Response to the Treatment With Antimicrobial Growth Promoter, Tylosin,” HB Kim, K Borewicz, BA White, RS Singer, S Sreevatsan, ZJ Tu, and RE Isaacson, PNAS, 109:15485, DOI: 10.1073/pnas.1205147109 (2012). The figure above shows an analysis that used the Ribosomal Database Project (RDP) classifier to show the composition of the fecal microbiome of pigs receiving tylosin (an antimicrobial growth promoter) and those that did not, and how it changed over time. The graphs show results for treated (T) and non-treated (NT) pigs at different ages at two different farms. (A) RDP classification of the sequence reads from farm 1. (B) RDP classification of the sequence reads from farm 2.
Professor Isaacson and his group also use MSI for other projects, including investigations into the effect of pathogenic bacteria on the gut microbiome and analysis of the human lung microbiome (see “The Lung Microbiome in Moderate and Severe Chronic Obstructive Pulmonary Disease,” AA Pragman, HB Ki, CS Reilly, C Wendt, RE Isaacson,” PLos One, 7:e47305, DOI: 10.1371/journal.pone.0047305 (2012)).
The research group of Professor Laura Gagliardi (Chemistry) uses quantum chemistry methods to study chemical systems containing transition metals and even heavier atoms like lanthanides and actinides. Gagliardi group projects that currently use MSI include: simulations of actinide chemistry in the gas phase; the understanding of uranyl nanoclusters; modeling of water-splitting catalysts in dye-sensitized solar cells; simulations of carbon capture in metallorganic frameworks; and prediction of novel metal-metal multiply bounded compounds that can be employed in CO2 activation.
An article relating to this research appeared in the Journal of the American Chemical Society in June 2012 (“Differentiating Between Trivalent Lanthanides and Actinides,” MJ Polinski, DJ Grant, S Wang, EV Alekseev, JN Cross, EM Villa, W Depmeier, L Gagliardi, and TE Albrecht-Schmitt, JACS, 134:10682, DOI:10.1021/ja303804r (2012)). MSI resources were used for various kinds of electronic-structure calculations for this paper.
MSI also maintains some computational hardware for the Gagliardi group. They needed high-memory nodes for their work in quantum chemical method development. Multiconfigurational methods can require more than 50 GB of memory per node. To meet this need, MSI installed additional high-memory nodes, purchased with the Gagliardi group’s research funds, on Itasca and integrated them with the existing software and scheduling infrastructure. MSI maintains this additional hardware along with the rest of Itasca’s infrastructure.
Professor Gagliardi is a member of the Chemical Theory Center group in the Department of Chemistry. Another exciting development is the awarding, in Fall 2012, of a grant from the Department of Energy to create the Nanoporous Materials Genome Center (NMGC). Professor Gagliardi is the Director of this Center. The NMCG studies metal-organic frameworks (MOFs), a novel class of materials used in many energy-relevant processes. The goal of the Center is to develop state-of-the-art molecular- and material-simulation tools that will be used to characterize and predict the performance of millions of as-yet-unsynthesized materials. The NMGC will also provide a repository of experimental structures and associated properties that can be used by other researchers. The Center anticipates heavy use of MSI resources for the calculations necessary for this work.
Description of image: Depiction of the (a) three-dimensional framework and (b) sheet topology of Ln[B4O6(OH)2Cl] (Ln = La–Nd; Pu). The lanthanide and plutonium metal centers are depicted by the blue spheres, chlorine is depicted by the purple spheres, BO4 tetrahedra as light green unit, and BO3 triangles as dark green units.
On April 11, MSI held its 4th Annual Research Exhibition. This event included a judged poster competition for our users. The winner of this year’s competition was Feilong Liu, who submitted a poster entitled, “Numerical Modeling of Organic Semiconductor Heterostructure Devices.” Mr. Liu is a graduate student in the research group of Professor P. Paul Ruden in the Department of Electrical and Computer Engineering. MSI recently met with with Mr. Liu to discuss his research.
MSI: How long have you used MSI resources?
Feilong Liu: I started using MSI in 2010, so about three years. I came to the University during the fall semester of 2009.
MSI: What type of research do you use MSI for?
FL: Basically we use MSI for the numerical calculations of our organic hetero-structured device model. Organic-based semiconductors have an advantage in that their flexibility, low cost, and ease of fabrication makes these devices potentially very attractive for many different applications. The big difference between what our research group does and what other groups do is that, whereas they focus on the fabrication of the devices we focus on the theoretical perspectives. We try to understand the device physics. So, this is where MSI really helps out, we use MSI resources to do the physics-based calculations of the device model.
MSI: Could you talk about what your poster describes?
FL: The poster shows a complete device model. It shows the calculation for the electrostatics of the device. We do this by splitting the device into hundreds of segments and each of these segments has multiple differential equations attached to it. This leaves us with thousands of coupled equations that we need to use MSI resources to solve. With the results we can explore two types of real applications. The first is the light-emitting diode that converts electricity to light. The second is the photovoltaic cells, which conversely converts light to electricity. The poster shows that our model can work well for both applications.
MSI: In regards to the calculations you do, are there any systems here at MSI that you use in particular?
FL: I remotely access the Laboratory Interactive pool of resources to run a Fortran compiler.
MSI: Would you say your research is geared towards immediate applications or is more theoretical?
FL: First, we wanted to understand what is going on with the devices. Next, we asked, what can we do to improve existing devices? The recent research of our group has been aimed at improving the performance of the device models. What we do is come up with ideas of how to improve the performance and efficiency of devices like LEDs and solar panels, and these ideas enter the development of these products.
MSI: Would you like to continue this research once you become a PI of your own research group?
FL: I think this is a great project and group to be a part of. This project had been ongoing when I became a part of it. What I did was to improve the previously established model, which was basically generic for any bilayer structure. I incorporated the characteristic microscopic processes for organic-based devices. I think that in the future what needs to be done is to extend our model to more complicated devices. For instance the model we have now is applicable to a bilayer structure, with one layer of Material A and the other of Material B. In real experiments, however, it is becoming very popular to use an interpenetrated structure; people call this a bulk heterojunction. Going forward I think it would be very interesting to figure out how to model this type of structure.
MSI: Do you think MSI resources will be an important part of your future research?
FL: Of course, if I have access to MSI resources in the future it will be of great importance to my research. It is a very nice thing to have and something I hope to enjoy for some time to come.
NOTE: Mr. Liu was the lead author on a paper published in the journal Applied Physics Letters about this topic: "Electrostatic Capacitance in Single and Double Layer Organic Diodes," FL Liu, PP Ruden, IH Campbell, DL Smith, Applied Physics Letters, 101(2):023501, DOI: 10.1063/1.4734379 (2012).
One of the most exciting areas that researchers use MSI for is computer-generated visualizations. Avery Musbach, a graduate student in the Department of Computer Science and Engineering, is the lead author on a paper that demonstrates the power of scientific computing to create visualizations. The paper, “Full-Wave Modeling of Light Propagation and Reflection,” appeared recently in the journal Computer Graphics Forum (published online Feb 4, 2013, DOI: 10.1111/cgf.12012). Other authors include Associate Professor Gary Meyer (Computer Science and Engineering), Professor Fernando Reitich (Mathematics), and Assistant Professor Sang-Hyun Oh (Electrical and Computer Engineering).
The goal of this paper was to show a new way to use computer graphics to model how light interacts with objects. The authors used the finite difference time domain (FDTD) method to compute the propagation of electromagnetic energy in three dimensions. This is a more general approach to creating computer graphics than has been previously used. The authors created a video of a butterfly opening and closing its wings using this method. The image above is a still from the video.
MSI resources used for this project included the Scientific Development and Visualization Laboratory and MATLAB, a software package that is used for a wide variety of applications, including image and video processing. While the final rendering of the butterfly video was done using CSE computers, the high-performance computing work was done at MSI. Scientific Computing Consultant Dr. Shuxia Zhang, who is a member of the HPC Operations group, provided technical expertise on this project.
The research group of Professor Steven Kass (MSI Fellow, Chemistry) uses MSI resources in their investigations into hydrogen bond networks. The goal of this research is to understand enzyme catalysis and develop hydrogen bond catalysts, novel acids and bases, and molecular anion receptors. By mimicking nature, the researchers have found that hydrogen bond arrays stabilize charged centers to a greater degree than was previously recognized and that flexible alcohols can serve as anion receptors. The Kass group has published results of their research in several articles that appeared in the Journal of the American Chemical Society during 2012 and 2011:
- “Three Hydrogen Bond Donor Catalysts: Oxyanion Hole Mimics and Transition State Analogues,” EV Beletskiy, J Schmidt, XB Wang, and SR Kass, JACS:134(45):18534, DOI:10.1021/ja3085862 (2012)
- “Characterization of a Saturated and Flexible Aliphatic Polyol Anion Receptor,” A Shokri, J Schmidt, XB Wang, and SR Kass, JACS 134(41):16944, DOI:10.1021/ja3075456 (2012)
- “Effect of Hydrogen Bonds on pKa Values: Importance of Networking,” A Shokri, A Abedin, A Fattahi, and SR Kass, JACS 134(25):10646, DOI:10.1021/ja3037349 (2012)
- "Hydrogen Bonded Arrays: The Power of Multiple Hydrogen Bonds," A Shokri, J Schmidt, XB Wang, and SR Kass, JACS 134(4):2094, DOI:10.1021/ja2081907 (2011)
The group is modeling a number of polyols and comparing their thermodynamic properties and binding properties with different substrates. This work benefits from the use of the supercomputers because the molecules are large and flexible, which makes it computationally expensive to examine them. The catalyst-substrate complexes also involve very time-consuming calculations. Current research in 2013 involves modeling infrared spectra and electron binding energies of a number of deprotonated polyols (the conjugate bases of Bronsted acids) and polyol-substrate complexes (bound hydrogen bond catalysts). This work complements experimental efforts that entail synthesizing novel “green” acids, hydrogen bond catalysts, and hosts for molecular recognition, as well as probing their reactivities and properties (e.g. pKa’s), and examining their binding via mass spectrometry experiments (e.g. electron affinity measurements and IR spectra determinations of bound catalysts).
Description of image: The difference in the acidity of the two compounds shown is 21 orders of magnitude (i.e., 1021, a very large number!), due to the hydrogen bond network in the larger species. To put this number into context, it corresponds to the weight of an elephant (more precisely, a male African elephant) versus that of the entire world. That is, the ratio of the weight of the world to that of an elephant is the same as the ratio of the acidity difference of the polyol to the simple alcohol.