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With the recent appearance of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV), coronaviruses are once again in the news. These viruses are found worldwide and some of them can create serious illness in humans. SARS (severe acute respiratory syndrome), which is caused by a coronavirus, killed hundreds of people in 2002-2003.
Assistant Professor Fang Li, an MSI Principal Investigator from the Department of Pharmacology in the Medical School, uses structural biology to study diseases including viral infections. This research investigates the structural basis for the receptor recognition mechanisms of viruses. This includes studying the structures and functions of the receptor-binding proteins found on the surfaces of viruses, as well as how they interact with host receptors. These structural studies will allow researchers to develop therapy strategies to fight virus-caused diseases.
Recently, Professor Li and his colleagues determined the crystal structure of the spike protein N-terminal domains (NTDs) of bovine coronavirus (BCoV). This finding was published in the Journal of Biological Chemistry in December 2012 (“Crystal Structure of Bovine Coronavirus Spike Protein Lectin Domain,” GQ Peng, LQ Xu, YL Lin, L Chen, JR Pasquarella, KV Holmes, F Li, Journal of Biological Chemistry, 287:41931, DOI: 10.1074/jbc.M112.418210 (2012)). The research studied the differences in the structure of the NTDs of BCoV and another coronavirus, mouse hepatitis coronavirus (MHC). While both NTDs include a human galactose-binding lectin (galectin) in their NTD structures, the former binds to sugar and the latter to a protein, CEACAM1. The Li group’s studies of the crystal structure of the NTDs show subtle differences in the receptor-binding loops. These results indicate a possible evolution path where a coronavirus incorporated this galectin into its spike proteins, which was altered as the different modern coronaviruses evolved. The researchers used the BSCL for this research.
The Li group has also published additional papers related to their research using MSI. These include:
- “Structural basis for multifunctional roles of mammalian aminopeptidase N,” L Chen, YL Lin, GQ Peng, F Li, Proceedings of the National Academy of Sciences of the United States of America, 109:17966, DOI: 10.1073/pnas.1210123109 (2012)
- “Mechanisms of Host Receptor Adaptation by Severe Acute Respiratory Syndrome Coronavirus,” KL Wu, GQ Peng, M Wilken, RJ Geraghty, F Li, Journal of Biological Chemistry, 287:8904, DOI: 10.1074/jbc.M111.325803 (2012)
Image description: A. Overall structure of BCoV NTD. Two β-sheets of NTD core are colored green and magenta, respectively, and other parts of the NTD are color cyan. N*, N terminus; C*, C terminus. The β-sandwich core structure is indicated as “core.” The two potential sugar-binding pockets above and underneath the core structure are indicated as top and bottom, respectively. B. 2Fo – Fo electron density of a portion of BCoV NTD at 1.5σ. This region includes three of the critical sugar-binding residues. (Peng G et al., “Crystal Structure of Bovine Coronavirus Spike Protein Lectin Domain,” J. Biol. Chem., 287:41931 (2012); ©2012 by the American Society for Biochemistry and Molecular Biology.)
posted on July 17, 2013
Makenzie Provorse is a graduate student in Professor Jiali Gao’s (MSI Fellow) group in the Department of Chemistry. She entered the University of Minnesota in the fall of 2009 and joined the Gao group in January 2010. She’s been using MSI since then.
Ms. Provorse was a finalist at the 2013 MSI Research Exhibition, which was held on April 11, 2013. She submitted a poster entitled "Quantum Coherence in Singlet Fission From Multistate Density Functional Theory (MSDFT)." Recently, MSI talked with Ms. Provorse to discuss her poster and the work she does using MSI.
MSI: What do you use MSI for?
Makenzie Provorse: I mainly run molecular simulation and electronic structure programs on Calhoun and Itasca. They’re the two machines I use the most. For this specific project, we used a locally modified version of GAMESS, a molecular electronic structure theory program, and CHARMM, a molecular simulation package. We do what is called combined QM/MM - quantum mechanics and molecular mechanics - simulations, so we use CHARMM to run molecular dynamics and have it call GAMESS as a subroutine whenever a quantum calculation is needed.
MSI: Can you explain what your poster describes?
MP: Pentacene is a planar [flat] molecule with five hexagonal benzene rings fused together. In the crystal or thin film form, pentacene displays some very unusual properties. Say you have two pentacene molecules side by side in a crystalline lattice. When one molecule absorbs energy from, for example, the sun, this absorbed energy - called a photon - excites an electron from one molecular orbital to another, higher-energy, molecular orbital. This forms an excited electronic state, but - what’s interesting about pentacene - is that through a process called singlet fission, you actually end up with two excited electrons, each on one of the neighboring pentacene molecules. So you’re getting two excited-state molecules from the absorption of just one photon. It’s kind of a two-for-one energy conversion process. The potential application is that we can use pentacene to make much more efficient solar cells as a source for renewable energy.
MSI: And that’s not a violation of thermodynamics laws?
MP: Right, that’s the interesting part! Quantum mechanically, when a molecule is excited from its ground state, which is typically a singlet state - all electrons are paired with one spin up and one spin down - its lowest-energy excited state is also a singlet. That is, after excitation, one electron has moved to a higher-energy molecular orbital, which makes two electrons unpaired, but they retain their respective spin states - one up and one down. The two unpaired electrons can also have the same spin - both spin up or both spin down - called a triplet state, but transitions from a singlet ground state to an excited triplet state are not allowed quantum mechanically. Regardless, the two excited pentacene molecules produced by singlet fission are in fact in the triplet state. So, after a photon is absorbed by a pentacene molecule and it’s excited to the lowest-energy singlet state, then, through some quantum mechanical process, the singlet state transitions to two excited triplet states.
Thermodynamics come into play when looking at the relative energy of the singlet and triplet excited states. Typically, the singlet excited state is lower in energy, but in pentacene, the triplet state is slightly less than half of the singlet state energy, which means that twice the energy of a triplet state is less than the singlet state energy. This quantum phenomenon makes it thermodynamically favorable for pentacene to undergo singlet fission.
The fact that pentacene undergoes singlet fission has been known for a long time. What we’re interested in is how this transition occurs. It’s been hypothesized that singlet fission involves an intermediate state, called a multiexciton (ME), which consists of two excited triplet states coupled together to form an overall singlet excited state. This state is optically-forbidden, meaning that it cannot be populated directly from the ground state, but it’s thought that the excited state pentacene shares its energy with a neighboring pentacene molecule to form a pair of correlated triplet states, each on one pentacene molecule. We’re investigating the way this ME state is populated and how it is coupled with the singlet excited state of a pentacene molecule.
MSI: So, you use the computer programs on the supercomputers to model this process?
MP: Yes, we use the computer programs to model each state, with the electrons excited in various ways, and then we calculate the electronic coupling between the states. There are three states important to the singlet fission process: the initially excited singlet state (S1); a charge-transfer (CT) state; and a pair of correlated triplet states, or a multiexciton (ME). If you go directly from the S1 to ME states, there’s a much smaller coupling than if you couple with the charge-transfer state, S1-to-CT then CT-to-ME. So these calculations show that including the intermediate charge-transfer state is necessary to get significant coupling to produce two excited, triplet state pentacene molecules.
MSI: Is this research something that can be applied immediately, or is it more basic research?
MP: This is basic research, but yes, there have been efforts to fabricate solar cell devices that make use of singlet fission. Here, we focus on understanding the underlying mechanism of this process.
MSI: Do you know if there’s anything else this could be used for?
MP: Mostly, the current interest in singlet fission comes from its potential to improve the efficiency of solar cells. Right now, the theoretical efficiency of single-junction solar cells to convert solar energy into electricity is limited to about 33%, the so-called Shokley-Queisser limit. But, if materials that undergo singlet fission are used, we could exploit this two-for-the-price-of-one energy conversion process and potentially break this limit.
MSI: Would that reduce the cost, if they could be made more efficient?
MP: I don’t know if will reduce the cost. But looking at where solar cells are now, with the materials that are currently used, efficiency is around 11%. One of the key motivations for this project is this quantum-mechanical limit that even if the solar cell is completely 100% efficient in all these other ways, due to the quantum mechanics, 33% efficiency is all you’ll ever get. That’s if everything else is perfect. This project is a way to increase that limit, because we’re getting two excited electrons that can both, potentially, be harvested to generate an electrical current. So, that’s the major advantage of using pentacene, because it undergoes singlet fission, we can break that theoretical barrier. If that’s improved, everything will be improved.
MSI: So, the long-term goals for this research are to prove your theory?
MP: The goal is to investigate the mechanism of how singlet fission happens in these kinds of organic monolayers. If we can understand what drives the reaction and what molecular properties affect this process, then down the road, we can use that knowledge to our advantage.
MSI: Is there anything else you’d like to mention about your work?
MP: Yes, the multistate density functional theory method I used for this poster was developed in our group. Density functional theory is a well-known electronic structure theory method. It’s very efficient computationally, it’s easy, it’s inexpensive, but it’s delocalized. With multistate density functional theory we can localize states on individual pentacene molecules. That’s why we can calculate these couplings. I’m also currently using this MSDFT method to study other processes related to solar energy conversion, such as proton-coupled electron transfer in photosynthesis.
MSI: This method was developed before you joined the Gao group?
MP: Yes, and it’s been ongoing. This project is just one of its many applications. This is a group effort, involving a number of people developing the theory, writing the computer code, and applying and validating the method in practical applications.
MSI: So, this is something that needs the supercomputers.
MP: Oh, definitely.
posted July 3, 2013
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).