Current and future use of the UNLV National Supercomputing Institute's resources (non-exhaustive)

Rebecca Martin,
UNLV Department of Physics and Astronomy

Project Name:

• Planet formation in and around binary star systems: simulating the formation and evolution of protoplanetary discs in and around binary stars systems in order to understand the properties of observed exoplanets.
• Retrograde accretion in Be/X-ray binaries: understand outbursts in Be/X-ray binaries when material is transferred from the Be star to the neutron star companion.
• Formation of super-Earths around low mass stars: explain how there are so many observed super-Earth mass planets around very low-mass stars.
• Stability of circumbinary planets: exploring the stability of circumbinary planetary systems and the ejection of planets to form free-floating planets.

Grants: The first project is supported by a NASA grant.

Publications related to Cherry-Creek:

• Tilted circumbinary planetary systems as efficient progenitors of free floating planets, Chen. C., Martin R. G., Nixon C. J., Lubow S. H., 2024, ApJL, 961, L5
• Mergers of black hole binaries driven by tilted circumbinary discs, Martin R. G., Lepp S., Zhang B., Nixon C. J., Childs A. C., 2024, MNRAS Letters, 528, L161
• Retrograde discs around one component of a binary are unstable to tilting, Overton M., Martin R. G., Lubow S. H., Lepp S., 2024, MNRAS Letters, 528, L106
• Disc precession in Be/X-ray binaries drives superorbital variations of outbursts and colour, Martin R. G., Charles P. A., 2024, MNRAS Letters, 528, L59
• Can a binary host three giant planets? Chen C., Martin R. G., Nixon C. J., 2023, MNRAS, 525, 3781
• Tidal truncation of circumplanetary discs fails above a critical aspect ratio, Martin R. G., Armitage P. J., Lubow S. H., Price D. J., 2023, ApJ, 953, 2
• Superorbital periods of Be/X-ray binaries driven by stellar spin precession, Martin R. G., 2023, MNRAS Letters, 523, L75
• Orbital stability of two circumbinary planets around misaligned eccentric binaries, Chen C., Lubow S. H., Martin R. G., Nixon C. J., 2023, MNRAS, 521, 5033

Dr. Edwin Oh,
Nevada Institute of Personalized Medicine and
Dr. Amei Amei,
UNLV Department of Mathematical Sciences

Project Name:

• Longitudinal genome-wide-association analyses
• Longitudinal epigenome-wide-association-analyses: Testing if there are any SNPs that could convey time-dependent genetic effects in various diseases, mainly in AD and hypertension.

Grants or potential grants: preliminary data will be used in a R01 submission for the Feb 2024 cycle.

Publications related to Cherry-Creek

• Zhuang, X., Xu, G., Amei, A., Cordes, D., Wang, Z. and Oh, E., 2023. Detecting time-varying genetic effects in Alzheimer's disease using a longitudinal GWAS model. bioRxiv, pp.2023-10.
• Zhuang X, Xu G, Amei A, and Oh E. (2023) Longitudinal genome wide association studies in Alzheimer's disease. Alzheimer's Association International Conference 2023 (Oral Presentation). Amsterdam, Netherland.

Dr Nicole Pietrasiak, UNLV School of Life Sciences

Project Name:

• Phylogenomics and comparative genomics analysis of exopolysaccharides genes between aquatic and terrestrial filamentous cyanobacteria: insights into cyanobacteria terrestrialization

Publication related to Cherry-Creek:

• Chen, M. Y., Teng, W. K., Zhao, L., Hu, C. X., Zhou, Y. K., Han, B. P., ... & Shu, W. S. (2021). Comparative genomics reveals insights into cyanobacterial evolution and habitat adaptation. The ISME Journal, 15(1), 211-227.
• Sánchez-Baracaldo, P., Bianchini, G., Di Cesare, A., Callieri, C., & Chrismas, N. A. (2019). Insights into the evolution of picocyanobacteria and phycoerythrin genes (mpeBA and cpeBA). Frontiers in Microbiology, 10, 45.

Dr. Balakrishnan Naduvalath,
UNLV Department of Chemistry

Project Name:

• Quantum mechanical investigation of chemical reactions in diverse environments

Grants or potential grants: Supported by NSF, DOD and NASA grants.

Jeffery Shen,
UNLV School of Life Sciences

Project Name:

• The roles of WRKY transcription factors in seed germination and plant responses to drought: Mine rice genomes, transcriptomes, proteomes, and epigenomes to reveal the networks underlying plant dormancy and germination, and responses to abiotic stresses.

Grants or potential grants: Revising an NSF proposal for resubmission: use computing to improve our interior models and with observational data to characterize planets.

Publications related to Cherry-Creek:

• Villacastin, A.J., Adams, K.S., Boonjue, R., Rushton, P.J., Han, M., Shen, Q.J.: Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice, Scientific Reports, 2021, 11:14887

Jason H. Steffen,
UNLV Department of Physics and Astronomy

Project Name:

• Characterization of Planet Interiors with MAGRATHEA
• Stellar evolution and tidal dissipation in REBOUNDx

Publication related to Cherry-Creek

• Childs, A. C., Yang, C., Shakespeare, C., Rice, D.R., Steffen, J. H., (2023) Composition constraints of the TRAPPIST-1 planets from their formation, Submitted to MNRAS.
• Rice, D. R., Steffen, J. H., (2023) Stable lifetime of compact, evenly-spaced planetary systems with non-equal masses, Accepted to MNRAS, [arXiv:2206.11374].
• Huang, C. H., Rice, D. R., Steffen, J. H., (2022) MAGRATHEA: An open-source spherical symmetric planet interior structure code, MNRAS, 513, 5256 [arXiv:2201.03094].
• MacDonald, M. G., Feil, L., Quinn T., Rice, D. R., (2022) Confirming the 3:2 Resonant Chain of K2-138, AJ, 163, 162 [arXiv:2201.12687].
• Rice, D. R., Rasio, F. A., Steffen, J. H., (2018) Survival of non-coplanar, closely packed planetary systems after a close encounter, MNRAS, 481, 2205[arXiv:1807.07668].
• Stanley A Baronett, Noah Ferich, Daniel Tamayo, Jason H Steffen, Stellar evolution and tidal dissipation in REBOUNDx, Monthly Notices of the Royal Astronomical Society, Volume 510, Issue 4, March 2022, Pages 6001—6009, https://doi.org/10.1093/mnras/stac043

Francis Cucinotta and Sungmin Pak,
UNLV Department of Integrated Health Sciences

Project Name:

• Computational study for tissue-specific dosimetric quantities of secondary radiation for lunar and Mars exploration.

Publications related to Cherry-Creek:

• Pak & Cucinotta, 2024. Tissue-specific dose equivalents of secondary mesons and leptons during galactic cosmic ray exposures for Mars exploration. Life Sciences in Space Research, 41:29-42.

Louisa Messenger,
UNLV School of Life Sciences

Project Name:

• Comparative genomics of Anopheles vectors of malaria
• Population genomics of an invasive mosquito vector, Aedes aegypti, in Nevada
• Tracking the genetic origins of West Nile Virus in Clark County, Nevada

Grants or potential grants:

• Project 1: Funding: the Global Fund to Fight AIDS, Tuberculosis and Malaria.
• Project 2&3: UNLV startup

Lukasz Sznajder,
UNLV Department of Chemistry and Biochemistry

Project Name:

• Delineating Pathogenic RNA Species in Myotonic Dystrophy Type 2
• Identifying Tandem Repeat Expansion-mediated Mechanisms of Autism-risk Genes

Chris Papesh,
UNLV Department of Healthcare

Projects:

• Cardiff Violence Prevention Project: built AI models that identify and map the locations of violence-injuries and drug overdoses in Nevada.

Yu Kuang,
UNLV Department of Integrated Health Sciences

Projects:

• Preclinic/Clinic Multiple Modality Imaging and Image-guided Radiation Therapy/Particle therapy: investigate a highly integrated quad-modal on-board imaging configuration combining positron emission tomography (PET), single-photon emission computed tomography (SPECT), spectral CT, and cone-beam computed tomography (CBCT) in a small-animal radiation therapy (SART) platform using a Monte Carlo model as a proof-of-concept.

Grants or potential grants: UNLV Startup fund

Publication related to Cherry-Creek:

• H. Wang, K. Nie, J. Chang, and Y. Kuang, A Monte Carlo study to investigate the feasibility of an on-board SPECT/spectral-CT/CBCT imager for medical linear accelerator, Med. Phys., vol. 47, no. 10, pp. 5112-5122, Oct. 2020.
• H. Wang, and Y. Kuang, First demonstration of triple onboard imaging in a small-animal radiation therapy platform, Int. J. Radiat. Oncol. Biol. Phys., vol. 99, no. 2, pp. S68-S68, Oct. 2017.
• H. Wang, and Y. Kuang, The Feasibility of Simultaneous CBCT, spectral CT and SPECT Online Imaging Using a Novel Linac Gantry-Based On-Board Imager, Med. Phys., vol. 44, no. 6, pp. 3184-3184. 2017.
• H. Wang, K. Nie, and Y. Kuang, An On-Board Spectral-CT/CBCT/SPECT Imaging Configuration for Small-Animal Radiation Therapy Platform: A Monte Carlo Study, IEEE Trans. Med. Imaging, vol. 39, no. 3, pp. 588-600, Mar. 2020.

Linchuan Shen,
UNLV Department of Mathematical Sciences

Projects:

• Detection of interactions between genetic marker sets and environment in a genome-wide study of hypertension: Development of powerful quantitative tools capable of integrating in complex diseases has the potential to facilitate the accurate curation and analysis of large genetic epidemiological studies.

Grants or potential grants: National Science Foundation [DMS1916246], the National Institutes of Health [K01AA023321, R01LM014087], and the COBRE pilot grant [GR13574].

Abinash Kumar Shaw,
UNLV Department of Computer Science

Projects:

• The impact of first sources in the universe on the intergalactic medium during reionization epoch: simulate the underlying hydrogen distribution and the sources (formed stochastically) in the universe using high dynamic range hydrodynamic simulation.

Brian Hedlund,
UNLV Department of Life Sciences

Projects:

• Novel repair replicase: To develop workflows with a novel thermophilic UDG-PolA fusion to lower error rates during DNA amplification and sequencing. Includes large analyses of DNA polymerases.
• Collaborative Research: Investigating the link between modern spring activity and associated paleospring mounds in Death Valley, NP: To integrate microbial community composition and activity with modern travertine formation and Pleistocene spring mounds. Includes large analyses of microbial genomes.
• A systems-level approach to probe the effect of a high-fat/high-protein diet in Clostridioides difficile infection: Determine the effects of diet macronutrients on microbiome function and susceptibility to Clostridioides difficile infection severity.
• Single cell genome-to-phenome: Integrating genome and phenome analyses of individual microbial cells in complex microbiomes. To test the hypothesis that Omnitrophota that are abundant and widespread in springs are symbiotic and are either acetogenic or respiratory.
• Influence of tectonic- and climatic-driven habitat fragmentation on the evolution of crenophilic microbes in North America?s driest desert. Microbial genome evolution of crenophilic (spring-loving) microorganisms from the southern Great Basin. Grants or potential grants: Publication related to Cherry-Creek

Publications related to Cherry-Creek:

• Lai D, Hedlund BP*, Mau RL, Jiao JY, Li J, Hayer M, Dijkstra P, Schwartz E, Li WJ, Dong H, Palmer M, Dodsworth JA, Zhou EM, Hungate BA*. 2023. Resource partitioning and amino acid assimilation in a terrestrial geothermal spring. ISME Journal. 17(11):2112-2122. https://doi.org/10.1038/s41396-023-01517-7.
• Palmer M, Covington JK, Zhou EM, Thomas SC, Habib N, Seymour CO, Lai D, Johnston J, Hashimi A, Jiao JY, Muok AR, Liu L, Xian WD, Zhi XY, Li MM, Silva LP, Bowen BP, Louie K, Briegel A, Pett-Ridge J, Weber PK, Tocheva EI, Woyke T, Northen TR, Mayali X, Li WJ, Hedlund BP*. 2023. Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past. ISME Journal 17(7):952-966. https://doi.org/10.1038/s41396-023-01405-0.
• Seymour CO, Palmer M, Becraft ED, Stepanauskas R, Friel AD, Schulz F, Woyke T, Eloe-Fadrosh E, Lai D, Jiao JY, Hua ZS, Liu L, Lian ZH, Li WJ, Chuvochina M, Finley BK, Koch BJ, Schwartz E, Dijkstra P, Moser DP, Hungate BA, Hedlund BP*. 2023. Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota. Nature Microbiology 8(4):727-744. https://doi.org/10.1038/s41564-022-01319-1.
• Bhute S, Mefferd CC, Phan JR, Ahmed M, Fox-King AE, Alarcia S, Villarama JV, Abel-Santos EA*, Hedlund BP. 2022*. A high-carbohydrate diet prolongs dysbiosis and Clostridioides difficile carriage in a hamster model of infection. Microbiology Spectrum. 2022 Jun 16:e0180421. https://doi.org/10.1128/spectrum.01804-21.
• Phan J, Do D, Truong MC, Ngo C, Phan J, Sharma S, Schilke A, Mefferd C, Villarama J, Lai D, Hedlund BP, Firestine S, Abel-Santos EA*. 2022. An aniline-substituted bile salt analog protects both mice and hamsters from multiple Clostridioides difficile strains. Antimicrobial Agents and Chemotherapy 66(1):e0143521. https://doi.org/10.1128/AAC.01435-21
• Thomas SC, Payne DM, Tamadonfar KO, Seymour CO, Jiao J-Y, Murugapiran SK, Lai D, Lau R, Bowen BP, Silva LP, Louie K, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese NJ, Mikhailova N, Chen I-M, Stamatis D, Reddy TBK, O?Mally R, Daum C, Shapiro N, Ivanova N, Krypides N, Woyke T, Eloe-Fadrosh EA, Hamilton TL, Dijkstra P, Dodsworth JA, Northen TR, Li W-J, Hedlund BP*. 2021. Genomics, exometabolomics, and metabolic probing reveal conserved proteolytic metabolism of Thermoflexus hugenholtzii and three candidate species from China and Japan. Frontiers in Microbiology 12:632731. https://www.frontiersin.org/articles/10.3389/fmicb.2021.632731/full
• Mefferd CC, Bhute SS, Phan JR, Villarama JV, Do DM, Abel-Santos EA, Hedlund BP*. 2020. A high-fat/high-protein, Atkins-type diet exacerbates Clostridioides (Clostridium) difficile infection in mice, whereas a high-carbohydrate diet protects. mSystems. 5(1):e00765-19. https://doi.org/10.1128/msystems.00765-19 (Editor?s choice).
• Thomas SC, Tamadonfar KO, Seymour CO, Lai D, Dodsworth JA, Murugapiran SK, Eloe-Fadrosh EA, Dijkstra P, Hedlund BP*. 2019. Position-specific metabolic probing and metagenomics of microbial communities reveal conserved central carbon metabolic network activities at high temperatures. Frontiers in Microbiology. 10: 1427. https://doi.org/10.3389/fmicb.2019.01427
• Howerton A, Seymour CO, Murugapiran SK, Liao Z, Phan J, Estrada A, Wagner AJ, Mefferd CC, Hedlund BP, Abel-Santos E*. 2018. Effect of the synthetic bile salt analog CamSA on the hamster model of Clostridium difficile infection. Antimicrobial Agents and Chemotherapy. 62: e02251-17. https://doi.org/10.1128/AAC.02251-17

Zach Perzan,
UNLV Department of Geoscience

Projects

• Hybrid modeling of managed aquifer recharge across overdrafted groundwater basins in California
• Understanding subsurface biogeochemical responses to flash flooding in arid environments

Joseph Lombardo,
Executive Director
National Supercomputing Institute (NSI) and
Dedicated Research Network.

Projects:

• The sequenced rat brain transcriptome — its use in identifying networks predisposing alcohol consumption. Research collaboration with Boris Tabakoff, PhD, Skaggs School of Pharmacy & Pharmaceutical Sciences, Institute for Behavioral Genetics, University of Colorado Denver.
• Artificial Intelligence in support of drug discovery for neurodegenerative disorders. In collaboration with the “International Neurodegenerative Disorders Research Center” (INDRC). INDRC is the world- leading distributed international non-profit research center for Alzheimer's disease and other neurodegenerative disorders.
Associates:
• Ara S. Khachaturian, PhD, Chair and President of the National Biomedical Research Ethics Council (NBREC) a Nevada-based 501(c)(3) tax exempt public charity that leads an international effort to improve clinical and public health research ethics.
• Bruno Vellas, MD, PhD is Professor of Medicine and Chairman of the Department of Internal Medicine and Geriatric Medicine at the CHUT, and Chief of the Alzheimer's Disease Clinical and Research Center at the University Hospital Center in Toulouse, France.
• Wolfgang Wahlster is a Professor of Artificial Intelligence (AI) and a pioneer of AI in Germany and Europe.
• Maria Rossini, Director of the Neuroscience Area of the Policlinico Foundation.
• Dr. Bairu, Adjunct Professor at the University of California, San Francisco School of Medicine where he lectures on global clinical trial's design, development, and conduct.
• Jean-Marie Charles Bouteiller, Research Associate Professor of Biomedical Engineering, joined the University from University of Montpellier, FRANCE) to start a PhD in Computational Neuroscience with Prof. Michel Baudry.
• Zaven Khachaturian, PhD, is the President of Prevent Alzheimer's Disease 2020. Emeritus Founding Editor-in-Chief of Alzheimer's & Dementia: Journal of the Alzheimer's Association.

Publications:

• Title: Can Artificial Intelligence Advance New Pathways for Drug Discovery for Alzheimer's and other Neurodegenerative Disorders? Khachaturian AS, Khachaturian Z, Wahlster W, Lombardo J.M. Submitted Nov. 2023, currently under review by the Alzheimer's & Dementia Journal, Wiley.

Laura Saba,
University of Colorado School of Medicine
Department of Pharmacology

Projects:

• NIDA Core Center of Excellence in Omics, Systems Genetics, and the Addictome (P30 DA044223 from NIDA/NIH)