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The following are Research Outputs from all resources supported since 2010 that have been reported to Research Computing staff. To list your publications, presentations, grants, awards, students graduated, etc, please contact Alex Pacheco.

Publications

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title2022
  • K. Zhao, B. Duka, H. Xie, D. J. Oathes, V. Calhoun, and Y. Zhang. "A dynamic graph convolutional neural network framework reveals new insights into connectome dysfunctions in ADHD" NeuroImage, 246: 118774 (2022). DOI 10.1016/j.neuroimage.2021.118774


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title2021
  • M. Razizadeh, M. Nikfar, and Y. Liu, “Small molecule therapeutics to destabilize the ACE2-RBD complex: A molecular dynamics study,” Biophysical Journal, 120 (14), 2793–2804 (2021), doi: 10.1016/J.BPJ.2021.06.016.
  • G. Repa, L. A. Fredin, "Parameter Space Exploration Reveals Interesting Mn-doped SrTiO3 Structures", Phys. Chem. Chem. Phys, 23, 23486 (2021), (DOI: 10.1039/D1CP02417E)
  • S. M. Martin, A. N. Oldacre, C. A. Pointer, T. Huang, G. Repa, L. A.  Fredin, and E. R. Young, "Proton-controlled Non-exponential Photoluminescence in a Pyridyl-Amidine-substituted Re(I) complex", Dalton Transactions, 50, 7265 (2021). (DOI: 10.1039/D1DT01132D)
  • P. Schwarzenberg*, T. Ren*, K. Klein, B. von Rechenberg, S. Darwiche, and H. L. Dailey, "Domain-Independent Simulation of Physiologically Relevant Callus Shape in Mechanoregulated Models of Fracture Healing", Journal of Biomechanics, 118, 110300 (2021). PMID: 33601180 (*equal contribution)
  • P. Schwarzenberg, K. Klein, S. J. Ferguson, B. von Rechenberg, S. Darwiche, and H. L. Dailey, " Virtual Mechanical Tests Out-Perform Morphometric Measures for Assessment of Mechanical Stability of Fracture Healing In Vivo", Journal of Orthopaedic Research, 39(4), 727 (2021). PMID: 32970350
  • D. Holz, R. A. Hall, E.  Usukura, S. Yamashiro, N. Watanabe, and D. Vavylonis, "A mechanism with severing near barbed ends and annealing explains structure and dynamics of dendritic actin networks", 2021 (pending revisions for eLife) bioRxiv DOI: 10.1101/2021.03.31.437985 
  • D. M. Rutkowski and D. Vavylonis, "Discrete mechanical model of lamellipodial actin network implements molecular clutch mechanism and generates arcs and microspikes", 2021, PLOS Comp. Biol., accepted, bioRxiv doi: 10.1101/2021.05.03 
  • T. Litschel, C. F. Kelley, D. Holz, M. Adeli Koudehi, S. Kenjiro Vogel, L. Burbaum, N. Mizuno, D. Vavylonis, and  P. Schwille, "Reconstitution of Contractile Actomyosin Rings in Vesicles," Nature Communications 12, 2254 (2021) DOI: 10.1038/s41467-021-22422-7
  • A. Venzie, A. Portoff, C. Fares, M. Stavola, W. B. Fowler, F. Ren, and Stephen J. Pearton,  "OH-Si complex in hydrogenated n-type β-Ga2O3:Si", Appl. Phys. Lett. 119, 062109 (2021).
  • Y. Fan, X. Tian, X. Yang, X. Li, C. Webster, and Y. Yu, "An asymptotically compatible probabilistic collocation method for randomly heterogeneous nonlocal problems", Submitted (2021).
  • H. You, Y. Yu, S. Silling, and M. D’Elia, "A data-driven peridynamic continuum model for upscaling molecular dynamics", Preprint (2021).
  • H. You, Y. Yu, M. DÉlia, T. Gao, and S. Silling, "Nonlocal kernel network (NKN): a stable and resolution-independent deep neural network", Under Review (2021).
  • M. Foss, P. Radu, Y. Yu, "Convergence analysis and numerical studies for linearly elastic peridynamics with dirichlet-type boundary conditions", arXiv preprint arXiv:2106.13878 (2021).
  • M. DÉlia, and Y. Yu, "On the prescription of boundary conditions for nonlocal poisson’s and peridynamics models", arXiv preprint arXiv:2107.04450 (2021).
  • H. You, Y. Yu, N. Trask, M. Gulian, M. D’Elia, Data-driven learning of nonlocal physics from high fidelity synthetic data, Computer Methods in Applied Mechanics and Engineering 374 (2021) 113553.
  • B. N. Ezealigo, and C. E. Ekuma, "Influence of vacancy defect on the structural and optical properties of hexagonal barium titanate ceramics: Experimental and theoretical analysis", Materials Letters, 304, 130582 (2021) (DOI: 10.1016/j.matlet.2021.130582)
  • Lalrinkima,  C. E. Ekuma, T. C. Chibueze, L. A. Fomin, I. V. Malikov, L. Zadeng, and D. P. Rai, "Electronic, magnetic, vibrational, and X-ray spectroscopy of inverse full-Heusler Fe2IrSi alloy", Phys. Chem. Chem. Phys., 23, 11876 (2021) (DOI: 10.1039/D1CP00418B)
  • R.M. Obodo, T. C. Chibueze, I. Ahmad, C. E. Ekuma, A. T. Raji, M. Maaza, and F. I. Ezema, "Effects of copper ion irradiation on CuyZn1−2y−xMny/GOCuyZn1−2y−xMny/GO supercapacitive electrodes". J Appl Electrochem, 51, 829–845 (2021). (DOI: 10.1007/s10800-021-01543-3)
  • K. J. Fisher, R. C. Vignogna, and G. I. Lang, "Overdominant Mutations Restrict Adaptive Loss of Heterozygosity at Linked Loci", Genome Biol Evol., 13(8), evab181 (2021) doi: 10.1093/gbe/evab181. PMID: 34363476.
  • R. C. Vignogna, S. W. Buskirk, and G. I. Lang GI. "Exploring a local genetic interaction network using evolutionary replay experiments", Mol Biol Evol., 38(8), 3144–3152(2021). doi: 10.1093/molbev/msab087. PMID: 33749796.
  • Y. Zhang, W. Wu, R. Toll, S. Naparstek, A. Maron-Katz, M. Watts, J. Gordon, J. Jeong, L. Astolfi, E. Shpigel, P. Longwell, K. Sarhadi, D. EI-Said, Y. Li, C. Cooper, C. Chin-Fatt, M. Arns, M. Goodkind, M. Trivedi, C. Marmar, and A. Etkin, "Identification of psychiatric disorder subtypes from functional connectivity patterns in resting-state electroencephalography", Nature Biomedical Engineering, 5: 309-323 (2021) DOI 10.1038/s41551-020-00614-8
  • Y. Zhang, H. Zhang, E. Adeli, X. Chen, M. Liu, and D. Shen. "Multiview feature learning with multiatlas based functional connectivity networks for MCI diagnosis", IEEE Transactions on Cybernetics, 2021, Accepted. DOI 10.1109/TCYB.2020.3016953
  • Y. Zhang, T. Zhou, W. Wu, H. Xie, H. Zhu, G. Zhou, A. Cichocki, "Improving EEG decoding via clustering-based multi-task feature learning". IEEE Transactions on Neural Networks and Learning Systems, 2021, Accepted. DOI 10.1109/TNNLS.2021.3053576


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title2020
  • Wehrmann, C. M.; Imran, M.; Pointer, C. A.; Fredin, L. A.*; Young, E. R.*; Chen, M. S.*, Spin Multiplicity Effects in Doublet versus Singlet Emission: The Photophysical Consequences of a Single Electron. Chem. Sci., 2020, 11, 10212-10219. (DOI: 10.1039/d0sc04211k)          
  • Ren T and Dailey HL. Mechanoregulation Modeling of Bone Healing in Realistic Fracture Geometries. Biomechanics and Modeling in Mechanobiology, 19, pp. 2307-2322, 2020. PMID: 32524288
  • Horan B. G., Hall A., and Vavylonis D., Insights into actin polymerization and nucleation using a coarse grained model, 2020, Biophys. J. 119:553-566. DOI: 10.1016/j.bpj.2020.06.019
  • “Determination of dielectric axes and transition moment directions in β-Ga2O3 from the polarization dependence of vibrational spectra,” Amanda Portoff, Andrew Venzie, Michael Stavola, W. Beall Fowler, and Stephen J. Pearton, J. Appl. Phys. 127, 055702 (2020).
  •  “Trapping of multiple H atoms at the Ga(1) vacancy in β-Ga2O3,” W. Beall Fowler, Michael Stavola, Ying Qin, and Philip Weiser, Appl. Phys. Lett. 117, 142101 (2020).
  •  “Vibrational properties of oxygen-hydrogen centers in H+ - and D+  -implanted Ga2O3,” Amanda Portoff, Andrew Venzie, Ying Qin, Michael Stavola, W. Beall Fowler, and Stephen J. Pearton, ECS J. Solid State Sci. Technol. 9, 125006 (2020).

  • H. You, X. Lu, N. Task, Y. Yu, An asymptotically compatible approach for neumann-type boundary condition on nonlocal problems, ESAIM: Mathematical Modelling and Numerical Analysis 54 (4) (2020) 1373–1413. 

  • C. H. Rycroft, C.-H. Wu, Y. Yu, K. Kamrin, An eulerian approach for modeling passive and active soft solids in fluids, Journal of Fluid Mechanics 898 (2020) A9. 

  • M. D’Elia, X. Tian, Y. Yu, SIAM Journal on Scientific Computing 42 (4) (2020) A1935–A1949.

  • M. D’Elia, X. Li, P. Seleson, X. Tian, Y. Yu, A review of local-to-nonlocal coupling methods in nonlocal diffusion and nonlocal mechanics, Journal of Peridynamics and Nonlocal Modeling (2020).

  • H. You, Y. Yu, D. Kamensky, An asymptotically compatible formulation for local-to-nonlocal coupling problems without overlapping regions, Computer Methods in Applied Mechanics and Engineering 366 (2020) 113038. 

  • D. Wei, T. Gao, Y. Yu, Dags with no fears: A closer look at continuous optimization for learning bayesian networks, Advances in Neural Information Processing Systems 33 (2020).

  • L. Zhang, M. Yu, T. Gao, Y. Yu, Mcmh: Learning multi-chain multi-hop rules for knowledge graph rea soning, in: Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing: Findings, 2020, pp. 3948–3954. 

  • Y. Yu, T. Gao, Dags with no curl: Efficient dag structure learning, NeurIPS Workshop on Causal Discovery and Causality-Inspired Machine Learning (2020). 

  • “Determination of dielectric axes and transition moment directions in β-Ga2O3 from the polarization dependence of vibrational spectra,” Amanda Portoff, Andrew Venzie, Michael Stavola, W. Beall Fowler, and Stephen J. Pearton, J. Appl. Phys. 127, 055702 (2020).
  • “Trapping of multiple H atoms at the Ga(1) vacancy in β-Ga2O3,” W. Beall Fowler, Michael Stavola, Ying Qin, and Philip Weiser, Appl. Phys. Lett. 117, 142101 (2020).
  • “Vibrational properties of oxygen-hydrogen centers in H+ - and D+  -implanted Ga2O3,” Amanda Portoff, Andrew Venzie, Ying Qin, Michael Stavola, W. Beall Fowler, and Stephen J. Pearton, ECS J. Solid State Sci. Technol. 9, 125006 (2020).
  • Buskirk SW, Rokes AB, Lang GI. 2020. Adaptive evolution of nontransitive fitness in yeast. Elife. Dec 29;9:e62238. doi: 10.7554/eLife.62238.
  • T.C. Chibueze and C.E. Ekuma and A.T. Raji and F.I. Ezema and C.M.I. Okoye, Tetragonal and uniaxial strains in pristine and doped half-Heusler AuMnSn alloy, ournal of Alloys and Compounds, 2020, 848, 156186 (DOI: 10.1016/j.jallcom.2020.156186)
  • C.E. Ekuma, Z.-L. Liu, Mechanical properties and hardness of boron pnicogens BX (X = N, P, As), Materialia, 2020, 14, 100904 (DOI: 10.1016/j.mtla.2020.100904)
  • Egbo, Kingsley O. and Ekuma, Chinedu E. and Liu, Chao Ping and Yu, Kin Man, Efficient p-type doping of sputter-deposited NiO thin films with Li, Ag, and Cu acceptors, Phys. Rev. Materials, 2020, 4, 104603 (DOI: 10.1103/PhysRevMaterials.4.104603)

  • Kingsley O. Egbo, Chao Ping Liu, Chinedu E. Ekuma, and Kin Man Yu , "Vacancy defects induced changes in the electronic and optical properties of NiO studied by spectroscopic ellipsometry and first-principles calculations", Journal of Applied Physics 128, 135705 (2020) (DOI: 10.1063/5.0021650)

  • T C Chibueze and C E Ekuma and A T Raji and D P Rai and C M I Okoye, Ferromagnetic half-metallicity in half-Heusler {AuMnSn}:Te Alloy, Materials Research Express, 7, 076519 (2020) (DOI: 10.1088/2053-1591/ab88ff)

  • K. Aziz and C. E. Ekuma, "Electronic and vibrational spectroscopy of miscible MgO–ZnO ternary alloys", Journal of Applied Physics 127, 075706 (2020) (DOI: 10.1063/1.5141363)

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