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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 Ryan Bradley.

In early 2021, the computational cluster Hawk that was enabled by NSF support (Award #2019035) was put into production. A significant portion of the scholarly works produced since Hawk was deployed in 2021 were wholly or partly made possible by this computational resource, which is made available as a no-cost discovery platform for Lehigh University researchers, educators, and students.

Publications

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title2022
  1. Z. J. Knepp, L.A. Fredin, Real Temperature Model of Dynamic Disorder in Molecular Crystals. J. Phys. Chem A, (2022). doi: 10.1021/acs.jpca.2c02120
  2. 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
  3. Z. Liu, C.E. Ekuma, W. Li, J. Yang, X. Li, ElasTool: An automated toolkit for elastic constants calculation. Computer Physics Communications, 270, 108180 (2022). ISSN 0010-4655, doi: 10.1016/j.cpc.2021.108180

  4. Wei Sun, Keith Veenhuizen, Jacob Marsh, Volkmar Dierolf, Himanshu Jain, Determination of the structure of lithium niobosilicate glasses by molecular dynamics simulation with a new Nb-O potential. Computational Materials Science., 207, 111307 (2022) doi: 10.1016/j.commatsci.2022.111307

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title2010-2015
  1. “Detailed structure of the H-N-H center in GaAsyN1-y revealed by vibrational spectroscopy under uniaxial stress,” L. Wen, F. Bekisli, M. Stavola, W. B. Fowler, R. Trotta, A. Polimeni, M. Capizzi, S. Rubini, and F. Martinelli, Phys. Rev. B 81, 233201 (2010).
  2.  “Hydrogen impurities and shallow donors in SnO2 studied by infrared spectroscopy,” Figen Bekisli, Michael Stavola, W. Beall Fowler, Lynn Boatner, Erik Spahr, and Gunter Lüpke, Phys. Rev. B 84, 035213 (2011).
  3.  “Microscopic structure of a VH4 center trapped by C in Si,” Chao Peng, Haoxiang Zhang, Michael Stavola, W. Beall Fowler, Benjamin Esham, Stefan K. Estreicher, Andris Docaj, Lode Carnel, and Mike Seacrist, Phys. Rev. B 84, 195205 (2011).
  4. “Bond angles for O-H defects in SnO2 from polarization properties of their vibrational modes,” Figen Bekisli, W. Beall Fowler, Michael Stavola, Lynn A. Boatner, Erik Spahr, and Gunter Lüpke, Phys. Rev. B 85, 205202 (2012).
  5. “Microscopic origin of compressive strain in hydrogen-irradiated dilute GaAs1-yNy alloys: Role of  N-Hn centers with n>2 and their thermal stability,” L. Wen, M. Stavola, W. B. Fowler, S. Kleekajai, R. Trotta, A. Polimeni, M. Xapizzi, S. Rubini, F. Martelli, and C. W. Tu, Phys. Rev. B 86, 085206 (2012).
  6.  “Small polaron characteristics of an OD center in TiO2 studied by infrared spectroscopy,” Figen Bekisli, W. Beall Fowler, and Michael Stavola, Phys. Rev. B 86, 155208 (2012).
  7. “Contrasting the experimental properties of hydrogen in SnO2, In2O3, and TiO2,” Michael Stavola, Figen Bekisli, Weikai Yin, Kirby Smithe, W. Beall Fowler and Lynn A. Boatner, J. Appl. Phys. 115, 012001 (2014). 
  8. “Hydrogen centers and the conductivity of In2O3 single crystals,” Weikai Yin, Kirby Smithe, Philip Weiser, Michael Stavola, W. Beall Fowler, Lynn Boatner, Stephen J. Pearton, David C. Hays, and Sandro G. Koch, Phys. Rev. B 91, 075208 (2015).
  9. “Microscopic Structure of N-Hn Complexes in Dilute Nitride Semiconductors Revealed by Their Vibrational Properties,” Michael Stavola and W. Beall Fowler, in Hydrogenated Dilute Nitride Semiconductors, ed. by Gianluca Ciatto  (Pan Stanford, 2015), pp. 129-160.


Presentations

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title2022

  • Predicting Effects of Dynamic Disorder in Molecular Semiconductors (presentation, L.A. Fredin) American Conference on Theoretical Chemistry July 2022. 

  • Modeling Photoactive Organic Materials (presentation, L.A. Fredin) American Chemical Society (ACS) Midatlantic Regional Meeting (MARM) June 2022.

  • Modeling Vibrational Disorder in Organic Materials. (poster, Z.J. Knepp, L.A. Fredin) American Chemical Society (ACS) Midatlantic Regional Meeting (MARM) June 2022.
  • Developing models for oxide materials. (poster, G. Repa, L.A. Fredin) American Chemical Society (ACS) Midatlantic Regional Meeting (MARM) June 2022.

  • Accurate Models of Undercoordinated Photoactive Sites on Nanotitania (presentation, L.A. Fredin) 3rd Frontiers in Photochemistry Conference May 2022. 

  • Understanding Structure-Function Relationships in Disordered Materials (presentation, L.A. Fredin) Theory and Simulation of Electronic and Optical Processes in Molecules and Materials, Virtual.

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title2017
  • “Three-dimensional simulation of remodeling lamellipodial actin filament network.” (poster presentation, D. Holz, A. Hall, D. Vavylonis) 2017 American Society for Cell Biology Annual Meeting, Philadelphia PA.
  • “Multiscale Model of the Formin Homology 1 Domain Illustrates its Role in Regulation of Actin Polymerization.” (poster presentation, B.G. Horan, G. Zerze, G.L. Dignon, Y.C. Kim, D. Vavylonis, J. Mittal) 2017 American Society for Cell Biology Annual Meeting, Philadelphia PA.
  • “Multiscale Model of the Formin Homology 1 Domain Illustrates its Role in Regulation of Actin Polymerization” (oral presentation, B.G. Horan, G. Zerze, G.L. Dignon, Y.C. Kim, D. Vavylonis, J. Mittal) Cell Physics 2017 conference, Saarbrücken, Germany.
  • “Simulation of the effect of confinement in actin ring formation” (poster presentation, M. Adeli Koudehi, D. Vavylonis). 2017 Biophysical Society Annual Meeting, New Orleans, LA


Students Graduated

  1. Peter Schwarzenberg, Development and Validation of Virtual Mechanical Testing of Bone Fracture Healing, Ph.D. Dissertation (2021)
  2. Danielle Holz, Models of Dendritic Actin Network Dynamics in Lamellipodial Protrusions, Ph.D. Dissertation (2021)
  3. Brandon Horan, Molecular Dynamics Simulations Reveal Molecular Mechanisms of Actin Polymerization and its Regulation by Formin, Ph.D. Dissertation (2019)
  4. Maral Adeli Koudehi, Actin Bundle, Ring and Network Formation in Confining Environment, Ph. D. Dissertation (2019)
  5. Bashar Hassan Attiya, Energy harvesting devices operating near free surface, Ph. D. Dissertation (2019)
  6. Songul Kutlu, Monte-Carlo Simulations of Patch Models with Applications to Soft Matter,  Ph. D. Dissertation (2019)
  7. Cosan Daskiran, Large eddy simulations of ventilated micro-hydrokinetic turbine and pump-turbines, Ph. D. Dissertation (2018)
  8. I-Han Liu, Computational study of flow past arrays of plates in the vicinity of surfaces, Ph. D. Dissertation (2018)
  9. Thienbao Nguyen Carpency, Monte Carlo Studies of Patchy Ellipsoids, Ph. D. Dissertation (2018)
  10. Georgi Dimitrov Georgiev,  Algorithms in protein cavity classification, Masters Thesis (2018)
  11. Chanh Nguyen, Two approaches to defend against adversarial examples: Attention-based and Certificate-based, Masters Thesis (2018)
  12. Haolin Ma,  Direct Numerical Simulation of Rayleigh-Bénard Convection of Two Immiscible Fluids-Level Set Method, Ph. D. Dissertation (2017)
  13. Baiou Shi, Molecular Dynamics Studies on dynamic wetting, droplet rapid contact line advancement and nanosuspension drop self-pinning phenomenon, Ph. D. Dissertation (2017)
  14. Wei Wei,  Coarse Grain Molecular Model Development and Implementation for Describing von Willebrand Factor Behavior in Human Blood Flow, Ph. D. Dissertation (2017)
  15. Murat Al, Atomistic Mechanisms of Stress Evolution for Gold Thin Films on Nickel Substrates via Molecular Dynamics Simulations, Ph. D. Dissertation (2017)
  16. Kalin McDannell, Methods and application of deep-time thermochronology: Insights from slowly-cooled terranes of Mongolia and the North American craton, Ph. D. Dissertation (2017)
  17. Jien Zhang, Detection of Climate Extremes and Their Effects on Hydrology and Ecosystems: Case Studies in California and the Great Plains, USA, Ph. D. Dissertation (2017)
  18. Nicole Fortoul, Coarse-Grained and Analytical Models for Vesicle-to-Membrane Adhesion Mechanisms, Ph. D. Dissertation (2017)
  19. Frank A. Artmont, Evaluation of the Fatigue Performance and Dynamic Behavior of Single Support Bar Modular Bridge Expansion Joint Systems,  Ph. D. Dissertation (2017)
  20. Alexander P. Borselli, Galois Groups of CM Fields in Degrees 24, 28, and 30, Ph. D. Dissertation (2017)
  21. Ziyi Guo, Leveraging Structural Flexibility to Predict Protein Function,  Ph. D. Dissertation (2017)
  22. Jason Leigh Haaga, Study of the Effects of Anisotropy in Self-Assembling Systems, Ph. D. Dissertation (2017)
  23. Aman Karamlou, Multi-Scale Methodologies for Probabilistic Resilience Assessment and Enhancement of Bridges and Transportation Systems, Ph. D. Dissertation (2017)
  24. Nipun Goel, Effect of Dopants at the Grain Boundary on Thermal Transport in β-SiC at High Temperatures, Ph. D. Dissertation (2016)
  25. Mingkai Jiang, On the History and Evidence of the Colwell Index in Quantifying Environmental Predictability, and Its Applications in Characterizing Precipitation Predictability in the Conterminous United States, Ph. D. Dissertation (2016)

Grants Submitted/Awarded

  • Hannah Dailey (PI), CAREER: Multiscale Mechanical Characterization of Bone Fracture Callus, National Science Foundation (CMMI-1943287)
  • Vavylonis Dimitrios (PI) NIH R35GM136372: Modeling mechanisms in cytokinesis, cell polarization and motility (4/1/20-3/31/25)
  • Vavylonis Dimitrios (PI) NIH R01GM114201: Theoretical and experimental studies of distributed actin turnover (6/1/16-5/3/21)
  • Greg Lang (PI) NIH 1R01GM127420-01: Mapping genetic interactions between growth-promoting mutations in yeast (5/1/2018 - 4/30/2023)
  • Yue Yu (PI),  A Framework for Multiscale/Multiphysics Mathematical Modeling of Cerebral Aneurysm Rupture, National Science Foundation (08/01/2016-07/31/2020)
  • Yue Yu (PI), A Multiphysics Mathematical Framework on Modeling Cerebral Aneurysms, Simons Foundation Collaboration Grant(09/01/2015-08/31/2017)
  • Yue Yu (PI), CAREER: A Local–Nonlocal Coupling Framework for Tissue Damage in Fluid–Structure Interaction, National Science Foundation (09/01/2018-08/31/2023)