Research Computing Scholarly Products

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Last updated: May 01, 2023 by Ryan Bradley
16 min read

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

 2022
  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

 2021
  1. E.H. Spielvogel, B.G. Stevenson, M.J. Stringer, Y. Hu, L.A. Fredin, J.R. Sweirk, Insights into the Mechanism of an Allylic Arylation Reaction via Photoredox Coupled Hydrogen Atom Transfer. J. Org. Chem., 87, 223-230 (2021). doi: 10.1021/acs.joc.1c02235
  2. G. M. Repa, L. A. Fredin, Parameter Space Exploration Reveals Interesting Mn-doped SrTiO3 Structures, Phys. Chem. Chem. Phys, 23, 23486 (2021), doi: 10.1039/D1CP02417E
  3. 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
  4. 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 doi: 10.1016/j.jbiomech.2021.110300 (*equal contribution)
  5. 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 doi: 10.1002/jor.24866
  6. 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 
  7. 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: 10.1371/journal.pcbi.1009506 
  8. 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
  9. 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). doi: 10.1063/5.0059769
  10. 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).
  11. H. You, Y. Yu, S. Silling, and M. D’Elia, "A data-driven peridynamic continuum model for upscaling molecular dynamics", Preprint  arXiv:2108.04883 [cond-mat.mtrl-sci] (2021).
  12. 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).
  13. 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 [math.AP] (2021).
  14. M. DÉlia, and Y. Yu, "On the prescription of boundary conditions for nonlocal poisson’s and peridynamics models", arXiv preprint arXiv:2107.04450  [math.NA] (2021).
  15. 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, 113553 (2021). doi: 10.1016/j.cma.2020.113553
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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

  25. P. M. Wilson, M. L. Chin, C. E. Ekuma, S. Najmaei, K. M. Price, T. Schiros, and J. Hone, "Chlorine-mediated atomic layer deposition of HfO2 on graphene". J. Mater. Chem. C, 9, 17437-17443 (2021). doi:10.1039/D1TC03502A

  26. J. Munshi, A. Roy, S. Hansen, C.E. Ekuma, and G. Balasubramanian, "Effect of vacancy defects on the thermal transport of β-Ga2O3", Molecular Simulation, 47(12), 1017–1021 (2021). doi:10.1080/08927022.2021.1941943

  27. Wei Sun, Volkmar Dierolf, Himanshu Jain. Molecular dynamics simulation of the effect of cooling rate on the structure and properties of lithium disilicate glass. Journal of Non-Crystalline Solids. 569, 120991 (2021). doi: 10.1016/j.jnoncrysol.2021.120991

 2020
  1. 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)          
  2. 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
  3. 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
  4. “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).
  5.  “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).
  6.  “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).

  7. 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. 

  8. 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. 

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

  10. 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).

  11. 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. 

  12. 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).

  13. 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. 

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

  15. “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).
  16. “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).
  17. “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).
  18. Buskirk SW, Rokes AB, Lang GI. 2020. Adaptive evolution of nontransitive fitness in yeast. Elife. Dec 29;9:e62238. doi: 10.7554/eLife.62238.
  19. 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)
  20. 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)
  21. 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)

  22. 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)

  23. 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)

  24. 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)

 2019
  1. Adeli Koudehi M., Rutkowski D., and Vavylonis D., Organization of Associating or Crosslinked Actin Filaments in Confinement, 2019, Cytoskeleton, 76:532-548 DOI: 10.1002/cm.21565
  2. Xu T., Langouras C., Adeli Koudehi M., Vos B. E., Wang N., Koenderink G. H., Huang X., and Vavylonis D., Automated Tracking of Biopolymer Growth and Network Deformation with TSOAX, 2019, Scientific Reports, 9:1717  DOI: 10.1038/s41598-018-37182-6
  3. “Hydrogen in Ga2O3,” Michael Stavola, W. Beall Fowler, Ying Qin, Philip Weiser, and Stephen Pearton, in Gallium Oxide, ed. by Stephen Pearton, Fan Ren, and Michael Mastro (Elsevier, 2019), pp. 169-210.
  4. “Hydrogen Centers in β-Ga2O3: Infrared Spectroscopy and Density Functional Theory,” Ying Qin, Michael Stavola, W. Beall Fowler, Philip Weiser, and Stephen J. Pearton, ECS J. Solid State Sci. Technol. 8, Q3103 (2019).
  5. Fisher KJ, Kryazhimskiy S, Lang GI. 2019. Detecting genetic interactions using parallel evolution in experimental populations. Philos Trans R Soc Lond B Biol Sci. Jul 22;374(1777):20180237. doi: 10.1098/rstb.2018.0237. PMID: 31154981.
 2018
  1. Horan B. G., Zerze G., Kim Y. C, Vavylonis D., and Mittal J., Computational modeling highlights the role of the disordered Formin Homology 1 domain in profilin-actin transfer, 2018, FEBS Lett. 592:1804-1816. DOI: 10.1002/1873-3468.13088
  2. “Diffusivity of the interstitial hydrogen shallow donor in In2O3,” Ying Qin, Philip Weiser, Karla Villalta, Michael Stavola, W. Beall Fowler, Ivan Biaggio, and Lynn Boatner, J. Appl. Phys. 123, 161506 (2018).
  3. “Tutorial: Novel properties of defects in semiconductors revealed by their vibrational spectra,” Michael Stavola and W. Beall Fowler, J. Appl. Phys. 123, 161561 (2018).
  4. “Structure and vibrational properties of the dominant O-H center in β-Ga2O3,” Philip Weiser, Michael Stavola, W. Beall Fowler, Ying Qin, and Stephen Pearton, Appl. Phys. Lett. 112, 232104 (2018).

  5. Fisher KJ, Buskirk SW, Vignogna RC, Marad DA, and Lang GI. 2018. Adaptive genome duplication affects patterns of molecular evolution in Saccharomyces cerevisiae. PLoS Genetics. May 25;14(5):e1007396. doi: 10.1371/journal.pgen.1007396. PMID: 29799840

  6. Marad DM, Buskirk SW, and Lang GI. 2018. Altered access to beneficial mutations slows adaptation and biases fixed mutations in diploids. Nature Ecology & Evolution. May;2(5):882-889. doi: 10.1038/s41559-018-0503-9. PMID: 29581586

 2017
  1. Buskirk SW, Peace RE, and Lang GI. 2017. Hitchhiking and epistasis give rise to cohort dynamics in adapting populations. Proc Natl Acad Sci U S A. 2017 Jul 18. pii: 201702314. doi: 10.1073/pnas.1702314114. PMID: 28720700
 2016
  1. “Point Defects,” W. B. Fowler, in Reference Module in Materials Science and Materials Engineering, ed. by Saleem Hashmi (Oxford: Elsevier, 2016), pp. 1-5.
  2. “The structures of interstitial hydrogen centers in VO2 in the dilute limit from their vibrational properties and theory,” Weikai Yin, Ying Qin, W. Beall Fowler, Michael Stavola and Lynn A. Boatner, J. Phys.: Condens. Matter 28, 395401 (2016).
  3. “Symmetry and diffusivity of the interstitial hydrogen shallow-donor center in In2O3,” Philip Weiser, Ying Qin, Weikai Yin, Michael Stavola, W. Beall Fowler, and Lynn A. Boatner, Appl. Phys. Lett. 109, 202105 (2016).
 2010-2015
  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

 2022

  • 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.

 2021
  • Cytoskeletal and membrane flows for cell motility and polarization (D. Vavylonis), Talk at Mathematics of the Cell: Integrating Signaling, Transport and Mechanics, Banff International Research Station October 2021
  • Discrete mechanical model of lamellipodial actin networks (David Rutkowski, Dimitrios Vavylonis). Talk at American Physical Society March Meeting March 2021
  • Model of dendritic actin network with distributed turnover and structural remodeling (Danielle Holz, Aaron Hall, Dimitrios Vavylonis). Talk at American Physical Society March Meeting March 2021
  • Coarse-grained simulations of actin polymerization (Aaron Hall, Brandon Horan, Dimitrios Vavylonis). Talk at American Physical Society March Meeting March 2021
  • Turnover, Mechanics, And Structural Plasticity of Lamellipodial Actin Networks, Invited Speaker, “Building the Cell, 20 Years After” Subgroup, Cell Bio Virtual 2020 (D. Vavylonis, ASCB/EMBO Annual meeting) December 2020
  • Discrete mechanical model of lamellipodial actin networks (David Rutkowski, Dimitrios Vavylonis). Talk at American Physical Society March Meeting March 2021
  • Model of dendritic actin network with distributed turnover and structural remodeling (Danielle Holz, Aaron Hall, Dimitrios Vavylonis). Talk at American Physical Society March Meeting March 2021
  • Coarse-grained simulations of actin polymerization (Aaron Hall, Brandon Horan, Dimitrios Vavylonis). Talk at American Physical Society March Meeting March 2021
 2020
  • Computational Insights into Faceted Au Nanoparticle Photocatalysis (presentation, L.A. Fredin) American Chemical Society (ACS) Division of Inorganic Chemistry (DIC) Periodic Table Talks, Sustainable Energy and the Environment: Charge Transport in Molecules and Solids, Virtual.

  • Understanding Structure-Function Relationships in Disordered Materials (presentation, L.A. Fredin) North East Centre for Energy Materials (NECEM) and Newcastle University School of Natural Environmental Sciences, Virtual. 

  • Modeling Excited States of Organic Radicals (presentation, L.A. Fredin) Photochemistry Spotlight, Virtual.

  • Profilin-actin binding modes explored using a coarse-grained model (poster presentation, E. Koessler (*), B. G. Horan, D. Vavylonis) 2020 Annual Biophysical Society meeting, San Diego CA. (*) undergraduate REU student
  • Kinetic and mechanical modeling of the lamellipodial actin network (poster presentation, D. M. Rutkowski, D. Holz, A. Hall and D. Vavylonis). 2020 Annual Biophysical Society meeting, San Diego CA.
 2019
  • Insights into Actin Polymerization and Nucleation Using a Coarse-grained Model. (poster presentation B. G. Horan, D. Vavylonis). 2019 American Society for Cell Biology/EMBO Annual Meeting, Washington DC.
  • Coarse-grained Simulations of Cytokinetic Node Protein Mid1 and Path to Dimeric Structure. (poster presentation, A. Hall, B. G. Horan, D. Vavylonis). 2019 American Society for Cell Biology/EMBO Annual Meeting, Washington DC.
  • Model for Dendritic Actin Network Formation, Distributed Turnover, and Structural Remodeling. (D. Holz, A. Hall, D. Vavylonis). 2019 American Society for Cell Biology/EMBO Annual Meeting, Washington DC.
  • Discrete Mechanical Model of Lamellipodial Actin Networks, (poster presentation D. M. Rutkowski, D. Holz, D. Vavylonis). 2019 American Society for Cell Biology/EMBO Annual Meeting, Washington DC.
  • “Mechanism of formin-mediated actin polymerization: alternate delivery of profilin-actin to the barbed end" (poster presentation, F. Quintana*, A. Kodera, B. G. Horan, S. Yamashiro, J. Mittal, N. Watanabe, D. Vavylonis). 2019 Annual Biophysical Society Meeting, Baltimore MD. (*) undergraduate student.
  • “Discrete model of dendritic actin networks undergoing retrograde flow” (poster presentation, D. Rutkowski, D. Holz, D. Vavylonis). 2019 Annual Biophysical Society meeting, Baltimore MD.
  • “Mechanisms for dendritic actin network formation, distributed turnover, and structural remodeling” (oral presentation, D. Holz, A. Hall, D. Vavylonis). 2019 Annual Biophysical Society meeting, Baltimore MD.
  • “Elucidating steps in actin polymerization and nucleation using a coarse-grained model of multiprotein complex formation,” (poster presentation, B. G. Horan, D. Vavylonis, J. Mittal). 2019 Annual Biophysical Society meeting, Baltimore MD.
 2018
  • “Delivery Mechanism of Profilin-Actin Complex to Actin Filament Barbed End” (poster presentation, Felix Quintana*, B. Horan, J. Mittal, D. Vavylonis) Annual Biomedical Research Conference for Minority Students, Indianapolis, IN. (*) undergraduate student. Poster award.
  • “Lamellipodia Protrusion driven by Actin Polymerization: Excitable Dynamics and Dendritic Network Structure,” Invited talk, Fall Central Sectional AMS Meeting, session “Cell Motility: Models and Applications”, University of Michigan, Ann Arbor, October 2018 (Danielle Holz).
  • “Morphologies of cross-linked actin filament networks in confinement,” (D. Vavylonis and M. Adeli Koudehi) Invited talk, 8th World Congress of Biomechanics, Dublin, Ireland, July 2018
  • “Modeling Actin Dynamics in Cell Motility and Cell Division”, Invited talk, Generation and Control of Forces in Cells, NORDITA workshop, Stockholm, Sweden, June 2018
  • “Simulations of Branching Actin Filament Networks at the Leading Edge of Moving Cells” (poster presentation, A. Hall, D. Holz, D. Vavylonis) 2018 American Physical Society March Meeting, Los Angeles CA.
  • “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) 2018 Biophysical Society Annual Meeting, San Francisco CA.
 2017
  • “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)