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changes.mady.by.user Lisa Fredin

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Comment: updated fredin group pubs and presentations

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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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title2021
  1. G. RepaE.H. Spielvogel, B.G. Stevenson, M.J. Stringer, Y. Hu, L.A. Fredin, Parameter Space Exploration Reveals Interesting Mn-doped SrTiO3 Structures, Phys. Chem. Chem. 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

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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

  • 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
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title2021
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.


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title2021
  • 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
  • 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
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title
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title2020
  • 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.

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