Publications since 2019

Recently accepted / published papers and links (since 2019):

  1. Rheological Tuning of Entangled Polymer Networks by Transient Crosslinks, X. Cao, M.G. Forest, Journal of Physical Chemistry B 123(5), 974-982 DOI: 10.1021/acs.jpcb.8b09357 (2019)
  2. Partial demixing of RNA-protein complexes leads to intra-droplet patterning in phase-separated biological condensates, K. Gasior, J. Zhao, G. McLaughlin, M.G. Forest, A. Gladfelter, J.M. Newby, Physical Review E 99, No. 1 DOI: 10.1103/PhysRevE.99.012411 (2019)
  3. Mucus accumulation in the lungs precedes structural changes and infection in children with cystic fibrosis, C. Esther, M. Muhlebach, C. Ehre, D.B. Hill, M. Wolfgang, M. Kesimer, K. Ramsey, M. Markovetz, I. Garbarine, M.G. Forest, I. Seim, B. Zorn, C. Morrison, M. Delion, L. Turkovic, S. Ranganathan, S Stick, S. Conlan, R. Boucher, Science Translational Medicine 11, Issue 486 DOI: 10.1126/scitranslmed.aav3488 (2019)
  4. Antibody-mediated immobilization of virions in mucus, M. Jensen, Y-Y Wang, S. Lai, M.G. Forest, S. McKinley, Bulletin of Mathematical Biology 81, 4069–4099 DOI: 10.1007/s11538-019-00653-6 (2019)
  5. Limited processivity of single motors improves overall transport flux of self-assembled motor-cargo complexes, K. Patel, S. Mao, M.G. Forest, S. Lai, J. Newby, Physical Review E, 100, 022408 DOI: 10.1103/PhysRevE.100.022408 (2019)
  6. Modeling barrier properties of intestinal mucus reinforced with IgG and secretory IgA against motile bacteria, Xu, J. Newby, T. Wessler, A. Chen, J. Schiller, H. Schroder, M.G. Forest, S. Lai, ACS Infectious Diseases 5(9), 1570-1580 DOI: 10.1021/acsinfecdis.9b00109 (2019)
  7. Transient crosslinking kinetics optimize gene cluster interactions, B. Walker, D. Taylor, J. Lawrimore, C. Hult, D. Adalsteinsson, K. Bloom, M.G. Forest, PLoS Comp Biol 15(8): e1007124 DOI: 10.1371/journal.pcbi.1007124 (2019)
  8. Three-Dimensional Thermodynamic Simulation of Condensin as a DNA-Based Translocase, J. Lawrimore, Y. He, M.G. Forest, K. Bloom, SMC Complexes, Springer Methods in Molecular Biology, 2004, 291-318 Badrinarayanan A. (editor) (2019)
  9. Overcoming anti-PEG, antibody-mediated, accelerated blood clearance of PEGylated liposomes by pre-infusion with high molecular weight free PEG, M. McSweeney. L. Price, T. Wessler, E. Ciociola, L. Herity, J. Piscitelli, A. DeWalle, T. Harris, A. Chan, R. Saw, P. Hu, J. Jennette, M. G. Forest, Y. Cao, S. Montgomery, W. Zamboni, S. Lai, J. Controlled Release 311-312, 138-146 DOI 10.1016/j.jconrel.2019.08.017 (2019)
  10. Nanoparticle loading of unentangled polymers induces entanglement-like relaxation modes and a broad sol-gel transition, X. Cao, H. Merlitz, M.G. Forest, Physical Chem. Letters 10(17), 4968-4973 DOI: 10.1021/acs.jpclett.9b01954 (2019)
  11. Observation of transition cascades in sheared liquid crystalline polymers, R. Fox, M.G. Forest, S. Picken, T. Dingemans, Soft Matter, 16, 3891-3901 DOI: 10.1039/D0SM00275E (2020)
  12. Spatial heterogeneity of the cytosol revealed by machine-learning-based 3D particle tracking, G. McLaughlin, E. Langdon, J. Crutchley, L. Holt, M.G. Forest, J. Newby, A. Gladfelter, Molecular Biology of the Cell, 31(14) DOI: 10.1091/mbc.E20-03-0210 (2020)
  13. Fingerprinting the Nonlinear Rheology of a Liquid Crystalline Polyelectrolyte, R. Fox, M.G. Forest, C. Do, W-R Chen, S. Picken, T. Dingemans, Rheologica Acta, 59(10), 727-743 DOI: 10.1007/s00397-020-01234-4 (2020)
  14. LPS-binding IgG arrests actively motile Salmonella Typhimurium in gastrointestinal mucus, H. Schroeder, J. Newby, A. Schaefer, B. Subramani, A. Tubbs, MG Forest, E. Miao, and SK Lai, Mucosal Immunology, 13(5), 814-823 DOI: 10.1038/s41385-020-0267-9 (2020)
  1. Statistical mechanics of chromosomes: In vivo and in silico approaches reveal high-level organization and structure arise exclusively through mechanical feedback between loop extruders and substrate properties, Y. He, J. Lawrimore, D. Cook, E. Van Gorder, S. De Larimat, D. Adalsteinsson, M.G. Forest, K. Bloom, Nucleic Acids Research, 48(20), 11284–11303 DOI: 10.1093/nar/gkaa871 (2020)
  2. Modeling the mechanisms by which coexisting biomolecular RNA-protein condensates form, K. Gasior, A. Gladfelter, M.G. Forest, J. Newby, Bulletin of Mathematical Biology 82, 153 DOI: 10.1007/s11538-020-00823-x (2020)
  3. Chain stiffness boosts active nanoparticle transport in polymer gel networks, X. Cao, H. Merlitz, C. Wu, M.G. Forest, Physical Review E, 103(5), 052501 10.1103/PhysRevE.103.052501 (2021)
  4. Molecular dynamics simulations to explore the structure and rheological properties of normal and hyper-concentrated airway mucus, A. Ford, X. Cao, M. Papanikolas, M. Markovetz, D.B. Hill, T. Kato, R. Boucher, R. Freeman, M.G. Forest, Studies in Applied Mathematics 147(4), 1369-1387 DOI: 10.1111/sapm.12433 (2021)
  5. Existence and stability of kayaking orbits for nematic liquid crystals in simple shear flow, D. Chillingworth, M.G. Forest, R. Lauterbach, C. Wulff, Archives for Rational Mechanics and Analysis, 242(2), 1229-1287 DOI: 10.1007/s00205-021-01703-x (2021)
  6. Experimental data and PBPK modeling quantify antibody interference in PEGylated drug carrier delivery, A. Talkington, T. Wessler, Y. Cao, S.K. Lai, M.G. Forest, Bull Math Biol 83, 123 DOI: 10.1007/s11538-021-00950-z (2021)
  7. Simulating Dynamic Chromosome Compaction: Methods for Bridging in Silico to in Vivo, Y. He, D. Adalsteinsson, B. Walker, J. Lawrimore, M.G. Forest, K. Bloom, Methods Mol Biol. 2415:211-220 Chapter 16 of Mitosis: Methods and Protocols DOI: 10.1007/978-1-0716-1904-9_16 (2022)
  8. Measurement error correction in particle tracking microrheology, Y. Ling, M. Lysy, I. Seim, J. Newby, D. Hill, J. Cribb, M. G. Forest, Annals of Applied Statistics 16(3): 1747-1773 DOI: 10.1214/21-AOAS1565 (2022)
  9. Rigidity percolation in disordered 3D rod systems, S. Heroy, D. Taylor, F. Shi, M.G. Forest, P.J. Mucha, SIAM Multiscale Modeling and Simulation 20(1) (2022)
  10. A comprehensive PBPK model recapitulates early kinetics of anti-PEG antibody-mediated accelerated blood clearance of PEGylated liposomes in vivo, Talkington, M. McSweeney, T. Wessler, M. Rath, Z. Li, T. Zhang, H. Yuan, J. Frank, M.G. Forest, Y. Cao, S.K. Lai, Journal of Controlled Release 343:518-527 10.1016/j.jconrel.2022.01.022 (2022)
  11. Modeling insights into SARS-CoV-2 respiratory tract infections prior to immune protection, A. Chen, T. Wessler, K. Daftari, K. Hinton, R. C. Boucher, R. Pickles, R. Freeman, S. K. Lai, M. G. Forest, Biophysical Journal 11742 DOI: 10.1016/j.bpj.2022.04.003 (2022)
  12. Aerosol transport modeling: the key link between lung infections of individuals and populations, Darquenne, A. T. Borojeni, M. Colebank, M. G. Forest, B. Madas, M. Tawhai, Y. Jiang, Frontiers in Physiology 13:923945 DOI: 10.3389/fphys.2022.923945 (2022)
  13. Screening confinement of entanglements: Role of a self-propelling, end-inducing ballistic chain reptation, X. Cao, H. Merlitz, C. Wu, M.G. Forest, Physical Review E, 106(2) L022501, DOI: 1103/PhysRevE.106.L022501 (2022)
  14. A hybrid discrete-continuum model of antibody and interferon immune responses to SARS-CoV-2 infection in the lung alveolar region, A. Aristotelous, A. Chen, M.G. Forest, J. Theoretical Biology 555, 111293 DOI: 1016/j.jtbi.2022.111293 (2022)
  15. Mucus and mucus flake composition and abundance reflect inflammatory and infection status in cystic fibrosis. Markovetz MR, Garbarine IC, Morrison CB, Kissner WJ, Seim I, Forest MG, Papanikolas MJ, Freeman R, Ceppe A, Ghio A, Alexis NE, Stick SM, Ehre C, Boucher RC, Esther CR, Muhlebach MS, Hill DB. J Cyst Fibros. 21(6):959-966DOI: 10.1016/j.jcf.2022.04.008 (2022)
  16. Antibody protection from SARS-CoV-2 respiratory tract exposure and infection, A. Chen, T. Wessler, M.G. Forest, J. Theoretical Biology 557 111334 DOI: 1016/j.jtbi.2022.111334 (2023)
  17. Modeling identifies variability in SARS-CoV-2 uptake and eclipse phase by infected cells as principal drivers of extreme variability in nasal viral load in the 48 hours post infection, Pearson, T. Wessler, A. Chen, R. Boucher, R. Freeman, S.K. Lai, R. Pickles, M.G. Forest, J. Theoretical Biology 565 111470 DOI 10.1016/j.jtbi.2023.111470 (2023)
  18. The power of weak, transient interactions across biology: a paradigm of emergent behavior, P. Vasquez, B. Walker, K. Bloom, D. Kolbin, C. Hult, N. Caughman, C. Edelmaier, R. Freeman, M. Lysy, D. Adalsteinsson, K. Newhall, M. Papanikolas, M.G. Forest, Physica D: Nonlinear Phenomena 454, 133866 DOI: 10.1016/j.physd.2023.133866 (2023)
  19. Polymer Modeling Reveals Interplay between Physical Properties of Chromosomal DNA and the Size and Distribution of Condensin-Based Chromatin Loops, D. Kolbin, Walker, C. Hult, J.D. Stanton, D. Adalsteinsson, MG Forest, K. Bloom, Genes 14(12): 2193 DOI: 10.3390/genes14122193 (2023)
  20. Computational Modeling Insights into Extreme Heterogeneity in COVID-19 Nasal Swab Data, L. Zhang, H. Cao, K. Medlin, J. Pearson, A. Aristotelous, A. Chen, T. Wessler, MG Forest, Viruses 16, 69 DOI: 10.3390/v16010069(2024)
  21. Benchmarking the immersed boundary method for viscoelastic flows, C. Gruninger, F. Fang, MG Forest, A. Barrett, B. Griffith, Journal of Computational Physics 506, 112888, DOI: 10.1016/j.jcp.2024.112888 (2024)
  22. Transient crosslinking controls the condensate formation pathway within chromatin Networks, Z-P Wu, K. Bloom, MG Forest, X-Z Cao, Phys. Rev. E 109(4) L042401 DOI: 10.1103/PhysRevE.109.L042401 (2024)
  23. Depletion strategies for crystallized layers of two-dimensional nanosheets to enhance lithium-ion conductivity in polymer nanocomposites, Wei, Xiaohan; Z-P Wu, A. Peng, X. Zhang, H. Merlitz, MG Forest, C-X Wu, X-Z Cao, American Chemical Society (ACS) Macro Letters 13(4):453-460 March DOI:1021/acsmacrolett.3c00756 (2024)
  24. Flagellum Pumping Efficacy in Shear-Thinning Viscoelastic Fluids
    Barrett, A. Fogelson, A., M.G. Forest, C. Gruninger, S. Lim, B. Griffith, J. Fluid Mechanics 999 A2, DOI: https://doi.org/10.1017/jfm.2024.666 (2024)
  25. Experimental and statistical methods for microrheological characterization of heterogeneity in human respiratory mucus mimics of health and disease progression, Caughman, M. Papanikolas, R. Freeman, M. Markovetz, D.B. Hill, M.G. Forest, M. Lysy, J. Rheology 68, 995–1011 https://doi.org/10.1122/8.0000789 (2024)
  26. Charge distribution and helicity tune the binding of septin’s amphipathic helix domain to membranes, C. Edelmaier, S.J. Klawa, S.M. Mofidi, Q. Wang, B. Curtis,W. Shi, S. Hanson, D. Klotsa, M.G. Forest, A. Gladfelter, R. Freeman, E. Nazockdast, Biophysical Journal, online April 3 https://doi.org/10.1016/j.bpj.2025.03.008 (2025)