Tree Soft Matter Theory

@ BYU ChemE

Publications

Journal Articles

2023

29. The effect of local chain stiffness on the mechanism of crystal nucleation in an oligomer melt. P. Kawak, C. Akiki, and D. R. Tree. chemRxiv. (2023). doi: 10.26434/chemrxiv-2023-374qx, preprint
28. Coarsening dynamics of ternary polymer solutions with mobility and viscosity contrasts. J. U. Garcia, D. R. Tree, A. Bagoyo, T. Iwama, K. T. Delaney, and G. H. Fredrickson. The Journal of Chemical Physics. (2023). doi: 10.1063/5.0173992, preprint
27. Nonsolvent-induced phase separation inside liquid droplets. R. Alhasan, T. A. Wilcoxson, D. S. Banks, S. Jung, D. R. Tree. The Journal of Chemical Physics. (2023). doi: 10.1063/5.0143928, preprint
26. Simulations of Morphology Control of Self-Assembled Amphiphilic Surfactants. Q. Zhu and D. R. Tree. Journal of Polymer Science. (2023). doi: 10.1002/pol.20220771, preprint
25. Active Control of Equilibrium, Near-Equilibrium, and Far-from-Equilibrium Colloidal Systems. M. N. McDonald, Q. Zhu, W. F. Paxton, C. K. Peterson, and D. R. Tree. Soft Matter. 19, 1675-1694, (2023). doi: 10.1039/D2SM01447E, preprint
24. Steering particles via micro-actuation of chemical gradients using model predicitve control. M. N. McDonald, C. K. Peterson, and D. R. Tree. Biomicrofluidics. 17, 014107, (2023). doi: 10.1063/5.0126690, preprint

2022

23. Gibbs–Duhem relation for phase-field models of polymeric mixtures. R. Alhasan and D. R. Tree. Macromolecules. 55, 759--765, (2022). doi: 10.1021/acs.macromol.1c02021, preprint
22. A phase field model for dynamics simulations of reactive blending of polymers. M. D. Tikekar, K. T. Delaney, M. C. Villet, D. R. Tree, and G. H. Fredrickson. Soft Matter. 18, 877--893(2021). doi: 10.1039/D1SM01686E, preprint

2021

21. Semiflexible oligomers crystallize via a cooperative phase transition. P. Kawak, D. S. Banks, and D. R. Tree. Journal of Chemical Physics. 155, 214902 (2021). doi: 10.1063/5.0067788, preprint
20. Using Reactive Dissipative Particle Dynamics to Understand Local Shape Manipulation of Polymer Vesicles. Q. Zhu, T. R. Scott, D. R. Tree. Soft Matter. 17, 24--39 (2021). doi: 10.1039/D0SM01654C, preprint

2020

19. Mechanisms of Asymmetric Membrane Formation in Nonsolvent-Induced Phase Separation Garcia, J. U.; Iwama, T.; Chan, E. Y.; Tree, D. R.; Delaney, K. T.; Fredrickson, G. H. ACS Macro Letters. 9, 1617-1624 (2020). doi: 10.1021/acsmacrolett.0c00609, preprint

2019

18. Mass-transfer driven spinodal decomposition in a ternary polymer solution D. R. Tree, L. Fracisco dos Santos, C. B. Wilson, T. R. Scott, J. Ulric Garcia, and G. H. Fredrickson. Soft Matter. 23, 4614-4628 (2019). doi: 10.1039/C9SM00355J, preprint

2018

17. Marangonoi Flows during Nonsolvent Induced Phase Separation. D. R. Tree, T. Iwama K. T. Delaney, J. Lee, and G. H. Fredrickson. ACS Macro Letters. 7, 582--586 (2018). doi: 10.1021/acsmacrolett.8b00012, preprint

2017

16. A multi-fluid model for microstructure formation in polymer membranes. D. R. Tree, K. T. Delaney, H. D. Ceniceros, T. Iwama and G. H. Fredrickson. Soft Matter. 13, 3013--3030 (2017). doi: 10.1039/C6SM02839J, preprint

2014

15. Hydrodynamics of DNA confined in nanoslits and nanochannels. K. D. Dorfman, D. Gupta, A. Jain, A. Muralidhar and D. R. Tree. Eur. Phys. J. Spec. Top. 223, 3179--3200 (2014). doi: 10.1140/epjst/e2014-02326-4, preprint
14. Backfolding of Wormlike Chains Confined in Nanochannels. A. Muralidhar, D. R. Tree, and K. D. Dorfman. Macromolecules. 47, 8446--8458 (2014). doi: 10.1021/ma501687k, preprint
13. The Odijk Regime in Slits. D. R. Tree, W. F. Reinhart, and K. D. Dorfman. Macromolecules 47, 3672--3684 (2014). doi: 10.1021/ma500647v, preprint
12. Interplay between chain stiffness and excluded volume of semiflexible polymers confined in nanochannels. A. Muralidhar, D. R. Tree, Y. Wang and K. D. Dorfman. J. Chem. Phys. 140, 084905 (2014) doi: 10.1063/1.4865965, preprint

2013

11. Modeling the Relaxation Time of DNA Confined in a Nanochannel. D. R. Tree, Y. Wang and K. D. Dorfman. Biomicrofluidics 7, 054118 (2013) doi: 10.1063/1.4826156, preprint
10. Is DNA a Good Model Polymer? D. R. Tree, A. Muralidhar, P. S. Doyle, and K. D. Dorfman. Macromolecules 46, 8369--8382 (2013) doi: 10.1021/ma401507f, preprint
9. Extension of DNA in a Nanochannel as a Rod-to-Coil Transition. D. R. Tree, Y. Wang, and K. D. Dorfman. Phys. Rev. Lett. 110, 208103 (2013) doi: 10.1103/PhysRevLett.110.208103, preprint
8. Revisiting Blob Theory for DNA Diffusivity in Slitlike Confinement. L. Dai, D. R. Tree, J. R. C. van der Maarel, K. D. Dorfman, and P. S. Doyle. Phys. Rev. Lett. 110, 168105 (2013) doi: 10.1103/PhysRevLett.110.168105, preprint
7. Beyond Gel Electrophoresis: Microfluidic Separations, Fluorescence Burst Analysis, and DNA Stretching. K. D. Dorfman, S. B. King, D. W. Olson, J. D. P. Thomas and D. R. Tree. Chem. Rev. 113, 2584--2667 (2013) doi: 10.1021/cr3002142, preprint
6. Entropic depletion of DNA in triangular nanochannels. W. F. Reinhart, D. R. Tree and K. D. Dorfman. Biomicrofluidics 7, 024102 (2013) doi: 10.1063/1.4794371, preprint
5. Syngas fermentation to biofuels: Effects of hydrogen partial pressure on hydrogenase efficiency. B. E. Skidmore, R. A. Baker, D. R. Banjade, J. M. Bray, D. R. Tree and R. S. Lewis. Biomass and Bioenergy 55, 156--162 (2013) doi: 10.1016/j.biombioe.2013.01.034

2012

4. Mobility of a Semiflexible Chain Confined in a Nanochannel. D. R. Tree, Y. Wang, and K. D. Dorfman. Phys. Rev. Lett. 108, 228105 (2012). doi: 10.1103/PhysRevLett.108.228105, preprint
3. Resolution limit for DNA barcodes in the Odijk regime. Y. Wang, W. F. Reinhart, D. R. Tree, and K. D. Dorfman. Biomicrofluidics 6, 014101--9 (2012). doi: 10.1063/1.3672691, preprint

2011

2. Simulation of DNA Extension in Nanochannels. Y. Wang, D. R. Tree, and K. D. Dorfman. Macromolecules, 44, 6594--6604 (2011). doi: 10.1021/ma201277e, preprint
1. The effects of syngas impurities on syngas fermentation to liquid fuels. D. Xu, D. R. Tree and R. S. Lewis. Biomass and Bioenergy 35, 2690--2696 (2011). doi: 10.1016/j.biombioe.2011.03.005