K. Uppulury, P. S. Coppock, and J. T. Kindt, "Molecular Simulation of the DPPE Lipid Bilayer Gel Phase: Coupling Between Molecular Packing Order and Tail Tilt Angle." J. Phys. Chem. B, Link
L. Yang and J. T. Kindt, "Simulation Study of the Permeability of a Model Lipid Membrane at the Fluid−Solid Phase Transition." Langmuir, 31 2187-2195 (2015). Link
A. West and J. T. Kindt, "On the Relationship Between Plateau Modulus and Shear Relaxation Time in Transient Networks." Macromolecular Theory and Simulations, 24 208-217 (2015). Link
J.T. Kindt, "Determining Bulk Equilibrium Constants for Cluster Formation from Constant NVT Ensemble Simulations at Small N." Physics Procedia, 53, 63-70 (2014). Link
W. Zheng, Y. Liu, A. West, E. E. Schuler, K. Yehl, R. B. Dyer, J. T. Kindt, and K. Salaita. "Quantum dots encapsulated within phospholipid membranes: phase-dependent structure, photostability, and site-selective functionalization." J. Am. Chem. Soc. 136, 1992-1999 (2014). Link
A. West, K. Ma, J. L. Chung, and J. T. Kindt, "Simulation studies of structure and edge tension of lipid bilayer edges: effects of tail structure and force-field." J. Phys. Chem. A 117, 7114-7123(2013). Link
J. T. Kindt, "Accounting for Finite-Number Effects on Cluster Size Distributions in Simulations of Equilibrium Aggregation." Journal of Chemical Theory and Computation 9, 147-152 (2013). Link
S. Nagarajan, E. E. Schuler, K. Ma, J. T. Kindt, and R. B. Dyer, "Dynamics of the gel to liquid-crystal phase transformation in lipid bilayer vesicles." J. Phys. Chem. B 116, 13749-13756 (2012). Link
D. C. Turner, F. Yin, J. T. Kindt, and H. Zhang. "Understanding pharmacokinetic food effects using molecular dynamics simulation coupled with physiologically based pharmacokinetic modeling." Biopharmaceutics and Drug Disposition. 33, 510-521(2012). Link
F. Yin and J. T. Kindt, "Hydrophobic Mismatch and Lipid Sorting Near OmpA in Mixed Bilayers: Atomistic and Coarse-Grained Simulations." Biophysical Journal 102, 2279-2287 (2012). Link
A. West and J. T. Kindt, "Effects of defects on the shear stress relaxation in self-assembled protein networks." Soft Matter 8, 2895-2906 (2012). Link
K.L.H. Lam, H. Wang, T.A. Siaw, M.R. Chapman, A.J. Waring, J.T. Kindt, and K.Y.C. Lee, "Mechanism of structural transformations induced by antimicrobial peptides in lipid membranes." Biochimica et Biophysica Acta - Biomembranes 1818 194-204 (2012). Link
J.T. Kindt, "Atomistic simulation of mixed-lipid bilayers: mixed methods for mixed membranes.” Molecular Simulation 37, 516-524 (2011). Link
Jason de Joannis, Patrick S. Coppock, Fuchang Yin, Makoto Mori, Absalom Zamorano and J.T. Kindt, "Atomistic Simulation of Cholesterol Effects on Miscibility of Saturated and Unsaturated Phospholipids: Implications for Liquid-Ordered/Liquid-Disordered Phase Coexistence.” J. Am. Chem. Soc. 133, 3625-3634 (2011). Link
Patrick S. Coppock and J. T. Kindt, "
Determination of phase transition temperatures for atomistic models of lipids from temperature-dependent stripe domain growth kinetics." J. Phys. Chem. B, 114, 11468-73 (2010). Link
Fuchang Yin and J. T. Kindt, "
Atomistic Simulation of Hydrophobic Matching Effects on Lipid Composition near a Helical Peptide Embedded in Mixed-Lipid Bilayers." J. Phys. Chem. B,
114, 8076-8080 (2010). Link
Yong Jiang, Hao Wang, and J. T. Kindt, "
Atomistic Simulations of Bicelle Mixtures." Biophysical Journal,
98, 2895-2903 (2010). Link
D. C. Turner, F. Yin, J. T. Kindt, and H. Zhang, "
Molecular dynamics simulations of glycocholate-oleic acid mixed micelle assembly." Langmuir,
26, 4687-4692 (2010).
P. S. Coppock and J. T. Kindt, "Atomistic simulations of
mixed-lipid bilayers in the gel and fluid phases." Langmuir,
25, 352-359 (2009).
H. Wang, J. de Jason, Y. Jiang, J. C. Gaulding, B. Albrecht, F.
Yin, K. Khanna and J. T. Kindt,
"Bilayer Edge and Curvature Effects on Partitioning of Lipids by
Tail Length: Atomistic Simulations.", Biophys. J.,
95, 2647 (2008). PDF format
L. S. Pam, L. L. Spell, and J. T. Kindt,
"Simulation and theory of flexible equilibrium polymers under poor solvent conditions.",
J. Chem. Phys.,
126,134906 (2007).PDF format
F. M. Menger, H. Zhang, J. de Joannis, and J. T. Kindt, "Solubilization of Paclitaxel (Taxol) by Peptoad Self-Assemblies.",
Langmuir, 23, 2308-2310 (2007).Link
Y. Jiang and J. T. Kindt, "Simulations of edge behavior in a mixed-lipid bilayer: Fluctuation analysis." J. Chem. Phys., 126, 045105 (2007).PDF format
J. de Joannis, Y. Jiang, F. Yin and J. T. Kindt, "Equilibrium distributions of dipalmitoyl phosphatidylcholine and dilauroyl phosphatidylcholine in a mixed lipid bilayer: Atomistic semigrand canonical ensemble simulations." J. Phys. Chem. B, 110, 25875-25882 (2006).Link
X. Lü and J. T. Kindt, "Theoretical analysis of polydispersity in the nematic phase of self-assembled semiflexible chains." J. Chem. Phys.,125, 054909 (2006).PDF format
K. Khanna, T. T. Chang, and J.T. Kindt, "Complementarity and clustering in a simple model mixed bilayer." J. Chem. Phys.,124, 036102 (2006).
J. de Joannis, F. Y. Jiang, and J.T. Kindt, "Coarse-grained model simulations of mixed-lipid systems: Composition and line tension of a stabilized bilayer edge." Langmuir, 22 998-1005 (2006). Link
J. T. Kindt, "Simulation and theory of self-assembly and network formation in reversibly cross-linked equilibrium polymers". J. Chem. Phys., 123, 144901 (2005).
Shi-Jin Zhao and J. T. Kindt, "Monte Carlo calculations of the free energy landscape
of vesicle formation and growth". Europhysics Letters, 69(5),
839 (2005). PDF format
X. Lü and J. T. Kindt, "Monte Carlo simulation of the
self-assembly and phase behavior of semiflexible equilibrium
polymers". Journal of Chemical Physics, 120,
10328 (2004). PDF Format
F. Y. Jiang, Y. Bouret, and J. T. Kindt,
"Molecular dynamics simulations of the lipid bilayer edge".
Biophysical Journal, 87,
182 (2004). PDF Format
J. T. Kindt, "Simulation and theory of self-assembled networks:
Ends, junctions, and loops". Journal of Physical Chemistry B,
106, 8223 (2002). Link
J. T. Kindt, "Pivot-coupled grand canonical Monte Carlo method
for ring simulations." Journal of Chemical Physics, 116,
6817 (2002). PDF Format
S. Tzlil, J. T. Kindt, W. M. Gelbart, and A. Ben-Shaul, "Forces
and Pressures in DNA Packaging and Release from Viral Capsids."
Biophysical Journal, 84, 1616 (2003).
J. Kindt, S. Tzlil, A. Ben-Shaul, and W. M. Gelbart. "DNA
packaging and ejection forces in bacteriophage." Proceedings of
the Nat'l Academy of Sciences, USA 98, 13671 (2001).
J. T. Kindt and W. M. Gelbart, "Chain self-assembly and phase
transitions in semiflexible polymer systems". Journal of Chemical
Physics, 114, 1432 (2001). PDF Format
J. T. Kindt and J. C. Tully, "Dynamical corrugation: simulations
of the sticking of CO on Cu (100)". Surface Science, 477,
J. T. Kindt and J. C. Tully, "Simulations of collision-induced
absorption of hydrogen on Ni(111)". Journal of Chemical Physics
111, 11060 (1999).
O. V. Prezhdo, J. T. Kindt, and J. C. Tully, "Perturbed ground
state method for electron transfer". Journal of Chemical Physics
111, 7818 (1999).
J. T. Kindt and C. A. Schmuttenmaer, "Theory for determination of
the low-frequency time-dependent response function in liquids using
time-resolved terahertz pulse spectroscopy". Journal of Chemical
Physics 110, 8589 (1999).
J. T. Kindt, J. C. Tully, M. Head-Gordon and M. A. Gomez,
"Electron-hole pair contributions to scattering, sticking, and
surface diffusion: CO on Cu(100)". Journal
of Chemical Physics 109, 3629 (1998).
J. T. Kindt and C. A. Schmuttenmaer, "Far-infrared absorption
spectra of water, ammonia, and chloroform calculated from
instantaneous normal mode theory". Journal of Chemical Physics
106, 4389 (1997).
J. T. Kindt and C. A. Schmuttenmaer, "Far-infrared dielectric
properties of polar liquids probed by femtosecond terahertz pulse
spectroscopy". Journal of Physical Chemistry 100,
R. C. Scarrow, B. A. Brennan, J. G. Cummings, H. Y. Jin, D. H. J.
Duong, J. T. Kindt, M. J. Nelson, "X-ray spectroscopy of nitrile
hydratase at pH 7 and 9". Biochemistry 35, 10078
J. T. Kindt, A. Woods, B. M. Martin, R. J. Cotter, and Y. Osawa,
"Covalent alteration of the prosthetic heme of human hemoglobin by
BrCCl3 : Cross-linking of heme to cysteine residue 93".
Journal of Biological Chemistry 267, (1992) 8739.