(* indicates an undergraduate co-author)
R. M. Pemberton, J. T. Kindt. “Orchid bee collects herbicide that mimics the fragrance of its orchid mutualists.” Accepted for publication in Florida Entomologist, 11/2023.
B. R. Deal, R. Ma, H. Ogasawara, J. T. Kindt, and K. Salaita. “Heteromultivalency enables enhanced detection of nucleic acid mutations”, Nature Chemistry, https://doi.org/10.1038/s41557-023-01345-4
L. A. Lowe, J. T. Kindt, C. Cranfield, B. Cornell, A. Macmillan, and A. Wang. “Subtle changes in pH affect the packing and robustness of fatty acid bilayers,” Soft Matter 18, 3498-3504 (2022). https://doi.org/10.1039/D2SM00272H
Xiaokun Zhang and James T. Kindt, “Free Energy of Micellization of Dodecyl Phosphocholine (DPC) from Molecular Simulation: Hybrid PEACH-BAR Method,” J. Comp. Chem. 42, 2221-2232 (2021). https://doi.org/10.1002/jcc.26751
James T. Kindt, Jack W. Szostak, and Anna Wang, “Bulk self-assembly of giant, unilammelar vesicles. ACS Nano 14, 14627-14634 (2020). https://doi.org/10.1021/acsnano.0c03125
B. R. Deal, R. Ma, V. Pui-Yan Ma, H. Su, J. T. Kindt, and K. Salaita, “Engineering DNA-Functionalized Nanostructures to Bind Nucleic Acid Targets Heteromultivalently with Enhanced Avidity.” J. Am. Chem. Soc.142, 9653-9660 (2020). https://doi.org/10.1021/jacs.0c01568
Ziwei Guo and James T. Kindt, “Competing factors in grain boundary loop shrinkage: two-dimensional hard sphere colloidal crystals,” J. Chem. Phys. 151, 084505 (2019) Accepted version ; link ; animations
Ziwei Guo, Peiyao Wu*, and James T. Kindt, “Ordering of colloidal hard spheres under gravity: From monolayer to multilayer,” Soft Matter, 15, 1027-1037 (2019). Accepted version ; link
Xiaokun Zhang, Jorge G. Arce Nunez*, and J. T. Kindt, “Derivation of micelle size-dependent free energies of aggregation for octyl phosphocholine from molecular dynamics simulation” Fluid Phase Equilibria 485, 83-93 (2019). Accepted version ; link
T. McGill. L. Williams, D. Mulford, S. Blakey, R. Harris, J. Kindt, D. Lynn, P. Marsteller, F. McDonald, N. Powell, “Chemistry Unbound: Designing a New Four-Year Undergraduate Curriculum” J. Chem. Ed., 96, 35-46 (2019); ACS Editors’ Choice article. link-open access
Z. Guo and J. T. Kindt, “Partitioning of Size-mismatched Impurities to Grain Boundaries in 2-d Solid Hard Sphere Monolayers” Langmuir 34, 12947–12956 (2018). link
L. A. Patel and J. T. Kindt, “Simulations of NaCl aggregation from solution: Solvent determines topography of free energy landscape” J. Comp. Chem. 40, 135-147 (2019) link
Z. Guo and J. T. Kindt, “Simulations of grain boundaries between ordered hard sphere monolayer domains: orientation-dependent stiffness and its correlation with grain coarsening dynamics” J. Chem. Phys. 149, 044503 (2018). Accepted version Link to journal version: link
Z. Guo and J. T. Kindt, “Size-asymmetrical Lennard-Jones solid solutions: Interstitials and substitutions.” J. Chem. Phys. 148, 164504 (2018). Editor’s Choice selection. Accepted version: Guo-Kindt-LJ-solids Link to journal version: link
K. A. Reid, C. M. Davis, R. B. Dyer, and J. T. Kindt, “Binding, folding, and insertion of a beta-hairpin peptide at a lipid bilayer surface: Influence of electrostatics and lipid tail packing.” Biochim. Biophys Acta – Biomembranes 1860, 792-800 (2018) link
Ziwei Guo and J. T. Kindt, “Gibbs Ensemble Monte Carlo with Solvent Repacking: Phase Coexistence of Size-asymmetrical Binary Lennard-Jones Mixtures.” Molecular Simulation 44, 300-308 (2018). link preprint
X. Zhang, L. A. Patel, O. Beckwith, R. Schneider, C. J. Weeden*, and J. T. Kindt. “Extracting Aggregation Free Energies of Mixed Clusters from Simulations of Small Systems: Application to Ionic Surfactant Micelles.” J. Chem. Theor. Comp. 13, 5195-5206 (2017). link
Lara A. Patel and J. T. Kindt, “Cluster free energies from simple simulations of small numbers of aggregants: Nucleation of liquid MTBE from vapor and aqueous phases.” J. Chem. Theory Comp. 13, 1023-1033 (2017). link
Lewen Yang and J. T. Kindt, “Line Tension Assists Membrane Permeation at the Transition Temperature in Mixed-Phase Lipid Bilayers.” J. Phys. Chem. B. 120, 11740-11750 (2016). link
L. A. Patel and J. T. Kindt, “Coarse-grained molecular simulations of the melting kinetics of small unilamellar vesicles.” Soft Matter, 12, 1765-1777 (2016). pdf link
J. T. Kindt, “Grand canonical Monte Carlo using solvent repacking: Application to phase behavior of hard disk mixtures.” J. Chem. Phys. 143, 124109 (2015). dx.doi.org/10.1063/1.4931731
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. 8725-8733 (2015). 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). Link
P. S. Coppock and J. T. Kindt, “Atomistic simulations of mixed-lipid bilayers in the gel and fluid phases.” Langmuir, 25, 352-359 (2009). Link
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). PDF format
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). PDF format
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
Publications from before Emory University:
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, 149 (2001).
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, 10373 (1996).
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 (1996).
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.