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- Warmflash, A., Adamson, D. N., & Dinner, A.R. How noise statistics impact models of enzyme cycles. J. Chem. Phys. 128, 225101.
- Hu, J., Ma, A., & Dinner, A.R. A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT. Proc. Natl. Acad. Sci. USA 105, 4615-4620.
- Li, Y., Bhimalapuram, P., Zhao, T. & Dinner, A.R. How the nature of an observation affects single-trajectory entropies. J. Chem. Phys. 128, 074102.
- Zhao, T. & Dinner, A.R. Apparent directional scanning for DNA repair. Biophys. J. 94, 47-52.
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- Warmflash, A., Bhimalapuram, P. & Dinner, A.R. Umbrella sampling for nonequilibrium processes. J. Chem. Phys. 127, 154112.
- Stewman, S. F. & Dinner, A.R. A lattice model for self-assembly with application to the formation of cytoskeletal-like structures. Phys. Rev. E 76, 016103.
- Nag, A., Zhao, T. & Dinner, A.R. Effects of non-productive binding on the kinetics of enzymatic reactions with patterned substrates. J. Chem. Phys. 126, 035103.
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- Ma, A., Hu, J., Karplus, M. & Dinner, A.R. Implications of alternative substrate binding modes for catalysis by uracil-DNA glycosylase: An apparent discrepancy resolved. Biochemistry, 45, 13687-13696.
- Hu, J., Ma, A. & Dinner, A.R. Bias annealing: a method for obtaining transition paths de novo. J. Chem. Phys. 125, 114101.
- Warmflash, A. & Dinner, A.R. A model for TCR gene use.J. Immunol.177, 3857-3864.
- Laslo, P., Spooner, C. J., Warmflash, A., Lancki, D.W., Lee, H.-J., Sciammas, R., Gantner, B.N., Dinner, A.R., & Singh, H. Multilineage transcriptional priming and stabilization of alternate hematopoietic cell fates. Cell, 126, 755-766.
- Wylie, D.C., Hori, Y., Dinner, A.R., & Chakraborty, A.K. A hybrid deterministic-stochastic algorithm for modeling cell signaling dynamics in spatially inhomogenous environments and under the influence of external fields. J. Phys. Chem. B, 110, 12749-12765.
- Hou, P., Araujo, E., Zhao, T., Massenburg, D., Veselits, M., Doyle, C., Dinner, A.R., & Clark, M.R. B cell antigen receptor signaling and internalization are mutually exclusive events. PLoS Biol. 4, 1147-1158.
- Bitetti-Putzer, R., Dinner, A.R., Yang, W., & Karplus, M. Conformational sampling via a self-regulating effective energy surface. J. Chem. Phys. 124, 174901.
- Ma, A., Nag, A., & Dinner, A.R. Dynamic coupling between coordinates in a model for biomolecular isomerization. J. Chem. Phys. 124, 144911.
- Nag, A. & Dinner, A.R. Enhancement of Diffusion-controlled reaction rates by surface-induced orientational restriction. Biophys. J. 90, 896-902.
- Hu, J., Ma, A. & Dinner, A.R. Monte Carlo simulations of biomolecules: The MC module in CHARMM. J. Comp. Chem. 27, 203-216.
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- Woo, H.-J., Dinner, A.R. & Roux, B. Grand canonical Monte Carlo simulation of water in protein environments. J. Chem. Phys. 121, 6392-6400.
- Li, Q.-J., Dinner, A.R., Qi, S., Irvine, D.J., Huppa, J., Davis, M.M. & Chakraborty, A.K. CD4 enhances T cell sensitivity to antigen by coordinating Lck accumulation at the immunological synapse. Nature Immunol. 5, 791-799.
- Maibaum, L., Dinner, A.R. & Chandler, D. Micelle formation and the hydrophobic effect. J. Phys. Chem. B 108, 6778-6781.
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- Hagan, M.F., Dinner, A.R., Chandler, D. & Chakraborty, A.K. An atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA. Proc. Natl. Acad. Sci. USA 100, 13922-13927.
- Lee, K.-H., Dinner, A.R., Tu, C., Campi, G., Raychaudrhuri, S., Varma, R., Sims, T.N., Burack, W.R., Wu, H., Wang, J., Kanagawa, O., Markiewicz, M., Allen, P.M., Dustin, M.L., Chakraborty, A.K. & Shaw, A.S. The immunological synapse balances TCR signaling and degradation. Science 302, 1218-1222.
- Sun, S.X., Chandler, D., Dinner, A.R. & Oster, G. Elastic energy storage in Beta-sheets with application to F1-ATPase. Eur. Biophys. J. 32, 676-683.
- Dinner, A.R., Lopez, X. & Karplus, M. A charge-scaling procedure to treat solvent in QM/MM simulations. Theor. Chem. Acc. 109, 118-124.
- Andricioeai, I., Dinner, A.R. & Karplus, M. Self-guided enhanced sampling methods for thermodynamic averages. J. Chem. Phys. 118, 1074-1084.
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- Dinner, A.R. & Karplus, M. Comment on the communication "The key to solving the protein-folding problem lies in an accurate description of the denatured state" by van Gunsteren et al. Angnew. Chem. Int. Ed. 40, 4615-4616.
- Dinner, A.R., Blackburn, G.M. & Karplus, M. Uracil-DNA glycosylase acts by substrate autocatalysis. Nature 413, 752-755.
- Dinner, A.R. & Karplus, M. The roles of stability and contact order in determining protein folding rates. Nature Struct. Biol. 8, 21-22.
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- Dinner, A.R. Local deformations of polymers with nonplanar rigid main chain internal coordinates. J. Comp. Chem. 21, 1132-1144.
- Dinner, A.R., Sali, A., Smith, L.J., Dobson, C.M. & Karplus, M. Understanding protein folding via free energy surfaces from theory and experiment. Trends Biochem. Sci. 25, 331-339.
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- Dinner, A.R., Lazaridis, T. & Karplus, M. Understanding Beta-hairpin formation. Proc. Natl. Acad. Sci. USA 96, 9068-9073.
- Dinner, A.R., Verosub, E. & Karplus, M. Use of a quantitative structure-property relationship to design larger model proteins that fold rapidly. Prot. Eng. 12, 909-917.
- Dinner, A.R. & Karplus, M. Is protein unfolding the reverse of protein folding? A lattice simulation analysis. J. Mol. Biol. 292, 403-419.
- Dinner, A.R. & Karplus, M. The thermodynamics and kinetics of protein folding: A lattice model analysis of multiple pathways with intermediates. J. Phys. Chem. B 103, 7976-7994.
- Dinner, A.R., Abkevich, V., Shakhnovich, E. & Karplus, M. Factors that affect the folding ability of proteins. Proteins, 35, 34-40.
- Jasanoff, A., Song, S., Dinner, A.R., Wagner, G. & Wiley, D.C. One of two unstructured domains of Ii becomes ordered in complexes with MHC class II molecules. Immunity 10, 761-768.
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