|
|
|
- Lin, Y., Li, Y., Crosson, S., Dinner, A. R., Scherer, N. F. Phase resetting reveals network dynamics underlying a
bacterial cell cycle. PLoS Comp. Biol. 8, e1002778.
- Maienschein-Cline, M., Dinner, A. R., Hlavacek, W. S., Mu, F.
Improved predictions of transcription factor binding sites using physicochemical features of DNA. Nuc. Acid Res. Advance Access.
- Pesic, J., Xu, X., Terdik, J. Z., Lopez, A., Rice, S. A., Dinner, A. R., Scherer, N. F. Structural responses of quasi-two-dimensional colloidal fluids to excitations elicited by nonequilibrium perturbations. Phys. Rev. E, 86, 031403.
- Guttenberg, N., Dinner, A. R. & Weare, J. Steered transition path sampling. J. Chem. Phys. 136, 234103.
- Yi, C., Chen, B., Qi, B., Zhang, W., Jia, G., Zhang, L., Li, C. Q., Dinner, A. R., Yang, C.-G. & He, C. Duplex interrogation by a direct DNA repair protein in search of base damage. Nature Struct. Mol. Biol., 19, 671-676.
- Lenz, M., Thoresen, T., Gardel, M. L. & Dinner, A. R. F-actin buckling underlies the contraction of non-sarcomeric actomyosin bundles. Phys. Rev. Lett. 108, 238107.
- Lenz, M., Gardel, M. L. & Dinner, A. R. Requirements for contractility in disordered cytoskeletal bundles. New J. Phys. 14, 033037.
- Ochiai, K., Maienschein-Cline, M., Mandal, M., Triggs, J., Bertolino, E., Sciammas, R., Dinner, A. R., Clark, M. R. & Singh, H. The regulatory and molecular logic of IL-7R and pre-BCR signaling in B cell development. Nature Immunol., 13, 300-307.
- Maienschein-Cline, M., Zhou, J., White, K. P., Sciammas, R. & Dinner, A. R. Discovering transcription factor regulatory targets using gene expression and binding data. Bioinformatics, 28, 206-213.
- Tabei, S. M. A., Li, Y., Weigert, M. & Dinner, A. R. Model for competition from self during passive immunization, with application to broadly neutralizing antibodies for HIV. Vaccine 30, 607-613.
- Cheng, X., Xu, X., Rice, S. A., Dinner, A. R., Cohen, I. Assembly of vorticity-aligned hard-sphere colloidal strings in a simple shear flow. Proc. Natl. Acad. Sci. USA 109, 63-67.
|
|
- Dickson, A., Tabei, S. M. A., & Dinner, A. R. Entrainment of a driven oscillator as a dynamical phase transition. Phys. Rev. E, 84, 061134.
- Mandal, M., Powers, S. E., Maienschein-Cline, M., Bartom, E. T., Hamel, K. M., Kee, B. L., Dinner, A. R. & Clark, M. R. Epigenetic repression of the Igk locus by STAT5-mediated recruitment of the histone methyltransferase Ezh2. Nature Immunol., 12, 1212-1220.
- Zheng, W., Qi, B., Rohrdanz, M. A., Caflisch, A., Dinner, A. R. & Clementi, C. Delineation of folding pathways of a beta-sheet miniprotein. J. Phys. Chem. B, 115, 13065-13074.
- Guttenberg, N., Tabei, S. M. A., & Dinner, A. R. Short-time evolution in the adaptive immune system. Phys. Rev. E, 84, 031932.
- Dickson, A., Maienschein-Cline, M., Tovo-Dwyer, A., Hammond, J. R. & Dinner, A. R. Flow-dependent unfolding and refolding of an RNA by nonequilibrium umbrella sampling. J. Chem. Theor. Comp., 7, 2710-2720.
- Sciammas, R., Li, Y., Warmflash, A., Song, Y., Dinner, A. R. & Singh, H. An incoherent regulatory network architecture that orchestrates B cell diversification in response to antigen signaling. Mol. Sys. Biol. 7, 495.
|
|
- Ren, M., Guo, Q., Guo, L., Lenz, M., Xu, H., Dinner, A. R., Schilling, A. B. & Tang, W.-J. Polymerization of human MIP-1 chemokines (CCL3 and CCL4) and clearance ofMIP-1 by human insulin degrading enzyme. EMBO J. 29, 3952-3966.
- Maienschein-Cline, M., Warmflash, A. & Dinner, A. R. Defining cooperativity in gene regulation locally through intrinsic noise. IET Sys. Biol. 4, 379-392.
- Graham, T. G. W., Tabei, S. M. A., Dinner, A. R. & Rebay, I. Modeling bistable cell-fate choices in the Drosophila eye:
qualitative and quantitative perspectives. Development, 137, 2265-2278.
- Qi, B., Muff, S., Caflisch, A. & Dinner, A. R. Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein. J. Phys. Chem. B, 114, 6979-6989.
- Dickson, A., Nasto, A., & Dinner, A. R. Incorporating friction and collective shear moves into a lattice gas. Phys. Rev. E, 81, 051111.
- Li, Y., Bhimalapuram, P. & Dinner, A. R. Model for how retrograde actin flow regulates adhesion traction stresses. J. Phys.: Condens. Matter. 22, 194113.
- Dickson, A. & Dinner, A. R. Enhanced sampling of nonequilibrium steady states. Annu. Rev. Phys. Chem. 61, 441-459.
- Stewman, S. F., Jones-Rhoades, M., Bhimalapuram, P., Tchernookov, M., Preuss, D. & Dinner, A. R. Mechanistic insights from a quantitative analysis of pollen tube guidance. BMC Plant Biol. 10, 32.
- Tchernookov, M. & Dinner, A. R. A list-based algorithm for evaluation of large deviation functions. J. Stat. Mech. 2010, P02006.
- Xu, X., Lin, B., Cui, B., Dinner, A. R. & Rice, S. A. Spreading of colloid clusters in a quasi-one-dimensional channel. J. Chem. Phys., 132, 084902.
- Tchernookov, M., Warmflash, A. & Dinner, A. R. Field theoretic treatment of an effective action for a model of catalyzed autoamplification. Phys. Rev. E 81, 011112.
|
|
- Dickson, A., Warmflash, A. & Dinner, A. R. Separating forward and backward pathways in nonequilibrium umbrella sampling. J. Chem. Phys. 131, 154104.
- Reynaud, D., Lancki, D. W., Pongubala, J. M. R., Warmflash, A., Dinner, A. R. & Singh,H. Gene regulatory networks directing cell fates within the hematopoietic system. Chapter 1 in Cell Determination during Hematopoiesis, R. Ceredig & G. Brown, eds. Nova Science Publishers.
- Brooks, B. R., Brooks, C. L. III, Mackerell, A. D. Jr., Nilsson, L., Petrella, R. J., Roux, B., Won, Y. et al. CHARMM: The biomolecular simulation program. J. Comp. Chem. B 30, 1545-1614.
- Li, Y., Qu, X., Ma, A., Smith, G. J., Scherer, N. F. & Dinner, A. R. Models of single-molecule experiments with periodic perturbations reveal hidden dynamics in RNA folding. J. Phys. Chem. B 113, 7579-7590.
- Tchernookov, M., Warmflash, A. & Dinner, A. R. Critical behavior of a model for catalyzed autoamplification. J. Chem. Phys. 130, 134906.
- Dickson, A., Warmflash, A. & Dinner, A. R. Nonequilibrium umbrella sampling in spaces of many order parameters. J. Chem. Phys. 130, 074104.
- Zhao, T., Li, Y. & Dinner, A. R. How focal adhesion size depends on integrin affinity. Langmuir 25, 1540-1546.
- Lin, Y., Zhao, T. Farooqui, Z., Qu, X., He, C., Dinner, A. R. & Scherer, N. F. Using the bias from flow to elucidate single DNA repair protein sliding and interactions with DNA. Biophys. J. 96, 1911-1917.
- Warmflash, A. & Dinner, A. R. Modeling gene regulatory networks for cell fate specification. Chapter 5 in Mechanics of Cellular Systems and Processes, M. Zaman, ed. Cambridge University Press.
|
|
- Warmflash, A. & Dinner, A.R. Signatures of combinatorial regulation in intrinsic biological noise. Proc. Natl. Acad. Sci. USA 105, 17262-17267.
- Chen, H., Hu, J., Chen, P. R., Lan, L., Li, Z., Hicks, L. M., Dinner, A.R. & He, C. The Pseudomonas aeruginosa multidrug efflux regulator MexR uses an oxidation-sensing mechanism. Proc. Natl. Acad. Sci. USA 105, 13586-13591.
- 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.
|
|
- 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.
|
|
- 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.
|
|
|
|
- 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.
|
|
- 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.
|
|
|
|
- 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. Angew. 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.
|
|
- 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.
[Just Figure 2]
|
|
- 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.
|
|
|
|
|
|
|
|
|
|
|
