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Aaron R. Dinner - Publications

Chemistry University of Chicago, Chicago, IL 
theoretical studies of cellular behavior

139 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Zhang R, Redford SA, Ruijgrok PV, Kumar N, Mozaffari A, Zemsky S, Dinner AR, Vitelli V, Bryant Z, Gardel ML, de Pablo JJ. Spatiotemporal control of liquid crystal structure and dynamics through activity patterning. Nature Materials. PMID 33603187 DOI: 10.1038/s41563-020-00901-4  0.52
2020 Lorpaiboon C, Thiede EH, Webber RJ, Weare J, Dinner AR. Integrated Variational Approach to Conformational Dynamics: A Robust Strategy for Identifying Eigenfunctions of Dynamical Operators. The Journal of Physical Chemistry. B. PMID 32955887 DOI: 10.1021/Acs.Jpcb.0C06477  0.84
2020 Triandafillou CG, Katanski CD, Dinner AR, Drummond DA. Transient intracellular acidification regulates the core transcriptional heat shock response. Elife. 9. PMID 32762843 DOI: 10.7554/Elife.54880  0.36
2020 Antoszewski A, Feng CJ, Vani BP, Thiede EH, Hong L, Weare J, Tokmakoff A, Dinner AR. Insulin Dissociates by Diverse Mechanisms of Coupled Unfolding and Unbinding. The Journal of Physical Chemistry. B. PMID 32515958 DOI: 10.1021/Acs.Jpcb.0C03521  0.84
2020 Gao X, Jiang Y, Lin Y, Kim KH, Fang Y, Yi J, Meng L, Lee HC, Lu Z, Leddy O, Zhang R, Tu Q, Feng W, Nair V, Griffin PJ, ... ... Dinner AR, et al. Structured silicon for revealing transient and integrated signal transductions in microbial systems. Science Advances. 6: eaay2760. PMID 32110728 DOI: 10.1126/Sciadv.Aay2760  0.52
2020 Scholz M, Weirich KL, Gardel ML, Dinner AR. Tuning molecular motor transport through cytoskeletal filament network organization. Soft Matter. PMID 32016200 DOI: 10.1039/C9Sm01904A  0.52
2019 Freedman SL, Suarez C, Winkelman JD, Kovar DR, Voth GA, Dinner AR, Hocky GM. Mechanical and kinetic factors drive sorting of F-actin cross-linkers on bundles. Proceedings of the National Academy of Sciences of the United States of America. PMID 31346091 DOI: 10.1073/Pnas.1820814116  0.84
2019 Thiede EH, Giannakis D, Dinner AR, Weare J. Galerkin approximation of dynamical quantities using trajectory data. The Journal of Chemical Physics. 150: 244111. PMID 31255053 DOI: 10.1063/1.5063730  0.84
2019 Xu F, Kula-Eversole E, Iwanaszko M, Hutchison AL, Dinner A, Allada R. Circadian Clocks Function in Concert with Heat Shock Organizing Protein to Modulate Mutant Huntingtin Aggregation and Toxicity. Cell Reports. 27: 59-70.e4. PMID 30943415 DOI: 10.1016/J.Celrep.2019.03.015  0.44
2019 Karki S, Banerjee S, Mclean K, Dinner A, Clark MR. Transcription factories in Igκ allelic choice and diversity. Advances in Immunology. 141: 33-49. PMID 30904132 DOI: 10.1016/Bs.Ai.2018.11.001  0.8
2019 Mayassi T, Ladell K, Gudjonson H, McLaren JE, Shaw DG, Tran MT, Rokicka JJ, Lawrence I, Grenier JC, van Unen V, Ciszewski C, Dimaano M, Sayegh HE, Kumar V, Wijmenga C, ... ... Dinner AR, et al. Chronic Inflammation Permanently Reshapes Tissue-Resident Immunity in Celiac Disease. Cell. PMID 30739797 DOI: 10.1016/J.Cell.2018.12.039  0.44
2018 Freedman SL, Hocky GM, Banerjee S, Dinner AR. Nonequilibrium phase diagrams for actomyosin networks. Soft Matter. PMID 30204203 DOI: 10.1039/C8Sm00741A  0.8
2018 Karki S, Kennedy DE, Mclean K, Grzybowski AT, Maienschein-Cline M, Banerjee S, Xu H, Davis E, Mandal M, Labno C, Powers SE, Le Beau MM, Dinner AR, Singh H, Ruthenburg AJ, et al. Regulated Capture of Vκ Gene Topologically Associating Domains by Transcription Factories. Cell Reports. 24: 2443-2456. PMID 30157436 DOI: 10.1016/J.Celrep.2018.07.091  1
2018 Hutchison AL, Allada R, Dinner AR. Bootstrapping and Empirical Bayes Methods Improve Rhythm Detection in Sparsely Sampled Data. Journal of Biological Rhythms. 33: 339-349. PMID 30101659 DOI: 10.1177/0748730418789536  0.44
2018 Boisclair Lachance JF, Webber JL, Hong L, Dinner A, Rebay I. Cooperative recruitment of Yan via a high-affinity ETS supersite organizes repression to confer specificity and robustness to cardiac cell fate specification. Genes & Development. PMID 29535190 DOI: 10.1101/Gad.307132.117  0.48
2017 Stam S, Freedman SL, Banerjee S, Weirich KL, Dinner AR, Gardel ML. Filament rigidity and connectivity tune the deformation modes of active biopolymer networks. Proceedings of the National Academy of Sciences of the United States of America. PMID 29114058 DOI: 10.1073/Pnas.1708625114  0.8
2017 Scholz M, Dinner AR, Levine E, Biron D. Stochastic feeding dynamics arise from the need for information and energy. Proceedings of the National Academy of Sciences of the United States of America. PMID 28802256 DOI: 10.1073/Pnas.1703958114  0.44
2017 Freedman SL, Banerjee S, Hocky GM, Dinner AR. A Versatile Framework for Simulating the Dynamic Mechanical Structure of Cytoskeletal Networks. Biophysical Journal. 113: 448-460. PMID 28746855 DOI: 10.1016/J.Bpj.2017.06.003  0.8
2017 Banerjee S, Lo K, Daddysman MK, Selewa A, Kuntz T, Dinner AR, Scherer NF. Biphasic growth dynamics control cell division in Caulobacter crescentus. Nature Microbiology. 2: 17116. PMID 28737755 DOI: 10.1038/Nmicrobiol.2017.116  1
2017 Pekow J, Hutchison AL, Meckel K, Harrington K, Deng Z, Talasila N, Rubin DT, Hanauer SB, Hurst R, Umanskiy K, Fichera A, Hart J, Dinner AR, Bissonnette M. miR-4728-3p Functions as a Tumor Suppressor in Ulcerative Colitis-associated Colorectal Neoplasia Through Regulation of Focal Adhesion Signaling. Inflammatory Bowel Diseases. PMID 28594651 DOI: 10.1097/Mib.0000000000001104  0.44
2016 Burov S, Figliozzi P, Lin B, Rice SA, Scherer NF, Dinner AR. Single-pixel interior filling function approach for detecting and correcting errors in particle tracking. Proceedings of the National Academy of Sciences of the United States of America. PMID 28028226 DOI: 10.1073/Pnas.1619104114  1
2016 Gibbons SM, Scholz M, Hutchison AL, Dinner AR, Gilbert JA, Coleman ML. Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System. Mbio. 7. PMID 27999158 DOI: 10.1128/Mbio.01372-16  0.44
2016 Perera J, Zheng Z, Li S, Gudjonson H, Kalinina O, Benichou JI, Block KE, Louzoun Y, Yin D, Chong AS, Dinner AR, Weigert M, Huang H. Self-Antigen-Driven Thymic B Cell Class Switching Promotes T Cell Central Tolerance. Cell Reports. 17: 387-398. PMID 27705788 DOI: 10.1016/J.Celrep.2016.09.011  0.56
2016 Thiede EH, Van Koten B, Weare J, Dinner AR. Eigenvector method for umbrella sampling enables error analysis. The Journal of Chemical Physics. 145: 084115. PMID 27586912 DOI: 10.1063/1.4960649  0.84
2016 Liang WG, Triandafillou CG, Huang TY, Zulueta MM, Banerjee S, Dinner AR, Hung SC, Tang WJ. Structural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3. Proceedings of the National Academy of Sciences of the United States of America. PMID 27091995 DOI: 10.1073/Pnas.1523981113  1
2016 Banerjee S, Scherer NF, Dinner AR. Shape dynamics of growing cell walls. Soft Matter. PMID 26953519 DOI: 10.1039/C5Sm02991K  1
2016 Chen Y, Kale S, Weare J, Dinner AR, Roux B. A Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics - Monte Carlo Canonical Propagation Algorithm. Journal of Chemical Theory and Computation. PMID 26918826 DOI: 10.1021/Acs.Jctc.5B00706  1
2016 Ishizuka IE, Chea S, Gudjonson H, Constantinides MG, Dinner AR, Bendelac A, Golub R. Single-cell analysis defines the divergence between the innate lymphoid cell lineage and lymphoid tissue-inducer cell lineage. Nature Immunology. PMID 26779601 DOI: 10.1038/Ni.3344  1
2015 Peláez N, Gavalda-Miralles A, Wang B, Navarro HT, Gudjonson H, Rebay I, Dinner AR, Katsaggelos AK, Amaral LA, Carthew RW. Dynamics and heterogeneity of a fate determinant during transition towards cell differentiation. Elife. 4. PMID 26583752 DOI: 10.7554/Elife.08924  1
2015 Perelis M, Marcheva B, Ramsey KM, Schipma MJ, Hutchison AL, Taguchi A, Peek CB, Hong H, Huang W, Omura C, Allred AL, Bradfield CA, Dinner AR, Barish GD, Bass J. Pancreatic β cell enhancers regulate rhythmic transcription of genes controlling insulin secretion. Science (New York, N.Y.). 350: aac4250. PMID 26542580 DOI: 10.1126/Science.Aac4250  0.44
2015 Flourakis M, Kula-Eversole E, Hutchison AL, Han TH, Aranda K, Moose DL, White KP, Dinner AR, Lear BC, Ren D, Diekman CO, Raman IM, Allada R. A Conserved Bicycle Model for Circadian Clock Control of Membrane Excitability. Cell. 162: 836-48. PMID 26276633 DOI: 10.1016/J.Cell.2015.07.036  0.44
2015 Leone V, Gibbons SM, Martinez K, Hutchison AL, Huang EY, Cham CM, Pierre JF, Heneghan AF, Nadimpalli A, Hubert N, Zale E, Wang Y, Huang Y, Theriault B, Dinner AR, et al. Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. Cell Host & Microbe. 17: 681-9. PMID 25891358 DOI: 10.1016/J.Chom.2015.03.006  0.44
2015 Constantinides MG, Gudjonson H, McDonald BD, Ishizuka IE, Verhoef PA, Dinner AR, Bendelac A. PLZF expression maps the early stages of ILC1 lineage development. Proceedings of the National Academy of Sciences of the United States of America. 112: 5123-8. PMID 25838284 DOI: 10.1073/Pnas.1423244112  1
2015 Hutchison AL, Maienschein-Cline M, Chiang AH, Tabei SM, Gudjonson H, Bahroos N, Allada R, Dinner AR. Improved statistical methods enable greater sensitivity in rhythm detection for genome-wide data. Plos Computational Biology. 11: e1004094. PMID 25793520 DOI: 10.1371/Journal.Pcbi.1004094  1
2015 Wright CS, Banerjee S, Iyer-Biswas S, Crosson S, Dinner AR, Scherer NF. Intergenerational continuity of cell shape dynamics in Caulobacter crescentus. Scientific Reports. 5: 9155. PMID 25778096 DOI: 10.1038/Srep09155  1
2014 Kale S, Sode O, Weare J, Dinner AR. Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol. Journal of Chemical Theory and Computation. 10: 5467-5475. PMID 25516726 DOI: 10.1021/Ct500852Y  1
2014 Iyer-Biswas S, Wright CS, Henry JT, Lo K, Burov S, Lin Y, Crooks GE, Crosson S, Dinner AR, Scherer NF. Scaling laws governing stochastic growth and division of single bacterial cells. Proceedings of the National Academy of Sciences of the United States of America. 111: 15912-7. PMID 25349411 DOI: 10.1073/Pnas.1403232111  1
2014 Iyer-Biswas S, Crooks GE, Scherer NF, Dinner AR. Universality in stochastic exponential growth. Physical Review Letters. 113: 028101. PMID 25062238 DOI: 10.1103/Physrevlett.113.028101  1
2014 Mathew R, Mao AP, Chiang AH, Bertozzi-Villa C, Bunker JJ, Scanlon ST, McDonald BD, Constantinides MG, Hollister K, Singer JD, Dent AL, Dinner AR, Bendelac A. A negative feedback loop mediated by the Bcl6-cullin 3 complex limits Tfh cell differentiation. The Journal of Experimental Medicine. 211: 1137-51. PMID 24863065 DOI: 10.1084/Jem.20132267  1
2014 Tempkin JO, Qi B, Saunders MG, Roux B, Dinner AR, Weare J. Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations. The Journal of Chemical Physics. 140: 184114. PMID 24832260 DOI: 10.1063/1.4872021  1
2014 Singh H, Khan AA, Dinner AR. Gene regulatory networks in the immune system. Trends in Immunology. 35: 211-8. PMID 24768519 DOI: 10.1016/J.It.2014.03.006  1
2014 Saunders MG, Tempkin J, Weare J, Dinner AR, Roux B, Voth GA. Nucleotide regulation of the structure and dynamics of G-actin. Biophysical Journal. 106: 1710-20. PMID 24739170 DOI: 10.1016/J.Bpj.2014.03.012  1
2014 Rice SA, Dinner AR. Advances in Chemical Physics Advances in Chemical Physics. 156: 1-518. DOI: 10.1002/9781118949702  1
2014 Rice SA, Dinner AR. Preface to the series Advances in Chemical Physics. 156: vii. DOI: 10.1002/9781118197714  1
2014 Rice SA, Dinner AR. Preface to the series Advances in Chemical Physics. 156: vii. DOI: 10.1002/9781118180396  1
2013 Dama JF, Sinitskiy AV, McCullagh M, Weare J, Roux B, Dinner AR, Voth GA. The Theory of Ultra-Coarse-Graining. 1. General Principles. Journal of Chemical Theory and Computation. 9: 2466-80. PMID 26583735 DOI: 10.1021/Ct4000444  0.84
2013 Burov S, Tabei SM, Huynh T, Murrell MP, Philipson LH, Rice SA, Gardel ML, Scherer NF, Dinner AR. Distribution of directional change as a signature of complex dynamics. Proceedings of the National Academy of Sciences of the United States of America. 110: 19689-94. PMID 24248363 DOI: 10.1073/Pnas.1319473110  1
2013 Ochiai K, Maienschein-Cline M, Simonetti G, Chen J, Rosenthal R, Brink R, Chong AS, Klein U, Dinner AR, Singh H, Sciammas R. Transcriptional regulation of germinal center B and plasma cell fates by dynamical control of IRF4. Immunity. 38: 918-29. PMID 23684984 DOI: 10.1016/J.Immuni.2013.04.009  1
2013 Guttenberg N, Dama JF, Saunders MG, Voth GA, Weare J, Dinner AR. Minimizing memory as an objective for coarse-graining. The Journal of Chemical Physics. 138: 094111. PMID 23485281 DOI: 10.1063/1.4793313  1
2013 Tabei SM, Burov S, Kim HY, Kuznetsov A, Huynh T, Jureller J, Philipson LH, Dinner AR, Scherer NF. Intracellular transport of insulin granules is a subordinated random walk. Proceedings of the National Academy of Sciences of the United States of America. 110: 4911-6. PMID 23479621 DOI: 10.1073/Pnas.1221962110  1
2013 Xu X, Rice SA, Dinner AR. Relation between ordering and shear thinning in colloidal suspensions. Proceedings of the National Academy of Sciences of the United States of America. 110: 3771-6. PMID 23431185 DOI: 10.1073/Pnas.1301055110  1
2013 Xu X, Rice SA, Dinner AR. Influence of interlayer exchanges on vorticity-aligned colloidal string assembly in a simple shear flow Journal of Physical Chemistry Letters. 4: 3310-3315. DOI: 10.1021/Jz401722J  1
2013 Dama JF, Sinitskiy AV, McCullagh M, Weare J, Roux B, Dinner AR, Voth GA. The theory of ultra-coarse-graining. 1. General principles Journal of Chemical Theory and Computation. 9: 2466-2480. DOI: 10.1021/ct4000444  1
2012 Lin Y, Li Y, Crosson S, Dinner AR, Scherer NF. Phase resetting reveals network dynamics underlying a bacterial cell cycle. Plos Computational Biology. 8: e1002778. PMID 23209388 DOI: 10.1371/Journal.Pcbi.1002778  1
2012 Lenz M, Gardel ML, Dinner AR. Requirements for contractility in disordered cytoskeletal bundles. New Journal of Physics. 14. PMID 23155355 DOI: 10.1088/1367-2630/14/3/033037  1
2012 Pesic J, Terdik JZ, Xu X, Tian Y, Lopez A, Rice SA, Dinner AR, Scherer NF. Structural responses of quasi-two-dimensional colloidal fluids to excitations elicited by nonequilibrium perturbations. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 86: 031403. PMID 23030916 DOI: 10.1103/Physreve.86.031403  1
2012 Lenz M, Thoresen T, Gardel ML, Dinner AR. Contractile units in disordered actomyosin bundles arise from F-actin buckling. Physical Review Letters. 108: 238107. PMID 23003998 DOI: 10.1103/Physrevlett.108.238107  1
2012 Maienschein-Cline M, Dinner AR, Hlavacek WS, Mu F. Improved predictions of transcription factor binding sites using physicochemical features of DNA. Nucleic Acids Research. 40: e175. PMID 22923524 DOI: 10.1093/Nar/Gks771  1
2012 Guttenberg N, Dinner AR, Weare J. Steered transition path sampling. The Journal of Chemical Physics. 136: 234103. PMID 22779577 DOI: 10.1063/1.4724301  1
2012 Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C. Duplex interrogation by a direct DNA repair protein in search of base damage. Nature Structural & Molecular Biology. 19: 671-6. PMID 22659876 DOI: 10.1038/Nsmb.2320  1
2012 Ochiai K, Maienschein-Cline M, Mandal M, Triggs JR, Bertolino E, Sciammas R, Dinner AR, Clark MR, Singh H. A self-reinforcing regulatory network triggered by limiting IL-7 activates pre-BCR signaling and differentiation. Nature Immunology. 13: 300-7. PMID 22267219 DOI: 10.1038/Ni.2210  1
2012 Cheng X, Xu X, Rice SA, Dinner AR, Cohen I. Assembly of vorticity-aligned hard-sphere colloidal strings in a simple shear flow. Proceedings of the National Academy of Sciences of the United States of America. 109: 63-7. PMID 22198839 DOI: 10.1073/Pnas.1118197108  1
2012 Ali Tabei SM, Li Y, Weigert M, Dinner AR. Model for competition from self during passive immunization, with application to broadly neutralizing antibodies for HIV. Vaccine. 30: 607-13. PMID 22119591 DOI: 10.1016/J.Vaccine.2011.11.048  1
2012 Maienschein-Cline M, Zhou J, White KP, Sciammas R, Dinner AR. Discovering transcription factor regulatory targets using gene expression and binding data. Bioinformatics (Oxford, England). 28: 206-13. PMID 22084256 DOI: 10.1093/Bioinformatics/Btr628  1
2012 Nicolis G, Maes D, Rice SA, Dinner AR. Kinetics and Thermodynamics of Multistep Nucleation and Self-Assembly in Nanoscale Materials: Advances in Chemical Physics Kinetics and Thermodynamics of Multistep Nucleation and Self-Assembly in Nanoscale Materials: Advances in Chemical Physics. 151: 1-339. DOI: 10.1002/9781118309513  1
2011 Dickson A, Maienschein-Cline M, Tovo-Dwyer A, Hammond JR, Dinner AR. Flow-Dependent Unfolding and Refolding of an RNA by Nonequilibrium Umbrella Sampling. Journal of Chemical Theory and Computation. 7: 2710-2720. PMID 26605464 DOI: 10.1021/Ct200371N  1
2011 Dickson A, Tabei SM, Dinner AR. Entrainment of a driven oscillator as a dynamical phase transition. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 84: 061134. PMID 22304067 DOI: 10.1103/Physreve.84.061134  1
2011 Guttenberg N, Tabei SM, Dinner AR. Short-time evolution in the adaptive immune system. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 84: 031932. PMID 22060428 DOI: 10.1103/Physreve.84.031932  1
2011 Mandal M, Powers SE, Maienschein-Cline M, Bartom ET, Hamel KM, Kee BL, Dinner AR, Clark MR. Epigenetic repression of the Igk locus by STAT5-mediated recruitment of the histone methyltransferase Ezh2. Nature Immunology. 12: 1212-20. PMID 22037603 DOI: 10.1038/Ni.2136  1
2011 Zheng W, Qi B, Rohrdanz MA, Caflisch A, Dinner AR, Clementi C. Delineation of folding pathways of a β-sheet miniprotein. The Journal of Physical Chemistry. B. 115: 13065-74. PMID 21942785 DOI: 10.1021/Jp2076935  1
2011 Sciammas R, Li Y, Warmflash A, Song Y, Dinner AR, Singh H. An incoherent regulatory network architecture that orchestrates B cell diversification in response to antigen signaling. Molecular Systems Biology. 7: 495. PMID 21613984 DOI: 10.1038/Msb.2011.25  1
2011 Dickson A, Maienschein-Cline M, Tovo-Dwyer A, Hammond JR, Dinner AR. Flow-dependent unfolding and refolding of an RNA by nonequilibrium umbrella sampling Journal of Chemical Theory and Computation. 7: 2710-2720. DOI: 10.1021/ct200371n  1
2010 Li Y, Bhimalapuram P, Dinner AR. Model for how retrograde actin flow regulates adhesion traction stresses. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 22: 194113. PMID 21386439 DOI: 10.1088/0953-8984/22/19/194113  1
2010 Maienschein-Cline M, Warmflash A, Dinner AR. Defining cooperativity in gene regulation locally through intrinsic noise. Iet Systems Biology. 4: 379-92. PMID 21073237 DOI: 10.1049/Iet-Syb.2009.0070  1
2010 Ren M, Guo Q, Guo L, Lenz M, Qian F, Koenen RR, Xu H, Schilling AB, Weber C, Ye RD, Dinner AR, Tang WJ. Polymerization of MIP-1 chemokine (CCL3 and CCL4) and clearance of MIP-1 by insulin-degrading enzyme. The Embo Journal. 29: 3952-66. PMID 20959807 DOI: 10.1038/Emboj.2010.256  1
2010 Dickson A, Nasto A, Dinner AR. Incorporating friction and collective shear moves into a lattice gas. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 81: 051111. PMID 20866189 DOI: 10.1103/Physreve.81.051111  1
2010 Graham TG, Tabei SM, Dinner AR, Rebay I. Modeling bistable cell-fate choices in the Drosophila eye: qualitative and quantitative perspectives. Development (Cambridge, England). 137: 2265-78. PMID 20570936 DOI: 10.1242/Dev.044826  1
2010 Qi B, Muff S, Caflisch A, Dinner AR. Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein. The Journal of Physical Chemistry. B. 114: 6979-89. PMID 20438066 DOI: 10.1021/Jp101476G  1
2010 Dickson A, Dinner AR. Enhanced sampling of nonequilibrium steady states. Annual Review of Physical Chemistry. 61: 441-59. PMID 20367083 DOI: 10.1146/Annurev.Physchem.012809.103433  1
2010 Tchernookov M, Warmflash A, Dinner AR. Field theoretic treatment of an effective action for a model of catalyzed autoamplification. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 81: 011112. PMID 20365328 DOI: 10.1103/Physreve.81.011112  1
2010 Xu X, Lin B, Cui B, Dinner AR, Rice SA. Spreading of colloid clusters in a quasi-one-dimensional channel. The Journal of Chemical Physics. 132: 084902. PMID 20192315 DOI: 10.1063/1.3330414  1
2010 Stewman SF, Jones-Rhoades M, Bhimalapuram P, Tchernookov M, Preuss D, Dinner AR. Mechanistic insights from a quantitative analysis of pollen tube guidance. Bmc Plant Biology. 10: 32. PMID 20170550 DOI: 10.1186/1471-2229-10-32  1
2010 Tchernookov M, Dinner AR. A list-based algorithm for evaluation of large deviation functions Journal of Statistical Mechanics: Theory and Experiment. 2010. DOI: 10.1088/1742-5468/2010/02/P02006  1
2009 Dickson A, Warmflash A, Dinner AR. Separating forward and backward pathways in nonequilibrium umbrella sampling. The Journal of Chemical Physics. 131: 154104. PMID 20568844 DOI: 10.1063/1.3244561  1
2009 Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, et al. CHARMM: the biomolecular simulation program. Journal of Computational Chemistry. 30: 1545-614. PMID 19444816 DOI: 10.1002/Jcc.21287  1
2009 Li Y, Qu X, Ma A, Smith GJ, Scherer NF, Dinner AR. Models of single-molecule experiments with periodic perturbations reveal hidden dynamics in RNA folding. The Journal of Physical Chemistry. B. 113: 7579-90. PMID 19415919 DOI: 10.1021/Jp900225Q  1
2009 Tchernookov M, Warmflash A, Dinner AR. Critical behavior of a model for catalyzed autoamplification. The Journal of Chemical Physics. 130: 134906. PMID 19355779 DOI: 10.1063/1.3101649  1
2009 Lin Y, Zhao T, Jian X, Farooqui Z, Qu X, He C, Dinner AR, Scherer NF. Using the bias from flow to elucidate single DNA repair protein sliding and interactions with DNA. Biophysical Journal. 96: 1911-7. PMID 19254550 DOI: 10.1016/J.Bpj.2008.11.021  1
2009 Dickson A, Warmflash A, Dinner AR. Nonequilibrium umbrella sampling in spaces of many order parameters. The Journal of Chemical Physics. 130: 074104. PMID 19239281 DOI: 10.1063/1.3070677  1
2009 Zhao T, Li Y, Dinner AR. How focal adhesion size depends on integrin affinity. Langmuir : the Acs Journal of Surfaces and Colloids. 25: 1540-6. PMID 19132823 DOI: 10.1021/La8026804  1
2009 Warmflash A, Dinner AR. Modeling gene regulatory networks for cell fate specification Statistical Mechanics of Cellular Systems and Processes. 121-154. DOI: 10.1017/CBO9780511576768.006  1
2009 Reynaud D, Lancki DW, Pongubala JMR, Warmflash A, Dinner AR, Singh H. Gene regulatory networks directing cell fates within the hematopoietic system Cell Determination During Hematopoiesis. 1-23.  1
2008 Warmflash A, Dinner AR. Signatures of combinatorial regulation in intrinsic biological noise. Proceedings of the National Academy of Sciences of the United States of America. 105: 17262-7. PMID 18981421 DOI: 10.1073/Pnas.0809314105  1
2008 Chen H, Hu J, Chen PR, Lan L, Li Z, Hicks LM, Dinner AR, He C. The Pseudomonas aeruginosa multidrug efflux regulator MexR uses an oxidation-sensing mechanism. Proceedings of the National Academy of Sciences of the United States of America. 105: 13586-91. PMID 18757728 DOI: 10.1073/Pnas.0803391105  1
2008 Warmflash A, Adamson DN, Dinner AR. How noise statistics impact models of enzyme cycles. The Journal of Chemical Physics. 128: 225101. PMID 18554058 DOI: 10.1063/1.2929841  1
2008 Hu J, Ma A, Dinner AR. A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT. Proceedings of the National Academy of Sciences of the United States of America. 105: 4615-20. PMID 18353991 DOI: 10.1073/Pnas.0708058105  1
2008 Li Y, Zhao T, Bhimalapuram P, Dinner AR. How the nature of an observation affects single-trajectory entropies. The Journal of Chemical Physics. 128: 074102. PMID 18298135 DOI: 10.1063/1.2828505  1
2008 Zhao T, Dinner AR. Apparent directional scanning for DNA repair. Biophysical Journal. 94: 47-52. PMID 17827238 DOI: 10.1529/Biophysj.107.110619  1
2007 Warmflash A, Bhimalapuram P, Dinner AR. Umbrella sampling for nonequilibrium processes. The Journal of Chemical Physics. 127: 154112. PMID 17949137 DOI: 10.1063/1.2784118  1
2007 Stewman SF, Dinner AR. Lattice model for self-assembly with application to the formation of cytoskeletal-like structures. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 76: 016103. PMID 17677529 DOI: 10.1103/Physreve.76.016103  1
2007 Nag A, Zhao T, Dinner AR. Effects of nonproductive binding on the kinetics of enzymatic reactions with patterned substrates. The Journal of Chemical Physics. 126: 035103. PMID 17249902 DOI: 10.1063/1.2428301  1
2006 Ma A, Hu J, Karplus M, Dinner AR. Implications of alternative substrate binding modes for catalysis by uracil-DNA glycosylase: an apparent discrepancy resolved. Biochemistry. 45: 13687-96. PMID 17105188 DOI: 10.1021/Bi061061Y  1
2006 Hu J, Ma A, Dinner AR. Bias annealing: a method for obtaining transition paths de novo. The Journal of Chemical Physics. 125: 114101. PMID 16999460 DOI: 10.1063/1.2335640  1
2006 Warmflash A, Dinner AR. A model for TCR gene segment use. Journal of Immunology (Baltimore, Md. : 1950). 177: 3857-64. PMID 16951348 DOI: 10.4049/Jimmunol.177.6.3857  1
2006 Laslo P, Spooner CJ, Warmflash A, Lancki DW, Lee HJ, Sciammas R, Gantner BN, Dinner AR, Singh H. Multilineage transcriptional priming and determination of alternate hematopoietic cell fates. Cell. 126: 755-66. PMID 16923394 DOI: 10.1016/J.Cell.2006.06.052  1
2006 Wylie DC, Hori Y, Dinner AR, Chakraborty AK. A hybrid deterministic-stochastic algorithm for modeling cell signaling dynamics in spatially inhomogeneous environments and under the influence of external fields. The Journal of Physical Chemistry. B. 110: 12749-65. PMID 16800611 DOI: 10.1021/Jp056231F  1
2006 Hou P, Araujo E, Zhao T, Zhang M, Massenburg D, Veselits M, Doyle C, Dinner AR, Clark MR. B cell antigen receptor signaling and internalization are mutually exclusive events. Plos Biology. 4: e200. PMID 16719564 DOI: 10.1371/Journal.Pbio.0040200  1
2006 Bitetti-Putzer R, Dinner AR, Yang W, Karplus M. Conformational sampling via a self-regulating effective energy surface. The Journal of Chemical Physics. 124: 174901. PMID 16689598 DOI: 10.1063/1.2171194  1
2006 Ma A, Nag A, Dinner AR. Dynamic coupling between coordinates in a model for biomolecular isomerization. The Journal of Chemical Physics. 124: 144911. PMID 16626249 DOI: 10.1063/1.2183768  1
2006 Hu J, Ma A, Dinner AR. Monte Carlo simulations of biomolecules: The MC module in CHARMM. Journal of Computational Chemistry. 27: 203-16. PMID 16323162 DOI: 10.1002/Jcc.20327  1
2006 Nag A, Dinner AR. Enhancement of diffusion-controlled reaction rates by surface-induced orientational restriction. Biophysical Journal. 90: 896-902. PMID 16299070 DOI: 10.1529/Biophysj.105.072785  1
2005 Ma A, Dinner AR. Automatic method for identifying reaction coordinates in complex systems. The Journal of Physical Chemistry. B. 109: 6769-79. PMID 16851762 DOI: 10.1021/Jp045546C  1
2005 Warmflash A, Weigert M, Dinner AR. Control of genotypic allelic inclusion through TCR surface expression. Journal of Immunology (Baltimore, Md. : 1950). 175: 6412-9. PMID 16272293 DOI: 10.4049/Jimmunol.175.10.6412  1
2004 Woo HJ, Dinner AR, Roux B. Grand canonical Monte Carlo simulations of water in protein environments. The Journal of Chemical Physics. 121: 6392-400. PMID 15446937 DOI: 10.1063/1.1784436  1
2004 Li QJ, Dinner AR, Qi S, Irvine DJ, Huppa JB, Davis MM, Chakraborty AK. CD4 enhances T cell sensitivity to antigen by coordinating Lck accumulation at the immunological synapse. Nature Immunology. 5: 791-9. PMID 15247914 DOI: 10.1038/Ni1095  1
2004 Maibaum L, Dinner AR, Chandler D. Micelle formation and the hydrophobic effect Journal of Physical Chemistry B. 108: 6778-6781. DOI: 10.1021/Jp037487T  1
2003 Hagan MF, Dinner AR, Chandler D, Chakraborty AK. Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA. Proceedings of the National Academy of Sciences of the United States of America. 100: 13922-7. PMID 14617777 DOI: 10.1073/Pnas.2036378100  1
2003 Lee KH, Dinner AR, Tu C, Campi G, Raychaudhuri S, Varma R, Sims TN, Burack WR, Wu H, Wang J, Kanagawa O, Markiewicz M, Allen PM, Dustin ML, Chakraborty AK, et al. The immunological synapse balances T cell receptor signaling and degradation. Science (New York, N.Y.). 302: 1218-22. PMID 14512504 DOI: 10.1126/Science.1086507  1
2003 Sun S, Chandler D, Dinner AR, Oster G. Elastic energy storage in beta-sheets with application to F1-ATPase. European Biophysics Journal : Ebj. 32: 676-83. PMID 12955360 DOI: 10.1007/S00249-003-0335-6  1
2003 Andricioaei I, Dinner AR, Karplus M. Self-guided enhanced sampling methods for thermodynamic averages Journal of Chemical Physics. 118: 1074-1084. DOI: 10.1063/1.1528893  1
2003 Dinner AR, Lopez X, Karplus M. A charge-scaling method to treat solvent in QM/MM simulations Theoretical Chemistry Accounts. 109: 118-124. DOI: 10.1007/S00214-002-0417-Z  1
2002 Dinner AR, So SS, Karplus M. Statistical analysis of protein folding kinetics Advances in Chemical Physics. 120: 1-34.  1
2001 Dinner AR, 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. We thank Eugene Shakhnovich (Harvard University) for pointing out the references on lattice polymer simulations and very helpful discussions. We also thank Wilfred van Gunsteren for comments on the manuscript. A.R.D. is a Burroughs Wellcome Fund Hitchings-Elion Postdoctoral Fellow. The work done at Harvard was supported in part by the National Institutes of Health. Angewandte Chemie (International Ed. in English). 40: 4615-4616. PMID 12404364 DOI: 10.1002/1521-3773(20011217)40:24<4615::Aid-Anie4615>3.0.Co;2-H  1
2001 Dinner AR, Blackburn GM, Karplus M. Uracil-DNA glycosylase acts by substrate autocatalysis. Nature. 413: 752-5. PMID 11607036 DOI: 10.1038/35099587  1
2001 Dinner AR, Karplus M. The roles of stability and contact order in determining protein folding rates. Nature Structural Biology. 8: 21-2. PMID 11135664 DOI: 10.1038/83003  1
2000 Dinner AR, Sali A, Smith LJ, Dobson CM, Karplus M. Understanding protein folding via free-energy surfaces from theory and experiment. Trends in Biochemical Sciences. 25: 331-9. PMID 10871884 DOI: 10.1016/S0968-0004(00)01610-8  1
2000 Kargi F, Dinner AR, Pala A. Characterization and biological treatment of pickling industry wastewater Bioprocess Engineering. 23: 371-374. DOI: 10.1007/s004499900174  1
2000 Dinner AR. Local Deformations of Polymers with Nonplanar Rigid Main-Chain Internal Coordinates Journal of Computational Chemistry. 21: 1132-1144. DOI: 10.1002/1096-987X(200010)21:13<1132::Aid-Jcc2>3.0.Co;2-5  1
1999 Dinner AR, Verosub E, Karplus M. Use of a quantitative structure-property relationship to design larger model proteins that fold rapidly. Protein Engineering. 12: 909-17. PMID 10585496 DOI: 10.1093/Protein/12.11.909  1
1999 Dinner AR, Karplus M. Is protein unfolding the reverse of protein folding? A lattice simulation analysis. Journal of Molecular Biology. 292: 403-19. PMID 10493884 DOI: 10.1006/Jmbi.1999.3051  1
1999 Dinner AR, Lazaridis T, Karplus M. Understanding beta-hairpin formation. Proceedings of the National Academy of Sciences of the United States of America. 96: 9068-73. PMID 10430896 DOI: 10.1073/Pnas.96.16.9068  1
1999 Jasanoff A, Song S, Dinner AR, Wagner G, Wiley DC. One of two unstructured domains of Ii becomes ordered in complexes with MHC class II molecules. Immunity. 10: 761-8. PMID 10403651 DOI: 10.1016/S1074-7613(00)80075-8  1
1999 Dinner AR, Abkevich V, Shakhnovich E, Karplus M. Factors that affect the folding ability of proteins. Proteins. 35: 34-40. PMID 10090284 DOI: 10.1002/(Sici)1097-0134(19990401)35:1<34::Aid-Prot4>3.0.Co;2-Q  1
1999 Dinner AR, Karplus M. The Thermodynamics and Kinetics of Protein Folding:  A Lattice Model Analysis of Multiple Pathways with Intermediates The Journal of Physical Chemistry B. 103: 7976-7994. DOI: 10.1021/Jp990851X  1
1999 Dinner AR, Karplus M. The thermodynamics and kinetics of protein folding: A lattice model analysis of multiple pathways with intermediates Journal of Physical Chemistry B. 103: 7976-7994.  1
1998 Dinner AR, So SS, Karplus M. Use of quantitative structure-property relationships to predict the folding ability of model proteins. Proteins. 33: 177-203. PMID 9779787 DOI: 10.1002/(Sici)1097-0134(19981101)33:2<177::Aid-Prot4>3.0.Co;2-G  1
1998 Dinner AR, Karplus M. A metastable state in folding simulations of a protein model. Nature Structural Biology. 5: 236-41. PMID 9501918 DOI: 10.1038/Nsb0398-236  1
1996 Dinner AR, Sali A, Karplus M. The folding mechanism of larger model proteins: role of native structure. Proceedings of the National Academy of Sciences of the United States of America. 93: 8356-61. PMID 8710875 DOI: 10.1073/Pnas.93.16.8356  1
1994 Dinner A, Šali A, Karplus M, Shakhnovich E. Phase diagram of a model protein derived by exhaustive enumeration of the conformations The Journal of Chemical Physics. 101: 1444-1451. DOI: 10.1063/1.467769  1
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