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Arup K. Chakraborty - Publications

Affiliations: 
1988-2005 Chemical Engineering University of California, Berkeley, Berkeley, CA, United States 
 2005- Chemical Engineering Massachusetts Institute of Technology, Cambridge, MA, United States 
Area:
cell-cell recognition in immunology, T cell biology, polymers and membranes statistical mechanics
Website:
http://web.mit.edu/cheme/people/profile.html?id=4
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92 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
2023 Schede HH, Natarajan P, Chakraborty AK, Shrinivas K. A model for organization and regulation of nuclear condensates by gene activity. Nature Communications. 14: 4152. PMID 37438363 DOI: 10.1038/s41467-023-39878-4  0.763
2023 Natarajan P, Shrinivas K, Chakraborty AK. A model for cis-regulation of transcriptional condensates and gene expression by proximal lncRNAs. Biophysical Journal. PMID 37277993 DOI: 10.1016/j.bpj.2023.05.032  0.756
2022 Conti S, Ovchinnikov V, Faris JG, Chakraborty AK, Karplus M, Sprenger KG. Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV. Plos Computational Biology. 18: e1009391. PMID 35442968 DOI: 10.1371/journal.pcbi.1009391  0.393
2021 Conti S, Kaczorowski KJ, Song G, Porter K, Andrabi R, Burton DR, Chakraborty AK, Karplus M. Design of immunogens to elicit broadly neutralizing antibodies against HIV targeting the CD4 binding site. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33637649 DOI: 10.1073/pnas.2018338118  0.384
2021 Murakowski DK, Barton JP, Peter L, Chandrashekar A, Bondzie E, Gao A, Barouch DH, Chakraborty AK. Adenovirus-vectored vaccine containing multidimensionally conserved parts of the HIV proteome is immunogenic in rhesus macaques. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33514660 DOI: 10.1073/pnas.2022496118  0.535
2021 Murugan A, Husain K, Rust M, Bass JT, Hepler C, Pietsch JMJ, Swain PS, Toettcher JE, Jena S, Chakraborty AK, Sprenger KG, Mora T, Walczak A, Rivoire O, Wang S, et al. Roadmap on biology in time varying environments. Physical Biology. PMID 33477124 DOI: 10.1088/1478-3975/abde8d  0.675
2020 Henninger JE, Oksuz O, Shrinivas K, Sagi I, LeRoy G, Zheng MM, Andrews JO, Zamudio AV, Lazaris C, Hannett NM, Lee TI, Sharp PA, Cissé II, Chakraborty AK, Young RA. RNA-Mediated Feedback Control of Transcriptional Condensates. Cell. PMID 33333019 DOI: 10.1016/j.cell.2020.11.030  0.75
2020 Zhang TH, Dai L, Barton JP, Du Y, Tan Y, Pang W, Chakraborty AK, Lloyd-Smith JO, Sun R. Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease. Plos Genetics. 16: e1009009. PMID 33085662 DOI: 10.1371/journal.pgen.1009009  0.514
2020 Klein IA, Boija A, Afeyan LK, Hawken SW, Fan M, Dall'Agnese A, Oksuz O, Henninger JE, Shrinivas K, Sabari BR, Sagi I, Clark VE, Platt JM, Kar M, McCall PM, ... ... Chakraborty A, et al. Partitioning of cancer therapeutics in nuclear condensates. Science (New York, N.Y.). 368: 1386-1392. PMID 32554597 DOI: 10.1126/Science.Aaz4427  0.754
2020 Quadeer AA, Barton JP, Chakraborty AK, McKay MR. Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape. Nature Communications. 11: 377. PMID 31953427 DOI: 10.1038/S41467-019-14174-2  0.575
2019 Shrinivas K, Sabari BR, Coffey EL, Klein IA, Boija A, Zamudio AV, Schuijers J, Hannett NM, Sharp PA, Young RA, Chakraborty AK. Enhancer Features that Drive Formation of Transcriptional Condensates. Molecular Cell. 75: 549-561.e7. PMID 31398323 DOI: 10.1016/J.Molcel.2019.07.009  0.766
2019 Barton JP, Rajkoomar E, Mann JK, Murakowski DK, Toyoda M, Mahiti M, Mwimanzi P, Ueno T, Chakraborty AK, Ndung'u T. Modelling and testing of the HIV-1 Nef fitness landscape. Virus Evolution. 5: vez029. PMID 31392033 DOI: 10.1093/Ve/Vez029  0.587
2018 Gao A, Shrinivas K, Lepeudry P, Suzuki HI, Sharp PA, Chakraborty AK. Evolution of weak cooperative interactions for biological specificity. Proceedings of the National Academy of Sciences of the United States of America. PMID 30404915 DOI: 10.1073/Pnas.1815912115  0.776
2018 Amitai A, Chakraborty AK, Kardar M. The low spike density of HIV may have evolved because of the effects of T helper cell depletion on affinity maturation. Plos Computational Biology. 14: e1006408. PMID 30161121 DOI: 10.1371/Journal.Pcbi.1006408  0.324
2018 Sabari BR, Dall'Agnese A, Boija A, Klein IA, Coffey EL, Shrinivas K, Abraham BJ, Hannett NM, Zamudio AV, Manteiga JC, Li CH, Guo YE, Day DS, Schuijers J, Vasile E, ... ... Chakraborty AK, et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science (New York, N.Y.). PMID 29930091 DOI: 10.1126/Science.Aar3958  0.77
2018 Ovchinnikov V, Louveau JE, Barton JP, Karplus M, Chakraborty AK. Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies. Elife. 7. PMID 29442996 DOI: 10.7554/Elife.33038  0.652
2018 Louie RHY, Kaczorowski KJ, Barton JP, Chakraborty AK, McKay MR. Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies. Proceedings of the National Academy of Sciences of the United States of America. PMID 29311326 DOI: 10.1073/Pnas.1717765115  0.583
2018 Ovchinnikov V, Louveau JE, Barton JP, Karplus M, Chakraborty AK. Author response: Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies Elife. DOI: 10.7554/Elife.33038.022  0.609
2017 Amitai A, Mesin L, Victora GD, Kardar M, Chakraborty AK. A Population Dynamics Model for Clonal Diversity in a Germinal Center. Frontiers in Microbiology. 8: 1693. PMID 28955307 DOI: 10.3389/Fmicb.2017.01693  0.305
2017 Bandaru P, Shah NH, Bhattacharyya M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J. Deconstruction of the Ras switching cycle through saturation mutagenesis. Elife. 6. PMID 28686159 DOI: 10.7554/Elife.27810  0.56
2017 Hnisz D, Shrinivas K, Young RA, Chakraborty AK, Sharp PA. A Phase Separation Model for Transcriptional Control. Cell. 169: 13-23. PMID 28340338 DOI: 10.1016/J.Cell.2017.02.007  0.774
2017 Chakraborty AK, Barton J. Rational design of vaccine targets and strategies for HIV: a crossroad of statistical physics, biology, and medicine. Reports On Progress in Physics. Physical Society (Great Britain). PMID 28059778 DOI: 10.1088/1361-6633/Aa574A  0.543
2017 Bandaru P, Shah NH, Bhattacharyya M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J. Author response: Deconstruction of the Ras switching cycle through saturation mutagenesis Elife. DOI: 10.7554/Elife.27810.040  0.52
2016 Lorenzi JC, Cohen YZ, Cohn LB, Kreider EF, Barton JP, Learn GH, Oliveira T, Lavine CL, Horwitz JA, Settler A, Jankovic M, Seaman MS, Chakraborty AK, Hahn BH, Caskey M, et al. Paired quantitative and qualitative assessment of the replication-competent HIV-1 reservoir and comparison with integrated proviral DNA. Proceedings of the National Academy of Sciences of the United States of America. PMID 27872306 DOI: 10.1073/Pnas.1617789113  0.567
2016 Shaffer JS, Moore PL, Kardar M, Chakraborty AK. Optimal immunization cocktails can promote induction of broadly neutralizing Abs against highly mutable pathogens. Proceedings of the National Academy of Sciences of the United States of America. PMID 27791170 DOI: 10.1073/Pnas.1614940113  0.302
2016 Thill PA, Weiss AW, Chakraborty AK. Phosphorylation of a Tyrosine residue on Zap70 by Lck and its subsequent binding via a SH2 domain may be a key gatekeeper of T cell receptor signaling in vivo. Molecular and Cellular Biology. PMID 27354065 DOI: 10.1128/Mcb.00165-16  0.326
2016 Barton JP, Goonetilleke N, Butler TC, Walker BD, McMichael AJ, Chakraborty AK. Relative rate and location of intra-host HIV evolution to evade cellular immunity are predictable. Nature Communications. 7: 11660. PMID 27212475 DOI: 10.1038/Ncomms11660  0.581
2016 Butler TC, Barton JP, Kardar M, Chakraborty AK. Identification of drug resistance mutations in HIV from constraints on natural evolution. Physical Review. E. 93: 022412. PMID 26986367 DOI: 10.1103/Physreve.93.022412  0.573
2016 Butler TC, Barton JP, Kardar M, Chakraborty AK. Identification of drug resistance mutations in HIV from constraints on natural evolution Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 93. DOI: 10.1103/PhysRevE.93.022412  0.506
2016 Barton JP, Chakraborty AK, Cocco S, Jacquin H, Monasson R. On the Entropy of Protein Families Journal of Statistical Physics. 162: 1267-1293. DOI: 10.1007/S10955-015-1441-4  0.572
2015 Ndhlovu ZM, Kamya P, Mewalal N, Kløverpris HN, Nkosi T, Pretorius K, Laher F, Ogunshola F, Chopera D, Shekhar K, Ghebremichael M, Ismail N, Moodley A, Malik A, Leslie A, ... ... Chakraborty A, et al. Magnitude and Kinetics of CD8(+) T Cell Activation during Hyperacute HIV Infection Impact Viral Set Point. Immunity. 43: 591-604. PMID 26362266 DOI: 10.1016/J.Immuni.2015.08.012  0.3
2015 Sjölin-Goodfellow H, Frushicheva MP, Ji Q, Cheng DA, Kadlecek TA, Cantor AJ, Kuriyan J, Chakraborty AK, Salomon AR, Weiss A. The catalytic activity of the kinase ZAP-70 mediates basal signaling and negative feedback of the T cell receptor pathway. Science Signaling. 8: ra49. PMID 25990959 DOI: 10.1126/Scisignal.2005596  0.303
2015 Wang S, Mata-Fink J, Kriegsman B, Hanson M, Irvine DJ, Eisen HN, Burton DR, Wittrup KD, Kardar M, Chakraborty AK. Manipulating the selection forces during affinity maturation to generate cross-reactive HIV antibodies. Cell. 160: 785-97. PMID 25662010 DOI: 10.1016/J.Cell.2015.01.027  0.717
2015 Barton JP, Kardar M, Chakraborty AK. Scaling laws describe memories of host-pathogen riposte in the HIV population. Proceedings of the National Academy of Sciences of the United States of America. 112: 1965-70. PMID 25646424 DOI: 10.1073/Pnas.1415386112  0.577
2014 Chakraborty AK, Unanue ER. Herman Eisen (1918-2014). Immunity. 41: 869-70. PMID 25667944 DOI: 10.1016/J.Immuni.2014.12.001  0.327
2014 Stepanek O, Prabhakar AS, Osswald C, King CG, Bulek A, Naeher D, Beaufils-Hugot M, Abanto ML, Galati V, Hausmann B, Lang R, Cole DK, Huseby ES, Sewell AK, Chakraborty AK, et al. Coreceptor scanning by the T cell receptor provides a mechanism for T cell tolerance. Cell. 159: 333-45. PMID 25284152 DOI: 10.1016/J.Cell.2014.08.042  0.313
2014 Chakraborty AK, Weiss A. Insights into the initiation of TCR signaling. Nature Immunology. 15: 798-807. PMID 25137454 DOI: 10.1038/Ni.2940  0.32
2014 Mann JK, Barton JP, Ferguson AL, Omarjee S, Walker BD, Chakraborty A, Ndung'u T. The fitness landscape of HIV-1 gag: advanced modeling approaches and validation of model predictions by in vitro testing. Plos Computational Biology. 10: e1003776. PMID 25102049 DOI: 10.1371/Journal.Pcbi.1003776  0.582
2014 Frushicheva MP, Weiss A, Chakraborty AK. Investigation of Novel Zap-70 Functionality in T Cell Signaling Pathways using Computational Modeling Biophysical Journal. 106: 376a-377a. DOI: 10.1016/J.Bpj.2013.11.2131  0.333
2013 Shekhar K, Ruberman CF, Ferguson AL, Barton JP, Kardar M, Chakraborty AK. Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 88: 062705. PMID 24483484 DOI: 10.1103/Physreve.88.062705  0.575
2013 Sok D, Laserson U, Laserson J, Liu Y, Vigneault F, Julien JP, Briney B, Ramos A, Saye KF, Le K, Mahan A, Wang S, Kardar M, Yaari G, Walker LM, ... ... Chakraborty AK, et al. The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies. Plos Pathogens. 9: e1003754. PMID 24278016 DOI: 10.1371/Journal.Ppat.1003754  0.722
2013 Chakraborty AK, Roose JP. Biochemical heterogeneity and developmental varieties in T-cell leukemia. Cell Cycle (Georgetown, Tex.). 12: 1480-1. PMID 23652920 DOI: 10.4161/Cc.24858  0.316
2013 Eisen HN, Chakraborty AK. Immunopaleontology reveals how affinity enhancement is achieved during affinity maturation of antibodies to influenza virus. Proceedings of the National Academy of Sciences of the United States of America. 110: 7-8. PMID 23284164 DOI: 10.1073/Pnas.1219396110  0.311
2013 Sok D, Laserson U, Laserson J, Liu Y, Vigneault F, Julien J, Briney B, Ramos A, Saye KF, Le K, Mahan A, Wang S, Kardar M, Yaari G, Walker LM, ... ... Chakraborty AK, et al. Correction: The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies Plos Pathogens. 9. DOI: 10.1371/annotation/f1f8c791-61e9-45c6-a455-92c6dadf9f06  0.682
2013 Shekhar K, Kardar M, Chakraborty AK. Faithful Models of Viral Fitness can be Inferred from Mutation Patterns in Viral DNA Sequences Sampled from a Population Biophysical Journal. 104: 495a-496a. DOI: 10.1016/J.Bpj.2012.11.2732  0.31
2012 Read EL, Tovo-Dwyer AA, Chakraborty AK. Stochastic effects are important in intrahost HIV evolution even when viral loads are high. Proceedings of the National Academy of Sciences of the United States of America. 109: 19727-32. PMID 23112156 DOI: 10.1073/Pnas.1206940109  0.669
2012 Chung W, Abel SM, Chakraborty AK. Protein clusters on the T cell surface may suppress spurious early signaling events. Plos One. 7: e44444. PMID 22973450 DOI: 10.1371/Journal.Pone.0044444  0.327
2012 Ferguson A, Chakraborty A. From HIV protein sequences to viral fitness landscapes: a new paradigm for in silico vaccine design Retrovirology. 9: 331. DOI: 10.1186/1742-4690-9-S2-P331  0.311
2012 Shekhar K, Dahirel V, Walker BD, Chakraborty AK. Analysis of Collective Coevolution in HIV Proteins Suggests Strategies for Rational Vaccine Design Biophysical Journal. 102: 22a-23a. DOI: 10.1016/J.Bpj.2011.11.149  0.323
2012 Ferguson AL, Chakraborty AK. In Silico Reconstruction of HIV Viral Fitness Landscapes Biophysical Journal. 102: 184a. DOI: 10.1016/J.Bpj.2011.11.1003  0.307
2012 Košmrlj A, Kardar M, Chakraborty AK. The Influence of T Cell Development on Pathogen Specificity and Autoreactivity Journal of Statistical Physics. 149: 203-219. DOI: 10.1007/S10955-011-0403-8  0.305
2011 Stone JD, Artyomov MN, Chervin AS, Chakraborty AK, Eisen HN, Kranz DM. Interaction of streptavidin-based peptide-MHC oligomers (tetramers) with cell-surface TCRs. Journal of Immunology (Baltimore, Md. : 1950). 187: 6281-90. PMID 22102724 DOI: 10.4049/Jimmunol.1101734  0.311
2011 Dahirel V, Shekhar K, Pereyra F, Miura T, Artyomov M, Talsania S, Allen TM, Altfeld M, Carrington M, Irvine DJ, Walker BD, Chakraborty AK. Coordinate linkage of HIV evolution reveals regions of immunological vulnerability. Proceedings of the National Academy of Sciences of the United States of America. 108: 11530-5. PMID 21690407 DOI: 10.1073/Pnas.1105315108  0.304
2010 Eisen HN, Chakraborty AK. Evolving concepts of specificity in immune reactions. Proceedings of the National Academy of Sciences of the United States of America. 107: 22373-80. PMID 21173256 DOI: 10.1073/Pnas.1012051108  0.319
2010 Mouquet H, Scheid JF, Zoller MJ, Krogsgaard M, Ott RG, Shukair S, Artyomov MN, Pietzsch J, Connors M, Pereyra F, Walker BD, Ho DD, Wilson PC, Seaman MS, Eisen HN, ... Chakraborty AK, et al. Polyreactivity increases the apparent affinity of anti-HIV antibodies by heteroligation. Nature. 467: 591-5. PMID 20882016 DOI: 10.1038/Nature09385  0.306
2010 Kosmrlj A, Read EL, Qi Y, Allen TM, Altfeld M, Deeks SG, Pereyra F, Carrington M, Walker BD, Chakraborty AK. Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection. Nature. 465: 350-4. PMID 20445539 DOI: 10.1038/Nature08997  0.679
2010 Chakraborty AK, Das J. Pairing computation with experimentation: a powerful coupling for understanding T cell signalling. Nature Reviews. Immunology. 10: 59-71. PMID 20029448 DOI: 10.1038/Nri2688  0.32
2009 Kosmrlj A, Chakraborty AK, Kardar M, Shakhnovich EI. Thymic selection of T-cell receptors as an extreme value problem. Physical Review Letters. 103: 068103. PMID 19792616 DOI: 10.1103/Physrevlett.103.068103  0.301
2009 Prasad A, Zikherman J, Das J, Roose JP, Weiss A, Chakraborty AK. Origin of the sharp boundary that discriminates positive and negative selection of thymocytes. Proceedings of the National Academy of Sciences of the United States of America. 106: 528-33. PMID 19098101 DOI: 10.1073/Pnas.0805981105  0.316
2008 Kosmrlj A, Jha AK, Huseby ES, Kardar M, Chakraborty AK. How the thymus designs antigen-specific and self-tolerant T cell receptor sequences. Proceedings of the National Academy of Sciences of the United States of America. 105: 16671-6. PMID 18946038 DOI: 10.1073/Pnas.0808081105  0.325
2008 Locasale JW, Chakraborty AK. Regulation of signal duration and the statistical dynamics of kinase activation by scaffold proteins. Plos Computational Biology. 4: e1000099. PMID 18584022 DOI: 10.1371/Journal.Pcbi.1000099  0.532
2008 Zheng H, Jin B, Henrickson SE, Perelson AS, von Andrian UH, Chakraborty AK. How antigen quantity and quality determine T-cell decisions in lymphoid tissue. Molecular and Cellular Biology. 28: 4040-51. PMID 18426917 DOI: 10.1128/Mcb.00136-08  0.306
2007 Artyomov MN, Das J, Kardar M, Chakraborty AK. Purely stochastic binary decisions in cell signaling models without underlying deterministic bistabilities. Proceedings of the National Academy of Sciences of the United States of America. 104: 18958-63. PMID 18025473 DOI: 10.1073/Pnas.0706110104  0.307
2007 Locasale JW, Shaw AS, Chakraborty AK. Scaffold proteins confer diverse regulatory properties to protein kinase cascades. Proceedings of the National Academy of Sciences of the United States of America. 104: 13307-12. PMID 17686969 DOI: 10.1073/Pnas.0706311104  0.54
2007 Wylie DC, Das J, Chakraborty AK. Sensitivity of T cells to antigen and antagonism emerges from differential regulation of the same molecular signaling module. Proceedings of the National Academy of Sciences of the United States of America. 104: 5533-8. PMID 17360359 DOI: 10.1073/Pnas.0611482104  0.687
2007 Cemerski S, Das J, Locasale J, Arnold P, Giurisato E, Markiewicz MA, Fremont D, Allen PM, Chakraborty AK, Shaw AS. The stimulatory potency of T cell antigens is influenced by the formation of the immunological synapse. Immunity. 26: 345-55. PMID 17346997 DOI: 10.1016/J.Immuni.2007.01.013  0.542
2006 Shao Y, Molnar LF, Jung Y, Kussmann J, Ochsenfeld C, Brown ST, Gilbert AT, Slipchenko LV, Levchenko SV, O'Neill DP, DiStasio RA, Lochan RC, Wang T, Beran GJ, Besley NA, ... ... Chakraborty AK, et al. Advances in methods and algorithms in a modern quantum chemistry program package. Physical Chemistry Chemical Physics : Pccp. 8: 3172-91. PMID 16902710 DOI: 10.1039/B517914A  0.525
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  0.771
2006 Eide JL, Chakraborty AK, Oster GF. Simple models for extracting mechanical work from the ATP hydrolysis cycle Biophysical Journal. 90: 4281-4294. PMID 16581833 DOI: 10.1529/Biophysj.105.073320  0.743
2006 Qi S, Krogsgaard M, Davis MM, Chakraborty AK. Molecular flexibility can influence the stimulatory ability of receptor-ligand interactions at cell-cell junctions. Proceedings of the National Academy of Sciences of the United States of America. 103: 4416-21. PMID 16537380 DOI: 10.1073/Pnas.0510991103  0.303
2006 Eide JL, Chakraborty AK. Effects of quenched and annealed macromolecular crowding elements on a simple model for signaling in T lymphocytes. The Journal of Physical Chemistry. B. 110: 2318-24. PMID 16471819 DOI: 10.1021/Jp054191+  0.749
2004 Peters B, Bell AT, Chakraborty A. Rate constants from the reaction path Hamiltonian. II. Nonseparable semiclassical transition state theory. The Journal of Chemical Physics. 121: 4461-6. PMID 15332875 DOI: 10.1063/1.1778162  0.526
2004 Peters B, Bell AT, Chakraborty A. Rate constants from the reaction path Hamiltonian. I. Reactive flux simulations for dynamically correct rates. The Journal of Chemical Physics. 121: 4453-60. PMID 15332874 DOI: 10.1063/1.1778161  0.528
2004 Peters B, Heyden A, Bell AT, Chakraborty A. A growing string method for determining transition states: comparison to the nudged elastic band and string methods. The Journal of Chemical Physics. 120: 7877-86. PMID 15267702 DOI: 10.1063/1.1691018  0.518
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  0.568
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  0.629
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  0.563
2003 Lee SJ, Hori Y, Chakraborty AK. Low T cell receptor expression and thermal fluctuations contribute to formation of dynamic multifocal synapses in thymocytes. Proceedings of the National Academy of Sciences of the United States of America. 100: 4383-8. PMID 12671067 DOI: 10.1073/Pnas.0630563100  0.551
2003 Ryder JA, Chakraborty AK, Bell AT. Density functional theory study of benzene oxidation over Fe-ZSM-5 Journal of Catalysis. 220: 84-91. DOI: 10.1016/S0021-9517(03)00275-6  0.611
2002 Chakraborty AK. Lighting up TCR takes advantage of serial triggering. Nature Immunology. 3: 895-6. PMID 12352963 DOI: 10.1038/Ni1002-895  0.307
2002 Lee SJ, Hori Y, Groves JT, Dustin ML, Chakraborty AK. The synapse assembly model. Trends in Immunology. 23: 500-2. PMID 12297422 DOI: 10.1016/S1471-4906(02)02325-6  0.529
2002 Lee SJ, Hori Y, Groves JT, Dustin ML, Chakraborty AK. Correlation of a dynamic model for immunological synapse formation with effector functions: two pathways to synapse formation. Trends in Immunology. 23: 492-9. PMID 12297421 DOI: 10.1016/S1471-4906(02)02285-8  0.55
2002 Chakraborty AK. How and why does the immunological synapse form? Physical chemistry meets cell biology. Science's Stke : Signal Transduction Knowledge Environment. 2002: pe10. PMID 11880685 DOI: 10.1126/Stke.2002.122.Pe10  0.325
2002 Lee SE, Chakraborty AK. Sequence dependence of polymer dynamics in quenched disordered media: Weak attraction facilitates transport The Journal of Chemical Physics. 117: 10869-10876. DOI: 10.1063/1.1519838  0.565
2002 Hori Y, Raychaudhuri S, Chakraborty AK. Analysis of pattern formation and phase separation in the immunological synapse Journal of Chemical Physics. 117: 9491-9501. DOI: 10.1063/1.1512642  0.52
2002 Ryder JA, Chakraborty AK, Bell AT. Density Functional Theory Study of Nitrous Oxide Decomposition over Fe- and Co-ZSM-5 The Journal of Physical Chemistry B. 106: 7059-7064. DOI: 10.1021/Jp014705E  0.618
2001 Chakraborty AK, Golumbfskie AJ. Polymer adsorption-driven self-assembly of nanostructures. Annual Review of Physical Chemistry. 52: 537-73. PMID 11326074 DOI: 10.1146/Annurev.Physchem.52.1.537  0.752
2000 Ryder JA, Chakraborty AK, Bell AT. Density functional theory study of proton mobility in zeolites: Proton migration and hydrogen exchange in ZSM-5 Journal of Physical Chemistry B. 104: 6998-7011. DOI: 10.1021/Jp9943427  0.618
2000 Ryder JA, Rice MJ, Gilardoni F, Chakraborty AK, Bell AT. Applications of density functional theory to identify reaction pathways for processes occurring in zeolites and on dispersed metal oxides Studies in Surface Science and Catalysis. 130: 407-412. DOI: 10.1016/S0167-2991(00)80991-X  0.621
1999 Golumbfskie AJ, Pande VS, Chakraborty AK. Simulation of biomimetic recognition between polymers and surfaces. Proceedings of the National Academy of Sciences of the United States of America. 96: 11707-12. PMID 10518514 DOI: 10.1073/Pnas.96.21.11707  0.76
1997 Trout BL, Chakraborty AK, Bell AT. Diffusion and reaction in ZSM-5 studied by dynamic Monte Carlo Chemical Engineering Science. 52: 2265-2276. DOI: 10.1016/S0009-2509(97)00010-9  0.518
1994 Chakraborty AK, Bratko D, Chandler D. Diffusion of ionic penetrants in charged disordered media The Journal of Chemical Physics. 100: 1528-1541. DOI: 10.1063/1.466632  0.424
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