2015 - Recent

Recent Publications

238. “Two-dose “extended priming” immunization amplified humoral immune responses by synchronizing vaccine delivery with the germinal center response”, with S. Bhagchandani et al, submitted to Science Immunology (2023).

237. “How persistent infection overcomes peripheral tolerance mechanisms to cause T cell-mediated autoimmune disease”, with R. Yin et al, submitted to PNAS (2023).

236. “Polymer folding through active processes recreates features of genome organization”, with A. Goychuk et al, Proc. Natl. Acad. Sci., (2023).

235. “A model for cis-regulation of transcriptional condensates and gene expression by proximal lncRNAs”, with P. Natarajan et al, Biophysical Journal, (2023).

234. “A model for the organization and regulation of nuclear condensates by gene activity”, with H. Schede et al, Nature Comm, (2023).

233. “Antigen presentation dynamics shapes the response to emergent variants like the Omicron strain of SARS-CoV-2 after multiple vaccinations with the wild type strain”, with L. Yang et al., Cell Reports, (2023).

232. “Two complementary features of humoral immune memory confer protection against the same or variant antigens”, with M. van Beek et al, Proc. Natl. Acad. Sci., (2022).

231. “Mechanisms that promote the evolution of cross-reactive antibodies upon vaccination with designed influenza immunogens”, with L. Yang et al, Cell Reports, 112160 (2023).

230. “Design of immunogens for eliciting antibody responses that may protect against SARS-CoV-2 variants” with E. Wang, PLOS Comp. Biol., (2022).

229. “Multiscale affinity maturation simulations to elicit HIV broadly neutralizing antibodies”, with K. Sprenger et al, PLOS Comp. Biol., (2021).

228. “Inferring the intrinsic mutational fitness landscape of influenza-like evolving antigens from temporally ordered sequence data”, with J. Doelger et al, Phys Rev. E, (2021).

227. “RNA in formation and regulation of transcriptional condensates”, with P. Sharp et al, RNA Journal, 28, 52 (2022)

226. “A simple model for how the risk of pandemics from different virus families depends on viral and human traits”, with J. Doelger et al, Mathematical Biosciences, 343, 108732 (2021).

225. “Learning from HIV-1 to predict the immunogenicity of T cell epitopes in SARS-CoV-2”, with A. Gao et al, iScience, 24, 23102311 (2021).

224.  “Predicting the immunogenicity of T cell epitopes: from HIV to SARS-CoV-2”, with A.  Gao et al, Cell Systems, under review (2020).

223. “Design of immunogens to elicit CD4bs-targeting broadly neutralizing antibodies against HIV”, with S. Conti et al, Proc. Natl. Acad. Sci, (2020).

222. “Mechanisms underlying vaccination protocols that may optimally elicit broadly neutralizing antibodies against highly mutable pathogens”, with R. Ganti, Physical Review E, 103, 052408

221. “Adenovirus-vectored vaccine containing multi-dimensionally conserved parts of the  HIV proteome is immunogenic in rhesus macaques”, with D. Murakowski et al, Proc.  Natl. Acad. Sci, in press.
Authors: Dariusz K. Murakowski, John P. Barton, Lauren Peter, Abishek Chandrashekar, Esther Bondzie, Ang Gao, Dan H. Barouch, Arup K. Chakraborty,

220. Imagining the future of vaccine development”, with B. Trout, The Bridge, 50, issue 5.  pp. 33-35, (2020).
Authors: Bernhardt L. Trout, Arup K. Chakraborty

219. Defining and manipulating B cell immunodominance hierarchies to elicit broadly neutralizing antibody responses against influenza virus”, with A. Amitai et al, Cell  Systems, 11(6):573-588, (2020).
Authors: Assaf Amitai, Maya Sangesland, Daniel Lingwood, Arup K. Chakraborty

218. “RNA-mediated feedback control of transcriptional condensates”, with J. Henninger et al,  Cell, 184:207-225, (2021).
Authors: Jonathan E. Henninger, Ozgur Oksuz, Krishna Shrinivas, Phillip A. Sharp, Ibrahim I. Cisse, Arup K. Chakraborty, Richard A. Young

217. Predominance of positive epistasis among drug resistance-associated mutations in HIV-1  protease“, with T Zhang et al, PLOS Genetics, 16(10): e1009009, (2020).

216. “How the T cell signalling network processes information to discriminate between self and cognate ligands”, with R. Ganti et al, Proc. Natl. Acad. Sci, 117(42):26020-26030.  (2020).
Authors: Raman S. Ganti, Wan-Lin Lo, Darren B. McAffee, Jay T. Groves, Arthur Weiss, Arup K. Chakraborty

215. “Partitioning of cancer therapeutics in nuclear condensates”, with I. Klein et al, Science368, 13386 (2020).

214. “Optimizing immunization protocols to maximize generation of broadly neutralizing antibodies against highly mutable pathogens”, with K. Sprenger et al, Proc. Natl. Acad.  Sci, 117 (33) 20077-20087; (2020).
Authors: Kayla G. Sprenger, Joy E. Loveau, Pranav M. Murugan, Arup K. Chakraborty

213. “Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape”, with A. Quadeer et al, Nature Comm., 11, 377 (2020).
Authors: Ahmed A. Quadeer, John P. Barton, Arup K. Chakraborty, Matthew R. McKay

212. “David Chandler: 1944-2017”, with J. Weeks, H. Anderson, Biographical Memoirs,  Proc. Natl. Acad. Sci (2019).
Authors: Hans C. Andersen, Arup K. Chakraborty, John D. Weeks

211. “CD45 functions as a signalling gatekeeper in T cells”, with A. Courtney et al., Science  Signaling, 12, (2019).
Authors: Adam Courtney, Alexey Shvets, Arup K. Chakraborty, Arthur Weiss

210. “Enhancer features that drive transcriptional condensate formation”, with K. Shrinivas et al, Mol Cell, 75, 549 (2019).
Authors: Ben Sabari, Krishna Shrinivas, Eliot L. Coffey, Phillip A. Sharp, Richard A. Young, Arup K. Chakraborty

209. The evolution of weak cooperative interactions for biological specificity”, with A. Gao et al, PNAS, 115 (47) (2018).
Authors: Ang Gao, Krishna Shrinivas, Paul Lepeudry, Hiroshi Suzuki, Phillip A. Sharp, Arup K Chakraborty

208. “The low spike density of HIV may have evolved because of the effects of T helper cell depletion on affinity maturation”, with A. Amitai et al., PLOS Comp. Biol. (2018).
Authors: Assaf Amitai, Arup K. Chakraborty, Mehran Kardar

207. “Divergent signaling pathways in P38 activation in lymphocytes” with J. Jun et al,  Science Signaling, 12, eaao0736 (2019).
Authors: J. Jun, Arup K. Chakraborty

206. “Coactivator condensation at super-enhancers links phase separation and gene control”, with B. Sabari et al, Science, 361, 412 (2018).
Authors: Ben Sabari, Arup K. Chakraborty

205. “Modeling and in vitro testing of the HIV-1 Nef fitness landscape”, with E. Rajkoomar, Virus Evolution, 5, (2019).
Authors: E. Rajkoomar, Arup K. Chakraborty

204. “The role of framework mutations on the evolution of broadly neutralizing antibodies against HIV”, with V. Ovchinnikov et al, eLife, eLife 2018; 7:e33038 DOI: 7554/eLife.33038 (2018).
Authors: Victor Ovchinnikov, Joy E Louveau, John P Barton, Martin Karplus,  Arup K Chakraborty

203. “How nonuniform contact profiles of T cell receptors modulate thymic selection outcomes”, with H. Chen et al, Phys Rev E, arXiv:1801.03921[q-bio.PE] Jan 2018.
Authors: Hanrong Chen, Arup K. Chakraborty, Mehran Kardar

202. “The fitness landscape of the Human Immunodeficiency Virus envelope protein that is targeted by antibodies”, with R. Louie et al, PNAS, (2018).
Authors: Raymond H. Y. LouieKevin J. KaczorowskiJohn P. BartonArup K. Chakraborty and Matthew R. McKay

201. “A population dynamics model for clonal diversity in a germinal center,” with A. Amitai, Frontiers in Microbiology 2017; DOI: 10.3389/fmicb.2017.01693.
Authors: Assaf Amitai, Luka Mesin, Gabriel D. Victora, Mehran Kardar, Arup K. Chakraborty

200. “Deconstruction of the Ras switching cycle through saturation mutagenesis”, with P. Bandaru et al, eLife 2017; 6:e27810 DOI:10.7554/ eLife.27810.
Authors: Arup K. Chakraborty, P. Bandaru

199. “Continuous immunotypes describe human immune variation and predict diverse responses”, with K. Kaczorowski et al, PNAS, vol.114 no.30, E6097-E6106, doi: 1073/pnas.1705065114.
Authors: Kevin Kaczrowski, Arup K. Chakraborty

198. “A Phase separation model for transcriptional control”, with K. Shrinivas et al, Cell, 169(1), 13-23.
Authors: Denes Hnisz, Krishna Shrinivas, Richard A. Young, Arup K. Chakraborty, Phillip A. Sharp

197. “Paired quantitative and qualitative assessment of the replication-competent HIV-1 reservoir and comparison to integrated proviral DNA”, with Lorenzi et al, Natl. Acad. Sci., (2016): 201617789.
Authors: Julio C. C. LorenziYehuda Z. Cohen,  Lillian B. Cohn, Edward F. KreiderJohn P. Barton, Gerald H. Learn, Thiago Oliveira, Christy L. Lavine, Joshua A. Horwitz, Allison Settler, Mila Jankovic, Michael S. Seaman, Arup K. Chakraborty, Beatrice H. Hahn, Marina Caskey, Michel C. Nussenzweig

196. “A perspective on the role of computational models in Immunology”, Annual Reviews: Immunology, 35.1 (2017).
Authors: Arup K. Chakraborty

195“Optimal immunization cocktails can promote induction of broadly neutralizing antibodies against highly mutable pathogens”, with J.S. Shaffer et al., Proc. Natl. Acad. Sci., (2016): 201614940. 
Authors: J. Scott ShafferPenny L. Moore, Mehran Kardar, Arup K. Chakraborty

194. “Rational design of vaccine targets and strategies for HIV: a crossroad of statistical physics, biology, and medicine”, with J.P. Barton, Reports on Progress in Physics, DOI: 10.1088/1361-6633/aa574a, Jan 10 (2017).
Authors: Arup K. Chakraborty, John P. Barton

193. “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”, with P. Thill et al, Molecular and Cell Biology, 36, 18 (2016): 2396-2402.
Authors: Peter A. Thill, Arthur Weiss, Arup K. Chakraborty

192. “Sustained antigen availability during germinal center initiation enhances antibody responses to vaccination”, with H. Tam et al, Natl. Acad. Sci, (2016): 201606050.
Authors: Hok Hei TamMariane B. Melo, Myung Sun Kang,  Jeisa M. Pelet,  Vera M. Ruda, Maria H. Foley, Joyce K. Hu, Sudha Kumari, Jordan Crampton, Alexis D. Baldeon, Rogier W. Sanders,  John P. Moore, Shane Crotty, Robert Langer, Daniel G. Anderson, Arup K. Chakraborty, Darrell J. Irvine

191. “Enhanced clearance of HIV-1-infected cells by anti-HIV-1 broadly neutralizing antibodies in vivo”, with C. Li et al., Science 20 May: 1001-1004 (2016).
Authors: Ching-Lan Lu, Dariusz K. Murakowski, Stylianos Bournazos, Till Schoofs, Debolina Sarkar, Ariel Halper-Stromberg, Joshua A. Horwitz, Lilian Nogueira, Jovana Golijanin, Anna Gazumyan, Jeffrey V. Ravetch, Marina Caskey, Arup K. Chakraborty, Michel C. Nussenzweig

190. “Hydrophobic CDR3 residues promote the development of self-reactive T cell repertoires of self-reactive T cell repertoires”, with B. Stadinski et al., Nature Immunology, DOI: 10.1038/ni.3491, Jun 27 (2016).
Authors: Brian D StadinskiKarthik ShekharIria Gómez-TouriñoJonathan JungKatsuhiro SasakiAndrew K SewellMark PeakmanArup K Chakraborty, Eric S Huseby

189. “The kinetic and location of intra-host HIV evolution to evade cellular immunity is predictable”, with J. Barton et al., Nature Communications, 7, (2016).
Authors: John P. Barton, Nilu Goonetilleke, Thomas C. Butler, Bruce D. Walker, Andrew J. McMichael, Arup K. Chakraborty

188“Identification of  drug resistance mutations in HIV from constraints on natural evolution”, with T. Butler et al., Rev E, 93, 022412 (2016).
Authors: Thomas C. Butler, John P. Barton, Mehran Kardar, Arup K. Chakraborty

 187. “On the entropy of protein families”, with J. Barton et al., Stat Phys., 162, 1267 (2015).
Authors: John P. Barton, Arup K. Chakraborty, Simona Cocco, Hugo Jacquin, Rémi Monasson

186. “Affinity inequality among serum antibodies that originate in lymphoid germinal centers” with M. Kang et al., PLOS ONE, DOI: 1371/journal.pone.0139222, October 7 (2015).
Authors: Myung Sun Kang, Timothy J. Eisen, Ellen A. Eisen, Arup K. Chakraborty, Herman N. Eisen

185. “Magnitude and kinetics of CD8+ T cell activation during hyperacute HIV infection impact viral set point”, with Z. Ndhlovu et al., Immunity, 43, 591 (2015).
Authors: Zaza M. Ndhlovu, Philomena Kamya, Nikoshia Mewalal, Henrik N.  Kløverpris, Thandeka Nkosi, Karyn Pretorius, Faatima Laher, Funsho Ogunshola, Denis Chopera, Karthik Shekhar, Musie Chebremichael, Nasreen Ismail, Amber Moodley, Amna Malik, Alasdair Leslie, Philip J. R. Goulder, Søren Buus, Arup K. Chakraborty, Krista Dong, Thumbi Ndung’u, Bruce D. Walker

184. “Theory, Models, and Biology”, with W. Shou et al., eLife, 4:e07158 (2015).
Authors: Wenying Shou, Carl T Bergstrom, Arup K Chakraborty, Frances K Skinner 

183. “ZAP-70 Catalytic Activity Regulates Basal Signaling and Negative Feedback on the Proximal TCR Signaling Pathway”, with H. Goodfellow, et al., Science Signaling, 8, ra49 (2015).
Authors: Hanna Sjölin-Goodfellow, Maria P. Frushicheva, Qinqin Ji, Debra A. Cheng, Theresa A. Kadlecek, Aaron J. Cantor, John Kuriyan, Arup K. Chakraborty, Arthur R. Salomon, Arthur Weiss

182. “Scaling Laws Describe Memories of Host-Pathogen Riposte in the HIV Population”, with J.P. Barton, et al., Natl. Acad. Sci., 112, 1965 (2015).
Authors: John P. Barton, Mehran Kardar, Arup K. Chakraborty

181. “Manipulating the Selection Forces During Affinity Maturation to Generate Cross-Reactive HIV Antibodies”, with S. Wang, et al., Cell, 160, 785 (2015).
Authors: Shenshen Wang, Jordi Mata-Fink, Barry Kriegsman, Melissa Hanson, Darrell J. Irvine, Herman N. Eisen, Dennis R. Burton, K. Dane Wittrup, Mehran Kardar, Arup K. Chakraborty


Publications: 2005-2014

180. “Herman Eisen (1918-2014)”, with E. Unanue, Immunity, 41, 869 (2014).
Authors: Arup K. Chakraborty, Emil R. Unanue

179. “Discovering Statistical Vulnerabilities in Highly Mutable Viruses: A Random Matrix Approach”, with A. Quadeer, et al., Conference proceedings, IEEE workshop on Statistical Signal Processing, 5-8 (2014).
Authors: A.A. Quadeer, R. H. Y. Louie, K. Shekhar, A. K. Chakraborty, I. Hsing, M. R. McKay

178. “Understanding Immunology: Fun at an Intersection of the Physical, Life, and Clinical Sciences”, A.K. Chakraborty, Physical Biology, 11: 053014 (2014).
Authors: Arup K. Chakraborty

177. “Insights into the Initiation of TCR Signaling”, with A. Weiss, Nature Immunology, 15: 798-807 (2014).
Authors: Arup K. Chakraborty, Arthur Weiss

176. “Coreceptor Scanning by the T Cell Receptor Provides a Mechanism for T Cell Tolerance”, with O. Stepanek, et al., Cell, 159: 333-345 (2014).
Authors: Ondrej Stepanek, Arvind S. Prabhakar, Celine Osswald, Carolyn G. King, Anna Bulek, Dieter Naeher, Marina Beaufils-Hugot, Michael L. Abanto, Virginie Galati, Barbara Hausmann, Rosemarie Lang, David K. Cole, Eric S. Huseby, Andrew K. Sewell, Arup K. Chakraborty, Ed Palmer

175. “Statistical Linkage Analysis of Substitutions in Patient-Derived Sequences of Genotype 1a Hepatitis C Virus Nonstructural Protein 3 Exposes Targets for Immunogen Design”, with A.A. Quadeer, et al. Virol., 88: 7628-7644 (2014).
AuthorsAhmed A. Quadeer, Raymond H. Y. Louie, Karthik Shekhar, Arup K. Chakraborty, I-Ming Hsing, Matthew R. McKay; Editor: M. S. Diamond

174. “Ras activation by SOS: Allosteric regulation by altered fluctuation dynamics”, with L. Iversen, et al., Science, 345: 50-54 (2014).
AuthorsLars Iversen, Hsiung-Lin Tu, Wan-Chen Lin, Sune M. Christensen, Steven M. AbelJeff Iwig, Hung-Jen Wu, Jodi GureaskoChristopher Rhodes, Rebecca S. PetitScott D. HansenPeter ThillCheng-Han Yu, Dimitrios StamouArup K. Chakraborty, John KuriyanJay T. Groves

173. “The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing”, with J.K. Mann, et al., PLOS Comp. Biol., 10: e1003776 (2014).
Authors: Jaclyn K. Mann, John P. Barton, Andrew L. Ferguson, Saleha Omarjee, Bruce D. Walker, Arup Chakraborty, Thumbi Ndung’u

172. “Monovalent Engagement of the BCR Activates Ovalbumin-Specific Transnuclear B Cells”, with A. Avalos, et al., Exp. Med., 211: 365-379 (2014).
AuthorsAna M. AvalosAngelina M. BilateMartin D. WitteAlbert K. TaiJiang HeMaria P. FrushichevaPeter D. ThillFriederike Meyer-WentrupChristopher S. TheileArup K. ChakrabortyXiaowei ZhuangHidde L. Ploegh

171. “Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE)”, with K. Shekhar, et al, Natl. Acad. Sci., 111 (1): 202-207 (2014).
AuthorsKarthik Shekhar, Petter Brodin, Mark M. Davis, Arup K. Chakraborty

170“Understanding and Harnessing the Immune System for the Rational Design of Therapies and Vaccines”, with M. Davis, The Bridge, 43(3): 16-25 (2013).
Authors: Arup K. Chakraborty, Mark M. Davis

169. “Spin Models Inferred from Patient-Derived Viral Sequence Data Faithfully Describe HIV Fitness Landscapes”, with K. Shekhar, et al., Rev. E, 88, 062705 (2013).
Authors: Karthik Shekhar, Claire F. Ruberman, Andrew L. Ferguson, John P. Barton, Mehran Kardar, Arup K. Chakraborty

168. “Therapeutic Efficacy of Potent Neutralizing HIV-1-sSpecific Monoclonal Antibodies in SHIV-Infected Rhesus Monkeys”, with D. Barouch, et al., Nature 503: 224-228 (2013).
Authors: Dan H. Barouch, James B. Whitney, Brian Moldt, Florian Klein, Thiago Y. Oliveira, Jinyan Liu, Kathryn E. Stephenson, Hui-Wen Chang, Karthik Shekhar, Sanjana Gupta, Joseph P. Nkolola, Michael S. Seaman, Kaitlin M. Smith, Erica N. Borducchi, Crystal Cabral, Jeffrey Y. Smith, Stephen Blackmore, Srisowmya Sanisetty, James R. Perry, Matthew Beck, Mark G. Lewis, William Rinaldi, Arup K. Chakraborty, Pascal Poignard, Michel C. Nussenzweig, Dennis R. Burton

167. “The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies”, with D. Sok, et al., PLOS Pathogens, 9(11), e1003754 (2013).
AuthorsDevin Sok, Uri Laserson, Jonathan Laserson, Yi Liu, Francois Vigneault, Jean-Philippe Julien, Bryan Briney, Alejandra Ramos, Karen F. Saye, Khoa Le, Alison Mahan, Shenshen Wang, Mehran Kardar, Gur Yaari, Laura M. Walker, Birgitte B. Simen, Elizabeth P. St. John, Po-Ying Chan-Hui, Kristine Swiderek, Stephen H. Kleinstein, Galit Alter, Michael S. Seaman, Arup K. Chakraborty, Daphne Koller, Ian A. Wilson, George M. Church, Dennis R. Burton, Pascal Poignard

166. “Quorum Sensing Allows T Cells to Discriminate Between Self and Nonself”, with T. Butler and M. Kardar, Natl. Acad. Sci., 110: 11833-11838 (2013).
AuthorsThomas Charles Butler, Mehran Kardar, Arup K. Chakraborty

165. “Computational Prediction of Broadly Neutralizing HIV-1 Antibody Epitopes from Neutralization Activity Data”, with A. Fergusson, et al., PLOS One, 8(12), e80562 (2013).
Authors: Andrew L. Ferguson, Emilia Falkowska, Laura M. Walker, Michael S. Seaman, Dennis R. Burton, Arup K. Chakraborty

164. “Coreceptor Affinity for MHC Defines Peptide Specificity Requirements for TCR Interaction with Coagonist Peptide–MHC”, with J. Hoerter, et al., J Exp Med, 210:1807-1821 (2013).
AuthorsJohn A.H. HoerterJoanna BrzostekMaxim N. ArtyomovSteven M. AbelJavier CasasVasily RybakinJeanette AmpudiaCarina LotzJanet M. ConnollyArup K. ChakrabortyKeith G. GouldNicholas R.J. Gascoigne

163. “Biochemical Heterogeneity and Developmental Varieties in T-Cell Leukemia”, with J. Roose, Cell Cycle 12:10, 1480–1481 (2013).
Authors: Arup K. Chakraborty, Jeroen P. Roose

162. “Activation of Extracellular Signal-Regulated Kinase but Not of p38 Mitogen-Activated Protein Kinase Pathways in Lymphocytes Requires Allosteric Activation of SOS”, with J. Jun, et al., Cell Biol. 33, 2470-2484 (2013).
AuthorsJesse E. Jun, Ming Yang, Hang Chen, Arup K. Chakraborty, Jeroen P. Roose

161. “Stochastic Responses May Allow Genetically Diverse Cell Populations to Optimize Performance with Simpler Signaling Networks”, with C. Govern, PLOS One, 8(8) e65086 (2013).
Authors: Christopher C. Govern, Arup K. Chakraborty

160. “Immunopaleontology Reveals How Affinity Enhancement is Achieved During Affinity Maturation of Antibodies to Influenza Virus”, with H.N. Eisen, Natl. Acad. Sci., 110: 7-8 (2013).
Authors: Herman N. Eisen, Arup K. Chakraborty

159. “Translating HIV Sequences into Quantitative Fitness Landscapes Predicts Viral Vulnerabilities for Rational Immunogen Design”, with A. Ferguson, et al., Immunity, 38, 606 (2013).
AuthorsAndrew L. Ferguson, Jaclyn K. Mann, Saleha Omarjee,  Thumbi Ndung’u, Bruce D. Walker, Arup K. Chakraborty

158. “Dysregulated RasGRP1 Responds to Cytokine Receptor Input in T Cell Leukemogenesis”, with C. Hartzell, et al., Science Signaling, 6 (268), ra21 (2013).
Authors: Catherine Hartzell, Olga Ksionda, Ed Lemmens, Kristen Coakley, Ming Yang, Monique Dail, Richard C. Harvey, Christopher Govern, Jeroen Bakker, Tineke L. Lenstra, Kristin Ammon, Anne Boeter, Stuart S. Winter, Mignon Loh, Kevin Shannon, Arup K. Chakraborty, Matthias Wabl, Jeroen P. Roose

157. “Statistical Physics of T-Cell Development and Pathogen Specificity”, with A. Kosmrlj and M. Kardar, Ann Rev. Con. Mat. Phys., 4, 339-360 (2013).
Authors: Andrej Košmrlj, Mehran Kardar, Arup K. Chakraborty

156. “Protein Clusters on the T Cell Surface May Suppress Spurious Early Signaling Events”, with W. Chung and S. Abel, PLOS One, 7(9)doi:10.1371 (2012).
Authors: Woo Chung, Steven M. Abel, Arup K. Chakraborty

155. “Stochastic Effects are Important in Intrahost HIV Evolution Even When Viral Loads are High”, with E. Read and A. Tovo-Dwyer, Proc. Natl. Acad. Sci., 109, 19727 (2012). 
Authors: Elizabeth L. Read, Allison A. Tovo-Dwyer, Arup K. Chakraborty

154. “The Membrane Environment Can Promote or Suppress Bistability in Cell Signaling Networks”, with S. Abel, et al., Phys. B., 116, 3630 (2012).AuthorsSteven M. Abel, Jeroen P. Roose, Jay T. Groves, Arthur Weiss, Arup K. Chakraborty

153. “A Model for How Signal Duration Can Determine Distinct Outcomes of Gene Transcription Programs”, with K. Fowler and V.K. Kuchroo, PLOS One, 7(3) e33018 (2012).
Authors: Kevin D. Fowler, Vijay K. Kuchroo, Arup K. Chakraborty

152. “Identifying Dynamic Bottlenecks of Stochastic Transitions in Biochemical Networks”, with M. Yang and C. Govern, Rev. Lett., 108, 058102 (2012).
Authors: Christopher C. Govern, Ming Yang, Arup K. Chakraborty

151. “The Influence of T Cell Development on Pathogen Specificity and Autoreactivity”, with Kosmrlj and M. Kardar, J. Stat. Phys., 149(2), pp 203-219 (2012).
AuthorsAndrej Košmrlj, Mehran Kardar, Arup K. Chakraborty

150. “Interaction of Streptavidin-Based Peptide–MHC Oligomers (Tetramers) with Cell-Surface TCRs”, with J.D. Stone, et al., Immunology, 187, 6281-6290 (2011).
Authors: Jennifer D. Stone, Maxim N. Artymov, Adam S. Chervin, Arup K. Chakraborty, Herman N. Eisen, David M. Krantz

149. “Coordinate Linkage of HIV Evolution Reveals Regions of Immunological Vulnerability”, with V. Dahirel, et al., Natl. Acad. Sci., 108, 11530-11535 (2011).
AuthorsVincent Dahirel, Karthik Shekhar, Florencia Pereyra, Toshiyuki Miura, Mikita Artyomov, Shiv Talsania, Todd M. Allen, Marcus Altfeld, Mary Carrington, Darrell J. Irvine, Bruce D. Walker, Arup K. Chakraborty

148. “The Effect of Mutations on the Alloreactive T Cell Receptor/Peptide–MHC Interface Structure: A Molecular Dynamics Study”, with M.Y. Wolfson and K. Nam, Phys. Chem. B, 115, 8317-8327 (2011).
AuthorsMikhail Y. Wolfson, Kwangho Nam, Arup K. Chakraborty

147. “Decreased Diacylglycerol Metabolism Enhances ERK Activation and Augments CD8+ T Cell Functional Responses”, with M.J. Riese, et al., Biol. Chem., 286, 5254-5265 (2011).
AuthorsMatthew J. RieseJashanpreet Grewal, Jayajit Das, Tao Zou, Vineet Patil, Arup K. Chakraborty, Gary A. Koretzky

146. “Understanding the Structure and Function of the Immunological Synapse”, with M.L. Dustin and A.S. Shaw, in Samelson, L.E. and Shaw, A.S. (Eds.) Immunoreceptor Signaling. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. 247-260 (2010).
AuthorsMichael L. Dustin, Arup K. Chakraborty, Andrey S. Shaw

145. “Evolving Concepts of Specificity in Immune Reactions”, with H.N. Eisen, Natl. Acad. Sci., 107 (52), 22373 (2010).
Authors: Herman N. Eisen, Arup K. Chakraborty

144. “CD4 and CD8 Binding to MHC Molecules Primarily Acts to Enhance Lck Delivery”, with M. Artyomov, et al., Natl. Acad. Sci., 107 (39), 16916 (2010).
AuthorsMaxim N. Artyomov, Mieszko Lis, Srinivas Devadas, Mark M. Davis, Arup K. Chakraborty

143. “Polyreactivity Increases the Apparent Affinity of Anti-Hiv antibodies by Heteroligation” with H. Mouquet, et al., Nature, 467, 591 (2010).
AuthorsHugo MouquetJohannes F. ScheidMarkus J. ZollerMichelle KrogsgaardRene G. OttShetha ShukairMaxim N. ArtyomovJohn PietzschMark ConnorsFlorencia PereyraBruce D. WalkerDavid D. HoPatrick C. WilsonMichael S. SeamanHerman N. EisenArup K. ChakrabortyThomas J. HopeJeffrey V. RavetchHedda Wardemann, Michel C. Nussenzweig

142. “Only Signaling Modules that Discriminate Sharply Between Stimulatory and Nonstimulatory Inputs Require Basal Signaling for Fast Cellular Responses”, with M. Artomov and M. Kardar, Chem. Phys., 133, 105101 (2010).
AuthorsMykyta Artomov, Mehran Kardar, and Arup K. Chakraborty

141. “For T Cell Receptors, Some Breakups Might Not Last Forever”, with C. Govern, Immunity, 32, 141 (2010).
Authors: Christopher C. Govern, Arup K. Chakraborty

140. “Fast On-Rates Allow Short Dwell Time Ligands to Activate T Cells”, with C. Govern, et al., Natl. Acad. Sci., 107, 8724 (2010).
AuthorsChristopher C. Govern,  Michelle K. Paczosa, Arup K. Chakraborty, Eric S. Huseby

139. “Effects of Thymic Selection of the T-Cell Repertoire on HLA Class I-Associated Control of HIV Infection”, with A. Kosmrlj, et al., Nature, 465, 350 (2010).
Authors: Andrej KošmrljElizabeth L. ReadYing QiTodd M. AllenMarcus AltfeldSteven G. DeeksFlorencia PereyraMary CarringtonBruce D. Walker, Arup K. Chakraborty

138. “Seeing in Numbers”, A.K. Chakraborty, The Scientist, 24(3): 40 (2010).
Authors: Arup K. Chakraborty

137. “A Model for Genetic and Epigenetic Regulatory Networks Identifies Rare Pathways for Transcription Factor Induced Pluripotency”, with M. Artyomov and A. Meissner, PLOS Comp. Biol., 6(5): e1000785 (2010).
Authors: Maxim N. Artyomov, Alexander Meissner, Arup K. Chakraborty

136. “Statistical Mechanical Concepts in Immunology”, with Andrej Košmrlj, Rev. Phys. Chem., 61, 283 (2010).
Authors: Arup K. Chakraborty, Andrej Košmrlj

135. “Pairing Computation with Experimentation: A Powerful Coupling for Understanding T Cell Signaling”, with J. Das, Nature Reviews Immunology, 10, 59 (2010).
Authors: Arup K. Chakraborty, Jayajit Das

134. “Molecular Origin and Functional Consequences of Digital Signaling and Hysteresis During Ras Activation in Lymphocytes”, with J. Das, et al., Sci. Signal., 2 (66) pt2 (2009).
Authors: Arup K. Chakraborty, Jayajit Das, Julie Zikherman, Ming Yang, Christopher C. Govern, Mary Ho, Arthur Weiss, Jeroen Roose

133. “Stochastic Bimodalities in Deterministically Monostable Reversible Chemical Networks Due to Network Topology Reduction”, with M. Artyomov, et al., Chem. Phys., 131, 195103 (2009).
AuthorsMaxim N. Artyomov, Manikandan Mathur, Michael S. Samoilov,  Arup K. Chakraborty

132. “The Impact of Negative Selection on Thymocyte Migration in The Medulla”, with M. Leborgne, et al., Nature Immunology, 10, 823-830 (2009).
Authors: Marie Le Borgne, Ena Ladi, Ivan Dzhagalov, Paul Herzmark, Ying Fang Liao, Arup K Chakraborty, Ellen A Robey

131. “Thymic Selection of T-Cell Receptors as an Extreme Value Problem”, with A. Kosmrlj, et al., Rev. Lett., 103, 068103 (2009).
Authors: Andrej Košmrlj, Arup K. Chakraborty, Mehran Kardar, Eugene I. Shakhnovich

130. “Efficient Stochastic Simulation of Reaction–Diffusion Processes Via Direct Compilation”, with M. Lis, et al., Bioinformatics, 25, 2289-2291 (2009).
Authors: Mieszko Lis, Maxim N. Artyomov, Srinivas Devadas, Arup K. Chakraborty

129“Self-Assembly of Dendronized Polymers”, with J. Das and J.M.J. Frechet, Phys Chem B, 113 (42), 13768 (2009).
AuthorsJayajit Das, J. M. J. Fréchet Arup K. Chakraborty

128. “Positive Feedback Regulation Results in Spatial Clustering and Fast Spreading of Active Signaling Molecules on a Cell Membrane”, with J. Das and M. Kardar, Chem. Phys., 130, 245102 (2009).
AuthorsJayajit Das, Mehran Kardar, Arup K. Chakraborty

127. “Signaling Cascades Modulate the Speed of Signal Propagation through Space”, with C. Govern, PLOS One, 4(2), e4639 (2009).
Authors: Christopher C. Govern, Arup K. Chakraborty

126. “Origin of the Sharp Boundary that Discriminates Positive and Negative Selection of Thymocytes”, with A. Prasad, et al., Natl. Acad. Sci., 106, 528 (2009).
AuthorsAshok Prasad, Julie Zikherman, Jayajit Das, Jeroen P. Roose, Arthur Weiss, Arup K. Chakraborty

125. “Digital Signaling and Hysteresis Characterize Ras Activation in Lymphoid Cells”, with J. Das, et al., Cell, 136, 337 (2009).
Authors: Jayajit Das, Mary Ho, Julie Zikherman, Christopher Govern, MIng Yang, Arup K. Chakraborty, Jeroen P. Roose

124. “How the Thymus Designs an Antigen-Specific and Self-Tolerant T Cell Receptor Sequences”, with A. Kosmrlj, et al., Natl. Acad. Sci., 105, 16671 (2008).
AuthorsAndrej Košmrlj, Abhishek K. Jha, Eric S. Huseby, Mehran Kardar, Arup K. Chakraborty

123. “The Balance between T Cell Receptor Signaling and Degradation at the Center of the Immunological Synapse Is Determined by Antigen Quality”, with S. Cemerski, et al., Immunity, 29, 414 (2008).
Authors: Sašo Cemerski, Jayajit Das, Emanuele Giursato, Mary Al. Markiewicz, Paul M. Allen, Arup K. Chakraborty, Andrey S. Shaw

122. “How Antigen Quantity and Quality Determine T-cell Decisions in Lymphoid Tissues” with H. Zheng, et al., Cell Biol., 28, 4040 (2008).
AuthorsHuan Zheng, Bo Jin, Sarah E. Henrickson, Alan S. Perelson, Ulrich H. von Andrian, Arup K. Chakraborty

121. “Regulation of Signal Duration and the Statistical Dynamics of Kinase Activation by Scaffold Proteins”, with J. Locasale, PLOS, Comp. Biol., 4(6):e1000099 (2008).
Authors: Jason W. Locasale, Arup K. Chakraborty

120. “Tug of War at the Exit Door”, with M. Dustin, Immunity, 28, 15 (2008).
Authors: Michael L. Dustin, Arup K. Chakraborty

119. “T cell Sensing of Antigen Dose Governs Interactive Behavior with Dendritic Cells and Sets a Threshold for T Cell Activation”, with S. Henrickson, et al., Nature Immunology, 9, 282 (2008).
Authors: Sarah E Henrickson, Thorsten R Mempel, Irina B Mazo, Bai Liu, Maxim N Artyomov, Huan Zheng, Antonio Peixoto, Michael P Flynn, Balimkiz Senman, Tobias Junt, Hing C Wong, Arup K Chakraborty, Ulrich H von Andrian

118. “Purely Stochastic Binary Decisions in Cell signaling Models without Underlying Deterministic Bistabilities”, with M. Artyomov, J. Das and M. Kardar, Natl. Acad. Sci., 104, 18958 (2007).
AuthorsMaxim N. Artyomov, Jayajit Das, Mehran Kardar, Arup K. Chakraborty

117“Scaffold Proteins Confer Diverse Regulatory Properties to Protein Kinase Cascades”, with J. Locasale and A.S. Shaw, Natl. Acad. Sci., 104, 13307 (2007).
AuthorsJason W. Locasale, Andrey S. Shaw, Arup K. Chakraborty

116“Empty Class II Major Histocompatibility Complex Created by Peptide Photolysis Establishes the Role of DM in Peptide Association”, with G.M. Grotenbreg, et al., Biol. Chem., 282, 21425 (2007).
AuthorsGijsbert M. Grotenbreg, Melissa J. Nicholson, Kevin D. Fowler, Kathrin Wilbuer, Leah Octavio, Maxine Yang, Arup K. Chakraborty, Hidde L. Ploegh, Kai W. Wucherpfennig

115“The Stimulatory Potency of T Cell Antigens is Influenced by the Formation of the Immunological Synapse”, with S. Cemerski, et al., Immunity, 26, 345 (2007).
Authors: Sašo Čemerski, Jayajit Das, Jason Locasale, Phoebe Arnold, Emanuale Giurisato, Mary A. Markiewicz, Daved Fremont, Paul M. Allen, Arup K. Chakraborty, Andrey S. Shaw

114. Sensitivity of T cells to Antigen and Antagonism Emerges from Differential Regulation of the same Molecular Signaling Module”, with D. Wylie, et al., Natl. Acad. Sci., 104, 5533 (2007).
Authors: Dennis C. WylieJayajit Das, Arup K. Chakraborty

113. “A Hybrid Deterministic-Stochastic Algorithm for Modeling Cell Signaling Dynamics in Spatially Inhomogenous Environments and Under the Influence of External Fields” with D. Wylie, et al., Phys. Chem. B, 110, 12749 (2006).
AuthorsDennis C. Wylie, Yuko Hori, Aaron R. Dinner, Arup K. Chakraborty

112. “Effect of Cross-linking on the Structure and Thermodynamics of Lamellar Block Copolymers”, with E.D. Gomez, et al., Macromolecules, 39, 4848 (2006).
Authors: Enrique D. Gomez, Jayajit Das, Arup K. Chakraborty, John A. Pople, Nitash P. Balsara

111. “Advances in Methods and Algorithms for a Modern Quantum Chemistry Program Package”, with Y. Shao, et al., Chem. Chem. Phys., 8, 3172 (2006).
AuthorsYihan ShaoLaszlo Fusti MolnarYousung JungJörg KussmannChristian OchsenfeldShawn T. BrownAndrew T.B. GilbertLyudmila V. SlipchenkoSergey V. LevchenkoDarragh P. O’NeillRobert A. DiStasio JrRohini C. LochanTao WangGregory J.O. BeranNicholas A. BesleyJohn M. HerbertChing Yeh LinTroy Van VoorhisSiu Hung ChienAlex SodtRyan P. SteeleVitaly A. RassolovPaul E. MaslenPrakashan P. KorambathRoss D. AdamsonBrian AustinJon BakerEdward F. C. ByrdHolger DachselRobert J. Doerksen,  Andreas DreuwBarry D. DunietzAnthony D. Dutoi,Thomas R. FurlaniSteven R. GwaltneyAndreas HeydenSo HirataChao-Ping HsuGary KedzioraRustam Z. KhalliulinPhil KlunzingerAaron M. LeeMichael S. LeeWanZhen LiangItay LotanNikhil NairBaron PetersEmil I. ProynovPiotr A. PieniazekYoung Min RheeJim RitchieEdina RostaC. David SherrillAndrew C. SimmonettJoseph E. SubotnikH. Lee Woodcock IIIWeimin ZhangAlexis T. BellArup K. ChakrabortyDaniel M. ChipmanFrerich J. KeilArieh WarshelWarren J. HehreHenry F. Schaefer IIIJing KongAnna I. KrylovPeter M. W. Gill, Martin Head-Gordon

110. “Kinetic Pathways of Phase Ordering in Lipid Raft Model Systems”, with J. Liu and J.T. Groves, Phys. Chem. B, 110, 8416 (2006).
AuthorsJian Liu, Jay T. Groves, Arup K. Chakraborty

109. “Simple Models for Extracting Mechanical Work from the ATP Hydrolysis Cycle”, with J. Eide and G.F. Oster, J., 90, 4281 (2006).
Authors: Jonathan L. Eide, Arup K. Chakraborty, George F. Oster

108. “Molecular Flexibility can Influence the Stimulatory Ability of Receptor-Ligand Interactions at Cell-Cell Junctions”, with Mark M. Davis, et al., Natl. Acad. Sci., 103, 4416 (2006). COVER
AuthorsShuyan QiMichelle KrogsgaardMark M. Davis, Arup K. Chakraborty

107. “Effects of Quenched and Annealed Macromolecular Crowding Elements on a Simple Model for Signaling in T Lymphocytes”, with J. Eide, Phys. Chem. B, 110, 2318 (2006).
AuthorsJonathan L. Eide, Arup K. Chakraborty

106. Chemomechanics of Surface Stresses Induced by DNA Hybridization”, with J. Stachowiak, et al., Langmuir, 22, 263 (2006).
AuthorsJeanne C. Stachowiak, Min Yue, Kenneth Castelino, Arup Chakraborty, Arun Majumdar

105. “Phase Segregation on Different Length Scales in a Model Cell Membrane System”, with J. Liu and S.Y. Qi, Phys. Chem. B, 109, 19960 (2005).
AuthorsJian Liu, Shuyan Qi, Jay T. Groves, Arup K. Chakraborty

104. Directed Migration of Positively Selected Thymocytes Visualized in Real Time”, with C. Witt, et al., PLOS Biology, 3(6), 1062 (2005).
Authors: Colleen M. Witt, Subhadip Raychaudhuri, Brian Schaefer, Arup K. Chakraborty, Ellen A. Robey

103. “A Dendronized Polymer is a Single-Molecule Glass”, with J. Das, et al., Phys. Chem. 109, 6535 (2005).
AuthorsJayajit Das, Masaru Yoshida, Zachary M. Fresco, Tae-Lim Choi, J. M. J. Fréchet, Arup K. Chakraborty

102. “Movies, Measurements, and Modeling: the Three M’s of Mechanistic Immunology”, with C. Witt and S. Raychaudhuri, Exp. Med., 201, 501 (2005).
AuthorsColleen WittSubhadip RaychaudhuriArup K. Chakraborty

101. “Order-Disorder Transitions in Cross-Linked Block Copolymer Solids”, with H. Han, et al., Macromolecules, 38, 1277 (2005).
AuthorsHyeok Hahn, Arup K. Chakraborty, Jayajit Das, John A. Pople, Nitash P. Balsara


Publications: 2000-2004

100. “Signatures of the Order-Disorder Transition in Copolymers with Quenched Sequence Disorder”, with H.B. Eitouni, et al., Macromolecules, 37, 8487 (2004).
Authors: H. B. Eitouni, T. J. Rappl, E. D. Gomez, N. P. Balsara, A. K. Chakraborty, J. M. J. Fréchet, J. A. Pople

99. “Rate Constants from the Reaction Path Hamiltonian. II. Nonseparable Semiclassical Transition State Theory”, with B. Peters and A.T. Bell, Chem. Phys., 121, 4461 (2004).
AuthorsBaron Peters, Alexis T. Bell, Arup K. Chakraborty

98. “Rate Constants from the Reaction Path Hamiltonian. I. Reactive Flux Simulations for Dynamically Corrected Rates”, with B. Peters and A.T. Bell, Chem. Phys., 121, 4453 (2004).
AuthorsBaron Peters, Alexis T. Bell, Arup K. Chakraborty

97. “CD4 Enhances T Cell Sensitivity to Antigen by Coordinating Lck Accumulation at the Immunological Synapse”, with Q. Li, et al., Nature Immunol., 5, 791 (2004).
Authors: Qi-Jing Li, Aaron R Dinner, Shuyan Qi, Darrell J Irvine, Johannes B Huppa, Mark M Davis,  Arup K Chakraborty

96. “A Growing String Method for Determining Transition States: Comparison to the Nudged Elastic Band and String Methods”, with B. Peters, et al., Chem. Phys., 120, 7877 (2004).
AuthorsBaron Peters, Andreas Heyden, Alexis T. Bell, Arup Chakraborty

95. “Hybridization Dynamics of Surface Immobilized DNA”, with M. Hagan, Chem. Phys., 120, 4958 (2004).
Authors: Michael F. Hagen, Arup K. Chakraborty

94. “Atomistic Understanding of Kinetic Pathways for Single Base-Pair Binding and Unbinding in DNA”, with M. Hagan, et al., Natl. Acad. Sci., 100, 13922 (2003).
AuthorsMichael F. Hagan, Aaron R. Dinner, David Chandler, Arup K. Chakraborty

93. “Density Functional Theory Study of Benzene Oxidation over Fe-ZSM-5”, with J. Ryder, et al., Catalysis, 220, 84 (2003).
Authors: Jason A. Ryder, Arup K. Chakraborty, Alexis T. Bell 

92. “Effective Membrane Model of the Immunological Synapse”, with S. Raychaudhuri and M. Kardar, Rev. Lett., 92, 208101 (2003).
Authors: Subhadip Raychaudhuri, Arup K. Chakraborty, Mehran Kardar

91. “The Immunological Synapse Balances T Cell Receptor Signaling and Degradation”, with K.H. Lee, et al., Science, 302, 1218 (2003).
AuthorsKyeong-Hee Lee, Aaron R. Dinner3Chun Tu, Gabriele Campi, Subhadip Raychaudhuri, Rajat Varma, Tasha N. Sims, W. Richard Burack, Hui Wu, Julia Wang, Osami Kanagawa, Mary Markiewicz, Paul M. Allen, Michael L. Dustin, Arup K. Chakraborty, Andrey S. Shaw

90. “Macromolecules at Surfaces: Research Challenges and Opportunities from Tribology to Biology”, with S. Granick, et al., Polym. Sci. Part B: Polym. Phys., 41, 2755 (2003).
Authors: Steve Granick, Sanat K. Kumar, Eric J. Amis, Markus Antonietti, Anna C. Balazs, Arup K. Chakraborty, Gary S. Grest, Craig Hawker, Paul Janmey, Edward J. Kramer, Ralph Nuzzo, Thomas P. Russell, Cyrus R. Safinya

89. In Silico Models for Cellular and Molecular Immunology: Successes, Promises, and Challenges”, with A.S. Shaw and M.L. Dustin, Nature Immunology, 4, 933 (2003).
Authors: Arup K. Chakraborty, Michael L. Dustin, Andrey S. Shaw

88. “Decoding Communications Between Cells in the Immune System Using Principles of Chemical Engineering”, A.K. Chakraborty, AIChE J., 49, 1614(2003).
Authors: Arup K. Chakraborty

87. “Biasing a Transition State Search to Locate Multiple Reaction Pathways”, with B. Peters, et al., Chem. Phys., 118, 9533 (2003).
AuthorsBaron Peters, WanZhen Liang,  Alexis T. Bell, Arup Chakraborty

86. “Low T Cell Receptor Expression and Thermal Fluctuations Contribute to Formation of Dynamic Multifocal Synapses in Thymocytes”, with S.J. Lee and Yuko Hori, Natl. Acad. Sci., 100, 4383 (2003).
AuthorsSung-Joo E. LeeYuko Hori, Arup K. Chakraborty

85. “Sequence Dependence of Polymer Dynamics in Quenched Disordered Media: Weak Attraction Facilitates Transport”, with S.J. Lee, Chem. Phys., 117, 10869 (2002).
AuthorsSung-Joo E. Lee, Arup K. Chakraborty

84. “Analysis of Pattern Formation and Phase Separation in the Immunological Synapse”, with Y. Hori and S. Raychaudhuri, Chem. Phys., 117, 9491 (2002).
AuthorsYuko Hori, Subhadip Raychaudhuri, Arup K. Chakraborty

83. “Thermodynamics and Phase Behavior of Block Copolymer/Homopolymer Blend with Attractive and Repulsive Interactions”, with J.H. Lee, et al., Macromolecules, 35, 7748 (2002).
AuthorsJ. H. Lee, N. P. Balsara,  A. K. Chakraborty, R. Krishnamoorti, B. Hammouda

82. “Nanomechanical Forces Generated by Surface Grafted DNA”, with M.F. Hagan and A. Majumdar, Phys. Chem. B, 106, 10163 (2002).
AuthorsMichael F. Hagan, Arun Majumdar, Arup K. Chakraborty

81. “Density Functional Theory Study of Nitrous Oxide Decomposition over Fe- and Co-ZSM-5”, with J. Ryder and A.T. Bell, Phys. Chem. B, 106, 7059 (2002).
AuthorsJason A. Ryder, Arup K. Chakraborty, Alexis T. Bell

80. “The Synapse Assembly Model”, with S.J. Lee, et al., Trends in Immunology, 23, 500 (2002).
Authors: Sung-Joo E. Lee, Yuko Hori, Jay T. Groves, Michael L. Dustin, Arup K. Chakraborty

79. “Correlation of a Dynamic Model for Immunological Synapse Formation with Effector Functions: Two Pathways to Synapse Formation”, with S.J. Lee, et al., Trends in Immunology, 23, 492 (2002).
Authors: Sung-Joo E. Lee, Yuko Hori, Jay T. Groves, Michael L. Dustin, Arup K. Chakraborty

78. “Lighting up TCR Takes Advantage of Serial Triggering”, A.K. Chakraborty, Nature Immunology, 3, 895 (2002).
Authors: Arup K. Chakraborty

77. “Immunological Synapse Formation: Physical Chemistry Meets Cell Biology”, Science STKE PE10 (2002).
Authors: Arup K. Chakraborty

76. “Micelle Formation of Randomly Grafted Copolymers in Slightly Selective Solvents”, with A. Kreig, et al., Chem. Phys., 115, 6243 (2001).
AuthorsAdam Kreig, Amy A. Lefebvre, Hyeok Hahn, Nitash P. Balsara, Shuyan Qi, Arup K. Chakraborty, Maria Xenidou, Nikos Hadjichristidis

75. “The Phase Diagram of Molten Randomly Grafted Copolymers”, with S.Y. Qi, Chem. Phys., 115, 3401 (2001).
Authors: Shuyan Qi, Arup K. Chakraborty

74. “Microphase segregation in Molten Randomly Grafted Copolymers”, with S.Y. Qi and N. Balsara, Chem. Phys., 115, 3387 (2001).
AuthorsShuyan Qi and Arup K. Chakraborty, Nitash P. Balsara

73. “Synaptic Pattern Formation During Cellular Recognition”, with S.Y. Qi, et al., Natl. Acad. Sci., 98, 6548 (2001).
Authors: Shuyan Qi, Jay T. Groves, Arup K. Chakraborty

72. “Polymer Adsorption-Driven Self-Assembly of Nanostructures”, with A.J. Golumbfskie, Rev. Phys. Chem., 52, 537-573 (2001).
Authors: Arup K Chakraborty,  Aaron J Golumbfskie

71. “Origin of Nanomechanical Cantilever Motion Generated from Biomolecular Interactions”, with G. Wu, et al., Natl. Acad. Sci., 98, 1560 (2001).
AuthorsGuanghua WuHaifeng JiKarolyn HansenThomas ThundatRam DatarRichard CoteMichael F. HaganArup K. ChakrabortyArunava Majumdar

70. “Disordered Heteropolymers: Models for Biomimetic Polymers and Polymers with Frustrating Quenched Disorder”, A.K. Chakraborty, Physics Reports, 342, 1 (2000).
Authors: Arup K. Chakraborty

69. “Theoretical Study of Polymeric Mixtures with Different Sequence Statistics. II. Brazovskii Class: Linear Random Copolymers with Diblock Copolymers”, with S.Y. Qi, Chem. Phys., 112, 1598 (2000).
AuthorsShuyan Qi and Arup K. Chakraborty

68. “Theoretical Study of Polymeric Mixtures with Different Sequence Statistics. I. Ising class: Linear Random Copolymers with Different Statistical Sequences and Ternary Blends of Linear Random Copolymers with Homopolymers”, with S.Y. Qi, Chem. Phys., 112, 1585 (2000).
AuthorsShuyan Qi and Arup K. Chakraborty

67. “Density Functional Theory Study of Proton Mobility in Zeolites: Proton Migration and Hydrogen Exchange in ZSM-5”, with J.A. Ryder and A.T. Bell, Phys. Chem. B., 104, 6998 (2000).
AuthorsJason A. Ryder, Arup K. Chakraborty, Alexis T. Bell

66. “Applications of Density Functional Theory to Identify Reaction Pathways for Processes Occurring in Zeolites and on Dispersed Metal Oxides”, with J.A. Ryder, et al., Surf. Sci. Catal., 130, 407-412 (2000).
Authors: Jason A. Ryder, Mark J. Rice, Francois Gilardoni, Arup K. Chakraborty, Alexis T. Bell

65. “Site Availability and Competitive Siting of Divalent Metal Cations in ZSM-5”, with M.J. Rice and A.T. Bell, Catal., 194, 278 (2000).
Authors: Mark J. Rice, Arup K. Chakraborty, Alexis T. Bell 

64. “Theoretical Studies of the Coordination and Stability of Divalent Cations in ZSM-5”, with M.J. Rice and A.T. Bell, Phys. Chem B, 104, 9987 (2000).
Authors: Mark J. Rice, Arup K. Chakraborty, Alexis T. Bell

63. “Density Functional Theory Calculations of the Oxidative Dehydrogenation of Propane on the (010) Surface of V2O5”, with F. Gilardoni, A.T. Bell, and P. Boulet, Phys. Chem. B., 104, 12250 (2000).
Authors: Francois Gilardoni, Alexis T. Bell, Arup K. Chakraborty, Pascal Boulet


Publications: 1995-1999

62. “Design and Synthesis of Materials with Precise Macroscopic Properties – Theoretical and Computational Approaches to Assist Rational Design: Biomimetic Recognition and Controlling Self-Assembly Processes by Tuning Polymer Architecture”, Frontiers of Engineering, (1999).
Authors: Arup K. Chakraborty

61. “Simulation of Biomimetic Recognition Between Polymers and Surfaces”, with A. Golumbfskie and V. Pande, Featured Article, Natl. Acad. Sci., 96, 11707 (1999).
Authors: Aron J. Golumbfskie, Vijay S. Pande, Arup K. Chakraborty

60. “A Density Functional Theory Study of Hydrogen Recombination and Hydrogen-Deuterium Exchange on Ga/H-ZSM-5”, with N. O. Gonzales and A. T. Bell, Topics in Catalysis, 9, 207 (1999).
Authors: Nick O. Gonzales, Arup K. Chakraborty, Alexis T. Bell

59. “Al Next Nearest Neighbor, Ring Occupation, and Proximity Statistics in ZSM-5”, with M. J. Rice and A. T. Bell, Catal., 186, 222 (1999).
Authors: Mark J. Rice, Arup K. Chakraborty, Alexis T. Bell

58. “Behavior of a Random Heteropolymer in Mixed Solvents”, A.K. Chakraborty, Chem. Phys. 111, 5232 (1999).
Authors: Arup K. Chakraborty

57. “Dynamic Monte-Carlo and Mean-field Study of the Effect of Strong Adsorption Sites on Self-Diffusion in Zeolites”, with M.-O. Coppens and A.T. Bell, Eng. Sci., 54, 3455 (1999).
Authors: Marc-Olivier Coppens, Alexis T. Bell, Arup K. Chakraborty

56. “Microphase Ordering in Melts of Randomly Grafted Copolymers”, with S. Qi, et al., Rev. Lett., 82, 2896 (1999).
Authors: Shuyan Qi, Arup K. Chakraborty, Hao Wang, Amy A. Lefebvre, Nitash P. Balsara, Eugene I. Shakhnovich, Maria Xenidou, Nikos Hadjichristidis

55. “Applications of Density Functional Theory to Study the Physical and Chemical Properties of Transition Metal Cation-Exchanged Zeolites”, with M.J. Rice, N.O. Gonzales, A.T. Bell, of 12th International Zeolite Conference, 1, 393-400 (1999).
Authors:Alexis T. Bell, Arup K. Chakraborty, N. O. Gonzales, Mark J. Rice

54. “Adhesion Promotion at a Homopolymer-Solid Interface Using Random Heteropolymers”, with R.E. Simmons, Chem. Phys., 109, 8667 (1998).
Authors: Edward Read Simmons, Arup K. Chakraborty

53. “Random Heteropolymer Adsorption on Disordered Multifunctional Surfaces: Effect of Specific Intersegment Interactions”, with S. Srebnik and D. Bratko, Chem. Phys., 109, 6415 (1998).
Authors: Simcha Srebnik, Arup K. Chakraborty, Dusan Bratko

52“A Density Functional Theory Study of the Interactions of H2O with H-ZSM-5, Cu-ZSM-5, and Co-ZSM-5”, with M.J. Rice and A.T. Bell, Phys. Chem., 102, 7498 (1998).
AuthorsMark J. Rice, Arup K. Chakraborty, Alexis T. Bell

51. “Effect of Topology and Molecular Occupancy on Self-Diffusion in Lattice Models of Zeolites—Monte-Carlo Simulations”, with M.O. Coppens and A.T. Bell, Eng. Sci., 53, 2053 (1998).
Authors: Marc-Olivier Coppensa, Alexis T. Bell, Arup K. Chakraborty

50. “Adsorption of Random Copolymers on Disordered Surfaces”, with D. Bratko and E. I. Shakhnovich, and Comp. Polym. Sci., 8, 113 (1998).
Authors: D. Bratko, Arup K. Chakraborty, E. I. Shakhnovich

49. “A Density Functional Theory Study of the Effects of Metal Cations on the Bronsted Acidity of H-ZSM-5”, with N. O. Gonzales and A. T. Bell, Catalysis Letters, 50, 135 (1998).
Authors: Nick O. Gonzales, Arup K. Chakraborty, Alexis T. Bell

48. “Freezing of Compact Random Heteropolymers with Correlated Sequence Fluctuations”, with E. I. Shakhnovich and V.S. Pande, Chem. Phys., 108, 1683 (1998).
Authors: Arup K. Chakraborty, Eugene I. Shakhnovich, Vijay S. Pande

47. “A Simple Theory and Monte Carlo Simulations for Recognition Between Random Heteropolymers and Disordered Surfaces”, with D. Bratko, Chem. Phys., 108, 1676 (1998).
Authors: Arup K. Chakraborty, D. Bratko

46. Reply to “Polymer Adsorption on Disordered Substrates””, with E.I. Shakhnovich, Rev. Lett., 79, 4931 (1997).
Authors: Arup K. Chakraborty, Eugene I. Shakhnovich

45. “Giovanni Astarita”, with T.W.F. Russell and A. B. Metzner, Physics Today, 50, 84 (1997).
Authors: Arup K. Chakraborty, T. W. Fraser Russell, Arthur B. Metzner

44. “Density Functional Theory Calculations of the Effects of Local Composition and Defect Structure on the Proton Affinity of H-ZSM-5”, with N. Gonzales and A.T. Bell, Phys. Chem. B., 101, 10058 (1997).
AuthorsNick O. Gonzales, Alexis T. Bell, Arup K. Chakraborty

43. “Recognition between Random Heteropolymers and Multifunctional Disordered Surfaces”, with E.I. Shakhnovich and D. Bratko, Phys. Lett., 280, 46 (1997).
Authors: . Bratko, Arup K. Chakraborty, E.I. Shakhnovich

42. “Diffusion and Reaction in ZSM-5 Studied by Dynamic Monte Carlo”, with B.L. Trout and A.T. Bell, Eng. Sci., 52 , 2265 (1997).
AuthorsBernhardt L. Trout, Arup K. Chakraborty, Alexis T. Bell

41. “The Structure of a Random Heteropolymer in a Disordered Medium: Ensemble Growth Simulation”, with D. Bratko and E.I. Shakhnovich, Chem. Phys., 106, 1264 (1997).
Authors: D. Bratko, Arup K. Chakraborty, E.I. Shakhnovich

40. “Analysis of the Thermochemistry of NOx Decomposition Over CuZSM-5 Based on Quantum Chemical and Statistical Mechanical Calculations”, with B.L. Trout and A.T.  Bell, Phys. Chem., 100, 17582 (1996).
AuthorsBernhardt L. Trout, Arup K. Chakraborty, Alexis T. Bell

39. “Exotic Transitions of Random Heteropolymers Interacting with Solid Surfaces”, with L. Gutman, Chem. Phys., 105, 7842 (1996).
Authors: Lorin Gutman, Arup K. Chakraborty

38. “Adsorption- Freezing Transition for Random Heteropolymers Near Disordered 2D Manifolds Due to “Pattern Matching””, with S. Srebnik and E.I. Shakhnovich, Rev. Letts, 77, 3157 (1996).
Authors: Simcha Srebnik, Arup K. Chakraborty, Eugene I. Shakhnovich

37. “Ion-Ion Correlations in Quenched Disordered Media”, with D. Bratko, Chem. Phys., 104, 7700 (1996).
Authors:D. Bratko, Arup K. Chakraborty

36. “Morton M. Denn “, with A.B. Metzner and T.W.F. Russell, Eng. Educ., 30, 88 (1996).
Authors: Arup K. Chakraborty, A. B. Metzner, T. W. F. Russell

35. “Sequence Fluctuation-Dependent Adsorption-Depletion Transition for Random Heteropolymers”, with L. Gutman, Chem. Phys., 104, 7306 (1996).
Authors: Lorin Gutman, Arup K. Chakraborty

34. “Local Spin Density Functional Theory Study of Copper Ion-Exchanged ZSM-5”, with B.L. Trout and A.T. Bell, Phys. Chem., 100, 4173 (1996).
AuthorsBernhardt L. Trout Arup K. Chakraborty ,* and Alexis T. Bell

33. “A Numerical Study of Polyampholyte Configuration”, with D. Bratko, Phys. Chem., 100, 1164 (1996).
Authors: D. Bratko, Arup K. Chakraborty

32. “Frozen Phases of Random Heteropolymers in Disordered Media”, with D. Bratko and E.I. Shakhnovich, Rev. Letts., 76, 1844 (1996).
Authors: D. Bratko, Arup K. Chakraborty, Eugene I. Shakhnovich

31. “Polymer Adsorption”, with M. Tirrell, feature article in Special issue of the MRS Bulletin on Polymer Surfaces and Interfaces, 21, 28 (1996).
Authors: Arup K. Chakraborty, Matthew Tirrell

30. “Schrodinger Equations and Diffusion Theory by M. Nagasawa”, AIChE Journal, 41, 2665 (1995).
Authors: Arup K. Chakraborty

29. “A Field Theory of Random Heteropolymers Near Solid Surfaces: Analysis of Interfacial  Organization and Adsorption-Desorption Phase Diagram”, with L. Gutman, Chem. Phys., 103, 10733 (1995).
Authors: Lorin Gutman, Arup K. Chakraborty

28. “Phase Behavior of Random Copolymers in Quenched Random Media”, with E.I. Shakhnovich, Chem. Phys., 103, 10751 (1995).
Authors: Arup K. Chakraborty, E. I. Shakhnovich

27. “Polyelectrolyte Configuration in a Disordered Medium”, with D. Bratko, Rev. E., 51, 5805 (1995).
Authors: D. Bratko, Arup K. Chakraborty

26. “Electronic Structure Calculations for Ammonia Adsorption in H-ZSM-5 Zeolites”, with A. Kyrlidis, A.T. Bell, and S.J. Cook, Phys. Chem., 99, 1505 (1995).
Authors: Agathagelos Kyrlidis, Stephen J. Cook, Arup K. Chakraborty, Alexis T. Bell, Doros N. Theodorou


Publications: 1986-1994

25. “Elastic Constants for Random Block Copolymers in the Strong Segregation Limit: Effects of Sequence Distribution”, with G.H. Fredrickson, Macromolecules, 27, 7079 (1994).
Authors: Arup K. Chakraborty, Glenn H. Fredickson

24. “Surface Induced Ordering for Confined Random Block Copolymers”, with L. Gutman, Chem. Phys., 101, 10074 (1994).
Authors: Lorin Gutman, Arup K. Chkraborty

23. “Solvation Thermodynamics of Simple Crown Ethers by the XRISM method”, with Y.L. Ha, Phys. Chem., 98, 11193 (1994).
Authors: Yuk Lung Ha, Arup K. Chakraborty

22. “Characterization of Crown Ethers as Macrocyclic Elements for Rotaxane Preparation: A Monte Carlo Simulation”, with Y.L. Ha, Eng Sci., 49, 2859 (1994).
Authors: Yuk Lung Ha, Arup K. Chakraborty

21. “Diffusion of Ionic Penetrants In Charged Disordered Media”, with D. Bratko, David Chandler, Chem. Phys., 100, 1528 (1994).
Authors: Arup K. Chakraborty, D. Bratko, David Chandler

20. “Ammonium Cation Complexation by 18-Crown-6 under Realistic Conditions: Simulations Using Proper Potentials”, with Y.L. Ha, Phys. Chem., 97, 11291 (1993).
Authors: Yuk Lung Ha, Arup K. Chakraborty

19. “Structural and Electronic Features of a Broensted Acid Site in H-ZSM-5”, with S.J. Cook et al., Phys. Chem., 97, 6679 (1993).
Authors: Stephen J. Cook, Arup K. Chakraborty, Alexis T. Bell, Doros N. Theodorou

18. “Dynamics of Poly(methyl methacrylate) Chains Adsorbed on Aluminum Surfaces” with J.S. Shaffer, Macromolecules, 26, 1120 (1993).
Authors: J. Scott Shaffer, Arup K. Chakraborty

17. “Dynamics of Relaxation at Strongly Interacting Polymer- Solid Interfaces: Effects of Chain Architecture”, with P.M. Adriani, Chem. Phys., 98, 4263 (1993).
Authors:  Paul M. Adriani, Arup K. Chakraborty

16. “The Nature of the Interactions of 18-Crown-6 with Ammonium Cations: A Computational Study”, with Y.L. Ha, Phys. Chem., 96, 6410 (1992).
Authors: Yuk L. Ha, Arup K. Chakraborty

15. “Glassy Relaxation at Polymer-Solid Interfaces”, with P.M. Adriani, Macromolecules, 25, 2470 (1992).
Authors: Arup K. Chakraborty, P.M. Adriani

14. “Structure and Dynamics at Polymer/Metal Interfaces”, with P.M. Adriani, J.S. Shaffer, Polymer Preprints, 33.1, 613-614 (1992).
Authors: Arup K. Chakraborty, P.M. Adriani, J.S. Shaffer

13. “Segment Level Chemistry and Chain Conformation in the Reactive Adsorption of Poly(methyl methacrylate) on Aluminum Oxide Surfaces”, with K. Konstandinidis et al., Langmuir, 8, 1307 (1992).
Authors: K. Konstadinidis, B. Thakkar, A. Chakraborty, L.W. Potts, R. Tannenbaum, M. Tirrell

12. “Progress and Future Directions in the Theory of Strongly Interacting Polymer/Solid Interfaces”, Proceedings of the First International Conference on Polymer/Solid Interfaces, page 3, I.O.P. Publishing Ltd., Bristol, U.K. (1992).
Authors: Arup K. Chakraborty

11. “The Effects of Local Structural Relaxation on Aluminum Siting within H-ZSM-5”, with S.R. Lonsinger et al., Catalysis Letters, 11, 209 (1991).
Authors: Stephen R. Lonsinger, Arup K. Chakraborty, Foros N. Theodorou, Alexis T. Bell

10. “Effects of Solvent Polarity and Temperature on the Conformational Statistics of a Simple Macrocyclic Polyether”, with Y.L. Ha, Phys. Chem., 95, 10781 (1991).
Authors: Yuk Lung Ha, Arup K. Chakraborty

9. “On the Existence of Quasi-Two-Dimensional, Glass-Like Structures at Strongly Interacting Polymer-Solid Interfaces”, with J.S. Shaffer, P.M. Adriani, Macromolecules, 24, 5226 (1991).
Authors: Arup K. Chakraborty, J. Scott Shaffer, Paul M. Adriani

8. “The Nature of the Interactions of poly (methyl methacrylate) Oligomers with an Aluminum Surface”, with J. S. Shaffer et al., Chem. Phys. 95, 8616 (1991).
Authors: J. Scott Shaffer, Arup K. Chakraborty, Matthew Tirrell, H. Ted Davis, Jose L. Martins

7. “Effect of Silicate Ratio on the Distribution of Silicate and Aluminosilicate Anions in TPA Aluminosilicate Solutions”, with R.F. Mortlock et al., Phys. Chem., 95, 4501 (1991).
Authors: R.F. Mortlock, A.T. Bell, A.K. Chakraborty, C.J. Radke

6. “Energetics and Near – Surface Structure at Polymer – Metal Interfaces”, with J.S. Shaffer, Polymer Preprints, 31, 546 (1990).
Authors: J. S. Shaffer, A.K. Chakraborty

5. “A Molecular Orbital Study of the Interactions of Acrylic Polymers with Aluminum: Implications for Adhesion”, with H.T. Davis, M. Tirrell, Polym. Sci.: Polym. Chem. Ed, 28, 3185 (1990).
Authors: Arup K. Chakraborty, H. Ted Davis, Matthew Tirrell

4. “Molecular Orbital Approach to Substituent Effects in Amine – CO2 Interactions”, with G. Astarita et al., Am. Chem. Soc., 110, 6947 (1988).
Authors: Arup K. Chakraborty, K. B. Bischoff, Gianni Astarita, J.R. Damewood, Jr.

3. “Boundary Layer Analysis for the Modeling of Noncatalytic Gas-Solid Reactions”, with G. Astarita, E.C. Research, 26, 972 (1987).
Authors: Arup K. Chakraborty, Gianni Astarita

2“C02 Absorption in Aqueous Solutions of Hindered Amines “, with G. Astarita and K.B. Bischoff, Eng Sci., 41, 997 (1986).
Authors: Arup K. Chakraborty, Gianni Astarita, K. B. Bischoff

1. “Sink Flows of Viscoelastic Fluids”, with A.B. Metzner, Rheo1., 30, 29 (1986).
AuthorsA. K. Chakraborty, A. B. Metzner



Edited Book: “Molecular Modeling and Theory in Chemical Engineering”, Academic Press, San Diego (2001).