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Items: 1 to 50 of 292

1.

Theory and simulations for RNA folding in mixtures of monovalent and divalent cations.

Nguyen HT, Hori N, Thirumalai D.

Proc Natl Acad Sci U S A. 2019 Sep 30. pii: 201911632. doi: 10.1073/pnas.1911632116. [Epub ahead of print]

PMID:
31570624
2.

Conformational heterogeneity in human interphase chromosome organization reconciles the FISH and Hi-C paradox.

Shi G, Thirumalai D.

Nat Commun. 2019 Aug 29;10(1):3894. doi: 10.1038/s41467-019-11897-0.

3.

Processivity, Velocity, and Universal Characteristics of Nucleic Acid Unwinding by Helicases.

Chakrabarti S, Jarzynski C, Thirumalai D.

Biophys J. 2019 Sep 3;117(5):867-879. doi: 10.1016/j.bpj.2019.07.021. Epub 2019 Jul 20.

PMID:
31400912
4.

Chicken egg yolk antibody (IgY) as diagnostics and therapeutics in parasitic infections - A review.

Thirumalai D, Visaga Ambi S, Vieira-Pires RS, Xiaoying Z, Sekaran S, Krishnan U.

Int J Biol Macromol. 2019 Sep 1;136:755-763. doi: 10.1016/j.ijbiomac.2019.06.118. Epub 2019 Jun 17. Review.

PMID:
31220492
5.

Universal Nature of Collapsibility in the Context of Protein Folding and Evolution.

Thirumalai D, Samanta HS, Maity H, Reddy G.

Trends Biochem Sci. 2019 Aug;44(8):675-687. doi: 10.1016/j.tibs.2019.04.003. Epub 2019 May 29. Review.

PMID:
31153683
6.

Ion Condensation onto Ribozyme Is Site Specific and Fold Dependent.

Hori N, Denesyuk NA, Thirumalai D.

Biophys J. 2019 Jun 18;116(12):2400-2410. doi: 10.1016/j.bpj.2019.04.037. Epub 2019 May 11.

PMID:
31130233
7.

Giant Casimir Nonequilibrium Forces Drive Coil to Globule Transition in Polymers.

Samanta HS, Mugnai ML, Kirkpatrick TR, Thirumalai D.

J Phys Chem Lett. 2019 Jun 6;10(11):2788-2793. doi: 10.1021/acs.jpclett.9b00695. Epub 2019 May 14.

PMID:
31066561
8.

Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular Machines.

Thirumalai D, Hyeon C, Zhuravlev PI, Lorimer GH.

Chem Rev. 2019 Apr 24. doi: 10.1021/acs.chemrev.8b00760. [Epub ahead of print]

PMID:
31017391
9.

Origin of superdiffusive behavior in a class of nonequilibrium systems.

Samanta HS, Thirumalai D.

Phys Rev E. 2019 Mar;99(3-1):032401. doi: 10.1103/PhysRevE.99.032401.

PMID:
30999548
10.

Share, but unequally: a plausible mechanism for emergence and maintenance of intratumour heterogeneity.

Li X, Thirumalai D.

J R Soc Interface. 2019 Jan 31;16(150):20180820. doi: 10.1098/rsif.2018.0820.

PMID:
30958159
11.

Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins.

Baul U, Chakraborty D, Mugnai ML, Straub JE, Thirumalai D.

J Phys Chem B. 2019 Apr 25;123(16):3462-3474. doi: 10.1021/acs.jpcb.9b02575. Epub 2019 Apr 15.

PMID:
30913885
12.

Donor Stabilized Diatomic Gr.14 E2 (E = C-Pb) Molecule D-E2-D (D = NHC, aNHC, NNHC, NHSi, NHGe, cAAC, cAASi, cAAGe): A Theoretical Insight.

Mondal T, Dutta S, De S, Thirumalai D, Koley D.

J Phys Chem A. 2019 Jan 17;123(2):565-581. doi: 10.1021/acs.jpca.8b11005. Epub 2019 Jan 3.

PMID:
30562460
13.

Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci.

Liu L, Shi G, Thirumalai D, Hyeon C.

PLoS Comput Biol. 2018 Dec 3;14(12):e1006617. doi: 10.1371/journal.pcbi.1006617. eCollection 2018 Dec.

14.

Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding.

Denesyuk NA, Hori N, Thirumalai D.

J Phys Chem B. 2018 Dec 20;122(50):11860-11867. doi: 10.1021/acs.jpcb.8b08142. Epub 2018 Dec 5.

PMID:
30468380
15.

One pot multi-component synthesis of functionalized spiropyridine and pyrido[2,3-d]pyrimidine scaffolds and their potent in-vitro anti-inflammatory and anti-oxidant investigations.

Lavanya M, Asharani IV, Thirumalai D.

Chem Biol Drug Des. 2019 Apr;93(4):464-472. doi: 10.1111/cbdd.13434. Epub 2018 Nov 28.

PMID:
30393996
16.

Charge fluctuation effects on the shape of flexible polyampholytes with applications to intrinsically disordered proteins.

Samanta HS, Chakraborty D, Thirumalai D.

J Chem Phys. 2018 Oct 28;149(16):163323. doi: 10.1063/1.5035428.

PMID:
30384718
17.

Synergy between intrinsically disordered domains and structured proteins amplifies membrane curvature sensing.

Zeno WF, Baul U, Snead WT, DeGroot ACM, Wang L, Lafer EM, Thirumalai D, Stachowiak JC.

Nat Commun. 2018 Oct 8;9(1):4152. doi: 10.1038/s41467-018-06532-3.

18.

Dynamics of Allosteric Transitions in Dynein.

Goldtzvik Y, Mugnai ML, Thirumalai D.

Structure. 2018 Dec 4;26(12):1664-1677.e5. doi: 10.1016/j.str.2018.08.005. Epub 2018 Sep 27.

PMID:
30270176
19.

Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover.

Hori N, Denesyuk NA, Thirumalai D.

J Phys Chem B. 2018 Dec 13;122(49):11279-11288. doi: 10.1021/acs.jpcb.8b07129. Epub 2018 Sep 18.

PMID:
30179471
20.

Interface Residues That Drive Allosteric Transitions Also Control the Assembly of l-Lactate Dehydrogenase.

Chen J, Thirumalai D.

J Phys Chem B. 2018 Dec 13;122(49):11195-11205. doi: 10.1021/acs.jpcb.8b06430. Epub 2018 Aug 27.

21.

Interphase human chromosome exhibits out of equilibrium glassy dynamics.

Shi G, Liu L, Hyeon C, Thirumalai D.

Nat Commun. 2018 Aug 8;9(1):3161. doi: 10.1038/s41467-018-05606-6.

22.

Regulatory element in fibrin triggers tension-activated transition from catch to slip bonds.

Litvinov RI, Kononova O, Zhmurov A, Marx KA, Barsegov V, Thirumalai D, Weisel JW.

Proc Natl Acad Sci U S A. 2018 Aug 21;115(34):8575-8580. doi: 10.1073/pnas.1802576115. Epub 2018 Aug 7.

23.

Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot.

Roca J, Hori N, Baral S, Velmurugu Y, Narayanan R, Narayanan P, Thirumalai D, Ansari A.

Proc Natl Acad Sci U S A. 2018 Jul 31;115(31):E7313-E7322. doi: 10.1073/pnas.1717582115. Epub 2018 Jul 16.

24.

Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.

Chakraborty D, Hori N, Thirumalai D.

J Chem Theory Comput. 2018 Jul 10;14(7):3763-3779. doi: 10.1021/acs.jctc.8b00091. Epub 2018 Jun 26.

25.

Signalling networks and dynamics of allosteric transitions in bacterial chaperonin GroEL: implications for iterative annealing of misfolded proteins.

Thirumalai D, Hyeon C.

Philos Trans R Soc Lond B Biol Sci. 2018 Jun 19;373(1749). pii: 20170182. doi: 10.1098/rstb.2017.0182. Review.

26.

Structure of APP-C991-99 and implications for role of extra-membrane domains in function and oligomerization.

Pantelopulos GA, Straub JE, Thirumalai D, Sugita Y.

Biochim Biophys Acta Biomembr. 2018 Apr 24. pii: S0005-2736(18)30112-3. doi: 10.1016/j.bbamem.2018.04.002. [Epub ahead of print]

27.

Forced-rupture of cell-adhesion complexes reveals abrupt switch between two brittle states.

Toan NM, Thirumalai D.

J Chem Phys. 2018 Mar 28;148(12):123332. doi: 10.1063/1.5011056.

28.

Computational Investigation of Carbene-Phosphinidenes: Correlation between 31P Chemical Shifts and Bonding Features to Estimate the π-Backdonation of Carbenes.

Dutta S, Maity B, Thirumalai D, Koley D.

Inorg Chem. 2018 Apr 2;57(7):3993-4008. doi: 10.1021/acs.inorgchem.8b00174. Epub 2018 Mar 12.

PMID:
29528628
29.

Optimal information transfer in enzymatic networks: A field theoretic formulation.

Samanta HS, Hinczewski M, Thirumalai D.

Phys Rev E. 2017 Jul;96(1-1):012406. doi: 10.1103/PhysRevE.96.012406. Epub 2017 Jul 14.

PMID:
29347079
30.

Denaturants Alter the Flux through Multiple Pathways in the Folding of PDZ Domain.

Liu Z, Thirumalai D.

J Phys Chem B. 2018 Feb 1;122(4):1408-1416. doi: 10.1021/acs.jpcb.7b11408. Epub 2018 Jan 22.

31.

Molecular chaperones maximize the native state yield on biological times by driving substrates out of equilibrium.

Chakrabarti S, Hyeon C, Ye X, Lorimer GH, Thirumalai D.

Proc Natl Acad Sci U S A. 2017 Dec 19;114(51):E10919-E10927. doi: 10.1073/pnas.1712962114. Epub 2017 Dec 7.

32.

Electrochemical reactive oxygen species detection by cytochrome c immobilized with vertically aligned and electrochemically reduced graphene oxide on a glassy carbon electrode.

Thirumalai D, Kathiresan V, Lee J, Jin SH, Chang SC.

Analyst. 2017 Nov 20;142(23):4544-4552. doi: 10.1039/c7an01387f.

PMID:
29114650
33.

Parsing the roles of neck-linker docking and tethered head diffusion in the stepping dynamics of kinesin.

Zhang Z, Goldtzvik Y, Thirumalai D.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E9838-E9845. doi: 10.1073/pnas.1706014114. Epub 2017 Oct 30.

34.

Oxidative environment causes molecular remodeling in embryonic heart-a metabolomic and lipidomic fingerprinting analysis.

Manickaraj S, Thirumalai D, Manjunath P, Sekarbabu V, Jeganathan S, Sundaresan L, Subramaniyam R, Jeganathan M.

Environ Sci Pollut Res Int. 2017 Oct;24(30):23825-23833. doi: 10.1007/s11356-017-9997-y. Epub 2017 Sep 2.

PMID:
28866837
35.

Ultrasensitivity of Water Exchange Kinetics to the Size of Metal Ion.

Lee Y, Thirumalai D, Hyeon C.

J Am Chem Soc. 2017 Sep 13;139(36):12334-12337. doi: 10.1021/jacs.7b04198. Epub 2017 Sep 1.

PMID:
28853881
36.

Kinematics of the lever arm swing in myosin VI.

Mugnai ML, Thirumalai D.

Proc Natl Acad Sci U S A. 2017 May 30;114(22):E4389-E4398. doi: 10.1073/pnas.1615708114. Epub 2017 May 16.

37.

Protein collapse is encoded in the folded state architecture.

Samanta HS, Zhuravlev PI, Hinczewski M, Hori N, Chakrabarti S, Thirumalai D.

Soft Matter. 2017 May 21;13(19):3622-3638. doi: 10.1039/c7sm00074j. Epub 2017 Apr 27.

PMID:
28447708
38.

Ripping RNA by Force Using Gaussian Network Models.

Hyeon C, Thirumalai D.

J Phys Chem B. 2017 Apr 20;121(15):3515-3522. doi: 10.1021/acs.jpcb.6b09402. Epub 2016 Dec 2.

PMID:
28423909
39.

One-pot cascade synthesis and in vitro evaluation of anti-inflammatory and antidiabetic activities of S-methylphenyl substituted acridine-1,8-diones.

Mallu L, Thirumalai D, Asharani IV.

Chem Biol Drug Des. 2017 Oct;90(4):520-526. doi: 10.1111/cbdd.12973. Epub 2017 Apr 12.

PMID:
28294548
40.

Theory and computations in biology: Kamal's legacy.

Thirumalai D.

Phys Biol. 2017 Feb 8;14(1):010401. doi: 10.1088/1478-3975/aa5564. No abstract available.

PMID:
28177933
41.

Collapse Precedes Folding in Denaturant-Dependent Assembly of Ubiquitin.

Reddy G, Thirumalai D.

J Phys Chem B. 2017 Feb 9;121(5):995-1009. doi: 10.1021/acs.jpcb.6b13100. Epub 2017 Jan 25.

PMID:
28076957
42.

Thermodynamics of Helix-Coil Transitions of Polyalanine in Open Carbon Nanotubes.

Suvlu D, Samaratunga S, Thirumalai D, Rasaiah JC.

J Phys Chem Lett. 2017 Jan 19;8(2):494-499. doi: 10.1021/acs.jpclett.6b02620. Epub 2017 Jan 11.

PMID:
28060517
43.

Chromatin Is Stretched but Intact When the Nucleus Is Squeezed through Constrictions.

Thirumalai D, Shi G.

Biophys J. 2017 Feb 7;112(3):411-412. doi: 10.1016/j.bpj.2016.11.902. Epub 2016 Dec 15. No abstract available.

44.

Discrete Step Sizes of Molecular Motors Lead to Bimodal Non-Gaussian Velocity Distributions under Force.

Vu HT, Chakrabarti S, Hinczewski M, Thirumalai D.

Phys Rev Lett. 2016 Aug 12;117(7):078101. doi: 10.1103/PhysRevLett.117.078101. Epub 2016 Aug 8.

PMID:
27564000
45.

Impact of membrane lipid composition on the structure and stability of the transmembrane domain of amyloid precursor protein.

Dominguez L, Foster L, Straub JE, Thirumalai D.

Proc Natl Acad Sci U S A. 2016 Sep 6;113(36):E5281-7. doi: 10.1073/pnas.1606482113. Epub 2016 Aug 24.

46.

Immunoglobulin Transporting Receptors Are Potential Targets for the Immunity Enhancement and Generation of Mammary Gland Bioreactor.

Jiang X, Hu J, Thirumalai D, Zhang X.

Front Immunol. 2016 Jun 10;7:214. doi: 10.3389/fimmu.2016.00214. eCollection 2016. Review.

47.

Directly measuring single-molecule heterogeneity using force spectroscopy.

Hinczewski M, Hyeon C, Thirumalai D.

Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):E3852-61. doi: 10.1073/pnas.1518389113. Epub 2016 Jun 17.

48.

Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension.

Hori N, Denesyuk NA, Thirumalai D.

J Mol Biol. 2016 Jul 17;428(14):2847-59. doi: 10.1016/j.jmb.2016.06.002. Epub 2016 Jun 15.

49.

Reply to Alberti: Are in vitro folding experiments relevant in vivo?

Zhuravlev PI, Hinczewski M, Chakrabarti S, Marqusee S, Thirumalai D.

Proc Natl Acad Sci U S A. 2016 Jun 7;113(23):E3192. doi: 10.1073/pnas.1603395113. Epub 2016 May 25. No abstract available.

50.

Noise Control in Gene Regulatory Networks with Negative Feedback.

Hinczewski M, Thirumalai D.

J Phys Chem B. 2016 Jul 7;120(26):6166-77. doi: 10.1021/acs.jpcb.6b02093. Epub 2016 May 12.

PMID:
27095600

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