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Items: 1 to 50 of 75

1.

Robustness of Clocks to Input Noise.

Monti M, Lubensky DK, Ten Wolde PR.

Phys Rev Lett. 2018 Aug 17;121(7):078101. doi: 10.1103/PhysRevLett.121.078101.

PMID:
30169070
2.

Optimal entrainment of circadian clocks in the presence of noise.

Monti M, Lubensky DK, Ten Wolde PR.

Phys Rev E. 2018 Mar;97(3-1):032405. doi: 10.1103/PhysRevE.97.032405.

PMID:
29776095
3.

Quantifying fluctuations in reversible enzymatic cycles and clocks.

Wierenga H, Ten Wolde PR, Becker NB.

Phys Rev E. 2018 Apr;97(4-1):042404. doi: 10.1103/PhysRevE.97.042404.

PMID:
29758603
4.

Rate constants for proteins binding to substrates with multiple binding sites using a generalized forward flux sampling expression.

Vijaykumar A, Ten Wolde PR, Bolhuis PG.

J Chem Phys. 2018 Mar 28;148(12):124109. doi: 10.1063/1.5012854.

PMID:
29604887
5.

The magnitude of the intrinsic rate constant: How deep can association reactions be in the diffusion limited regime?

Vijaykumar A, Ten Wolde PR, Bolhuis PG.

J Chem Phys. 2017 Nov 14;147(18):184108. doi: 10.1063/1.5009547.

PMID:
29141426
6.

Changes in microtubule overlap length regulate kinesin-14-driven microtubule sliding.

Braun M, Lansky Z, Szuba A, Schwarz FW, Mitra A, Gao M, Lüdecke A, Ten Wolde PR, Diez S.

Nat Chem Biol. 2017 Dec;13(12):1245-1252. doi: 10.1038/nchembio.2495. Epub 2017 Oct 16.

7.

Period Robustness and Entrainability of the Kai System to Changing Nucleotide Concentrations.

Paijmans J, Lubensky DK, Ten Wolde PR.

Biophys J. 2017 Jul 11;113(1):157-173. doi: 10.1016/j.bpj.2017.05.048.

8.

Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics.

Vijaykumar A, Ouldridge TE, Ten Wolde PR, Bolhuis PG.

J Chem Phys. 2017 Mar 21;146(11):114106. doi: 10.1063/1.4977515.

9.

A thermodynamically consistent model of the post-translational Kai circadian clock.

Paijmans J, Lubensky DK, Ten Wolde PR.

PLoS Comput Biol. 2017 Mar 15;13(3):e1005415. doi: 10.1371/journal.pcbi.1005415. eCollection 2017 Mar.

10.

Publisher's Note: Biochemical Machines for the Interconversion of Mutual Information and Work [Phys. Rev. Lett. 118, 028101 (2017)].

McGrath T, Jones NS, Ten Wolde PR, Ouldridge TE.

Phys Rev Lett. 2017 Jan 27;118(4):049902. doi: 10.1103/PhysRevLett.118.049902. Epub 2017 Jan 27.

PMID:
28186800
11.

Biochemical Machines for the Interconversion of Mutual Information and Work.

McGrath T, Jones NS, Ten Wolde PR, Ouldridge TE.

Phys Rev Lett. 2017 Jan 13;118(2):028101. doi: 10.1103/PhysRevLett.118.028101. Epub 2017 Jan 10. Erratum in: Phys Rev Lett. 2017 Jan 27;118(4):049902.

12.

The intrinsic rate constants in diffusion-influenced reactions.

Vijaykumar A, Bolhuis PG, Ten Wolde PR.

Faraday Discuss. 2016 Dec 22;195:421-441. doi: 10.1039/c6fd00104a.

PMID:
27727353
13.

Discrete gene replication events drive coupling between the cell cycle and circadian clocks.

Paijmans J, Bosman M, Ten Wolde PR, Lubensky DK.

Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):4063-8. doi: 10.1073/pnas.1507291113. Epub 2016 Mar 28.

14.

Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells.

Recouvreux P, Sokolowski TR, Grammoustianou A, ten Wolde PR, Dogterom M.

Proc Natl Acad Sci U S A. 2016 Feb 16;113(7):1811-6. doi: 10.1073/pnas.1419248113. Epub 2016 Feb 1.

15.

Optimal Prediction by Cellular Signaling Networks.

Becker NB, Mugler A, Ten Wolde PR.

Phys Rev Lett. 2015 Dec 18;115(25):258103. doi: 10.1103/PhysRevLett.115.258103. Epub 2015 Dec 17.

PMID:
26722947
16.

Combining molecular dynamics with mesoscopic Green's function reaction dynamics simulations.

Vijaykumar A, Bolhuis PG, ten Wolde PR.

J Chem Phys. 2015 Dec 7;143(21):214102. doi: 10.1063/1.4936254.

PMID:
26646864
17.

Non-monotonic dynamics and crosstalk in signaling pathways and their implications for pharmacology.

van Wijk R, Tans SJ, ten Wolde PR, Mashaghi A.

Sci Rep. 2015 Jun 18;5:11376. doi: 10.1038/srep11376.

18.

Diffusible crosslinkers generate directed forces in microtubule networks.

Lansky Z, Braun M, Lüdecke A, Schlierf M, ten Wolde PR, Janson ME, Diez S.

Cell. 2015 Mar 12;160(6):1159-68. doi: 10.1016/j.cell.2015.01.051. Epub 2015 Mar 5.

19.

Energy dissipation and noise correlations in biochemical sensing.

Govern CC, ten Wolde PR.

Phys Rev Lett. 2014 Dec 19;113(25):258102. Epub 2014 Dec 16.

PMID:
25554909
20.

Positive feedback can lead to dynamic nanometer-scale clustering on cell membranes.

Wehrens M, ten Wolde PR, Mugler A.

J Chem Phys. 2014 Nov 28;141(20):205102. doi: 10.1063/1.4901888.

PMID:
25429963
21.

Optimal resource allocation in cellular sensing systems.

Govern CC, Ten Wolde PR.

Proc Natl Acad Sci U S A. 2014 Dec 9;111(49):17486-91. doi: 10.1073/pnas.1411524111. Epub 2014 Nov 24.

22.

Lower bound on the precision of transcriptional regulation and why facilitated diffusion can reduce noise in gene expression.

Paijmans J, ten Wolde PR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Sep;90(3):032708. Epub 2014 Sep 25.

PMID:
25314474
23.

Multiplexing oscillatory biochemical signals.

de Ronde W, ten Wolde PR.

Phys Biol. 2014 Apr;11(2):026004. doi: 10.1088/1478-3975/11/2/026004. Epub 2014 Apr 1.

PMID:
24685537
24.

The Berg-Purcell limit revisited.

Kaizu K, de Ronde W, Paijmans J, Takahashi K, Tostevin F, ten Wolde PR.

Biophys J. 2014 Feb 18;106(4):976-85. doi: 10.1016/j.bpj.2013.12.030.

25.

Importance of crowding in signaling, genetic, and metabolic networks.

ten Wolde PR, Mugler A.

Int Rev Cell Mol Biol. 2014;307:419-42. doi: 10.1016/B978-0-12-800046-5.00012-6. Review.

PMID:
24380601
26.

Single-cell dynamics reveals sustained growth during diauxic shifts.

Boulineau S, Tostevin F, Kiviet DJ, ten Wolde PR, Nghe P, Tans SJ.

PLoS One. 2013 Apr 30;8(4):e61686. doi: 10.1371/journal.pone.0061686. Print 2013.

27.

Spatial partitioning improves the reliability of biochemical signaling.

Mugler A, Tostevin F, ten Wolde PR.

Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):5927-32. doi: 10.1073/pnas.1218301110. Epub 2013 Mar 25.

28.

Fundamental limits on sensing chemical concentrations with linear biochemical networks.

Govern CC, ten Wolde PR.

Phys Rev Lett. 2012 Nov 21;109(21):218103. Epub 2012 Nov 20.

PMID:
23215617
29.

Signaling noise enhances chemotactic drift of E. coli.

Flores M, Shimizu TS, ten Wolde PR, Tostevin F.

Phys Rev Lett. 2012 Oct 5;109(14):148101. Epub 2012 Oct 2.

PMID:
23083290
30.

Feed-forward loops and diamond motifs lead to tunable transmission of information in the frequency domain.

de Ronde WH, Tostevin F, Ten Wolde PR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Aug;86(2 Pt 1):021913. Epub 2012 Aug 13.

PMID:
23005791
31.

Mutual repression enhances the steepness and precision of gene expression boundaries.

Sokolowski TR, Erdmann T, ten Wolde PR.

PLoS Comput Biol. 2012;8(8):e1002654. doi: 10.1371/journal.pcbi.1002654. Epub 2012 Aug 30.

32.

Rare switching events in non-stationary systems.

Becker NB, ten Wolde PR.

J Chem Phys. 2012 May 7;136(17):174119. doi: 10.1063/1.4704812.

PMID:
22583222
33.

Non-stationary forward flux sampling.

Becker NB, Allen RJ, ten Wolde PR.

J Chem Phys. 2012 May 7;136(17):174118. doi: 10.1063/1.4704810.

PMID:
22583221
34.

Reliability of frequency and amplitude decoding in gene regulation.

Tostevin F, de Ronde W, ten Wolde PR.

Phys Rev Lett. 2012 Mar 9;108(10):108104. Epub 2012 Mar 8.

PMID:
22463459
35.

Membrane clustering and the role of rebinding in biochemical signaling.

Mugler A, Bailey AG, Takahashi K, ten Wolde PR.

Biophys J. 2012 Mar 7;102(5):1069-78. doi: 10.1016/j.bpj.2012.02.005. Epub 2012 Mar 6.

36.

Multiplexing biochemical signals.

de Ronde W, Tostevin F, ten Wolde PR.

Phys Rev Lett. 2011 Jul 22;107(4):048101. Epub 2011 Jul 19.

PMID:
21867046
37.

Effect of feedback on the fidelity of information transmission of time-varying signals.

de Ronde WH, Tostevin F, ten Wolde PR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Sep;82(3 Pt 1):031914. Epub 2010 Sep 24.

PMID:
21230115
38.

Robust circadian clocks from coupled protein-modification and transcription-translation cycles.

Zwicker D, Lubensky DK, ten Wolde PR.

Proc Natl Acad Sci U S A. 2010 Dec 28;107(52):22540-5. doi: 10.1073/pnas.1007613107. Epub 2010 Dec 13.

39.

Mutual information in time-varying biochemical systems.

Tostevin F, ten Wolde PR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jun;81(6 Pt 1):061917. Epub 2010 Jun 16.

PMID:
20866450
40.

Providing positional information with active transport on dynamic microtubules.

Tischer C, Ten Wolde PR, Dogterom M.

Biophys J. 2010 Aug 4;99(3):726-35. doi: 10.1016/j.bpj.2010.05.026.

41.

Shaping a morphogen gradient for positional precision.

He F, Saunders TE, Wen Y, Cheung D, Jiao R, ten Wolde PR, Howard M, Ma J.

Biophys J. 2010 Aug 4;99(3):697-707. doi: 10.1016/j.bpj.2010.04.073.

42.

Combinatorial gene regulation using auto-regulation.

Hermsen R, Ursem B, ten Wolde PR.

PLoS Comput Biol. 2010 Jun 10;6(6):e1000813. doi: 10.1371/journal.pcbi.1000813.

43.

Role of spatial averaging in the precision of gene expression patterns.

Erdmann T, Howard M, ten Wolde PR.

Phys Rev Lett. 2009 Dec 18;103(25):258101. Epub 2009 Dec 17.

PMID:
20366291
44.

Spatio-temporal correlations can drastically change the response of a MAPK pathway.

Takahashi K, Tanase-Nicola S, ten Wolde PR.

Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2473-8. doi: 10.1073/pnas.0906885107. Epub 2010 Jan 25.

45.

The switching dynamics of the bacterial flagellar motor.

van Albada SB, Tănase-Nicola S, ten Wolde PR.

Mol Syst Biol. 2009;5:316. doi: 10.1038/msb.2009.74. Epub 2009 Oct 13.

46.

Mutual information between input and output trajectories of biochemical networks.

Tostevin F, ten Wolde PR.

Phys Rev Lett. 2009 May 29;102(21):218101. Epub 2009 May 27.

PMID:
19519137
47.

Differential affinity and catalytic activity of CheZ in E. coli chemotaxis.

van Albada SB, Ten Wolde PR.

PLoS Comput Biol. 2009 May;5(5):e1000378. doi: 10.1371/journal.pcbi.1000378. Epub 2009 May 8.

48.

DNA looping provides stability and robustness to the bacteriophage lambda switch.

Morelli MJ, Ten Wolde PR, Allen RJ.

Proc Natl Acad Sci U S A. 2009 May 19;106(20):8101-6. doi: 10.1073/pnas.0810399106. Epub 2009 May 1.

49.

Homogeneous nucleation under shear in a two-dimensional Ising model: cluster growth, coalescence, and breakup.

Allen RJ, Valeriani C, Tănase-Nicola S, ten Wolde PR, Frenkel D.

J Chem Phys. 2008 Oct 7;129(13):134704. doi: 10.1063/1.2981052.

PMID:
19045113
50.

Regulatory control and the costs and benefits of biochemical noise.

Tănase-Nicola S, ten Wolde PR.

PLoS Comput Biol. 2008 Aug 15;4(8):e1000125. doi: 10.1371/journal.pcbi.1000125.

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