Publications Biochemical Networks

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Article(s) published in 2011

M.J. Morelli, R.J. Allen and P.R. ten Wolde, Effects of macromolecular crowding on genetic networks, Biophys. J. 101, 2882–2891 (2011).
S. Meyer, N.B. Becker, S.H. Syed, D. Goutte-Gattat, M.S. Shukla, J.J. Hayes, D. Angelov, J. Bednar, S. Dimitrov and R. Everaers, From crystal and NMR structures, footprints and cryo-electron-micrographs to large and soft structures: nanoscale modeling of the nucleosomal stem, Nucl. Acids Res. 39, 9139-9154 (2011).
W.H. de Ronde, F. Tostevin and P.R. ten Wolde, Multiplexing biochemical signals, Phys. Rev. Lett. 107, 048101 (2011).
F. Tostevin, Precision of sensing cell length via concentration gradients, Biophys. J. 100, 294-303 (2011).

Article(s) published in 2010

D. Zwicker, D.K. Lubensky and P.R. ten Wolde, Robust circadian clocks from coupled protein-modification and transcription–translation cycles, PNAS 107, 22540-22545 (2010).
W.H. de Ronde, F. Tostevin and P.R. ten Wolde, Effect of feedback on the fidelity of information transmission for time-varying signals, Phys. Rev. E 82, 031914 1-21 (2010).
F. He, T. Saunders, Y. Wen, R. Jiao, P.R. ten Wolde, M. Howard and J. Ma, Shaping a morphogen gradient for positional information, Biophys. J. 99, 697–707 (2010).
C. Tischer, P.R. ten Wolde and M. Dogterom, Providing positional information with active transport on dynamic microtubules, Biophys. J. 99, 726-735 (2010).
F. Tostevin and P.R. ten Wolde, Mutual information in time-varying biochemical systems, Phys. Rev. E 81, 061917 1-15 (2010).
R. Hermsen, B. Ursem and P.R. ten Wolde, Combinatorial gene regulation using auto-regulation, PLoS Comput. Biol. 6, e1000813 1-13 (2010).
K. Takahashi, S. Tanase-Nicola and P.R. ten Wolde, Spatio-temporal correlations can drastically change the response of a MAPK pathway, PNAS 107, 2473-2478 (2010).

Article(s) published in 2009

T. Erdmann, M. Howard and P.R. ten Wolde, Role of spatial averaging in the precision of gene expression patterns, Physical Review Letters 103, 258101 1-4 (2009).
R.J. Allen, C. Valeriani and P.R. ten Wolde, Forward flux sampling for rare event simulations, Journal of Physics: Condensed Matter 21, 463102 1-21 (2009).
S.B. van Albada, S. Tanase-Nicola and P.R. ten Wolde, The switching dynamics of the bacterial flagellar motor, Molecular Systems Biology 5, 316 1-8 (2009).
W.H. de Ronde, B.C. Daniels, A. Mugler, N.A. Sinitsyn and I. Nemenman, Mesoscopic statistical properties of multistep enzyme-mediated reactions, IET Syst. Biol. 3, 429-437 (2009).
M.J. Morelli, P.R. ten Wolde and R.J. Allen, DNA looping provides stability and robustness to the bacteriophage λ switch, PNAS 106, 8101-8106 (2009).
F. Tostevin and P.R. ten Wolde, Mutual information between input and output trajectories of biochemical networks, Physical Review Letters 102, 218101 1-4 (2009).
S.B. van Albada and P.R. ten Wolde, Differential affinity and catalytic activity of CheZ in E. coli chemotaxis, PLoS Computational Biology 5, e1000378 1-13 (2009).

Article(s) published in 2008

M.J. Morelli, R.J. Allen, S. Tanase-Nicola and P.R. ten Wolde, Eliminating fast reactions in stochastic simulations of biochemical networks : a bistable genetic switch, Journal of Chemical Physics 128, 045105 1--13 (2008).
M.J. Morelli, S. Tanase-Nicola, R.J. Allen and P.R. ten Wolde, Reaction coordinates for the flipping of genetic switches, Biophys. J. 94, 3413--3423 (2008).
M.J. Morelli and P.R. ten Wolde, Reaction Brownian dynamics and the effect of spatial fluctuations on the gain of a push-pull network, Journal of Chemical Physics 129, 054112 1--11 (2008).
S. Tanase-Nicola and P.R. ten Wolde, Regulatory control and the costs and benefits of biochemical noise, PLoS Computational Biology 4, e1000125 1--13 (2008).
R.J. Allen, C. Valeriani, S. Tanase-Nicola, P.R. ten Wolde and D. Frenkel, Homogeneous nucleation under shear in a two-dimensional ising model : cluster growth, coalescence and breakup, Journal of Chemical Physics 129, 134704 1--11 (2008).
R. Hermsen, P.R. ten Wolde and S. Teichmann, Chance and necessity in chromosomal gene distributions, Trends in Genetics 24, 216--219 (2008).

Article(s) published in 2007

F. Tostevin, P.R. ten Wolde and M. Howard, Fundamental limits to position determination by concentration gradients, PLoS Computational Biology 3, e78 0763-0771 (2007).
C. Valeriani, R.J. Allen, M.J. Morelli, D. Frenkel and P.R. ten Wolde, Computing stationary distributions in equilibrium and nonequilibrium systems with forward flux sampling, Journal of Chemical Physics 127, 114109 1--11 (2007).
S.B. van Albada and P.R. ten Wolde, Enzyme localization can drastically affect signal amplification in signal transduction pathways, PLoS Computational Biology 3, e195 1--10 (2007).
J.S. van Zon, D.K. Lubensky, P.R.H. Altena and P.R. ten Wolde, An allosteric model of circadian KaiC phosphorylation, PNAS 104, 7420--7425 (2007).
Z. Qin, H.L. Tepper and G.A. Voth, Effect of membrane environment on proton permeation through gramicidin A channels, Journal of Physical Chemistry B 111, 9931--9939 (2007).

Article(s) published in 2006

R.J. Allen, D. Frenkel and P.R. ten Wolde, Simulating rare events in equilibrium or nonequilibrium stochastic systems, Journal of Chemical Physics 124, 024102 1--16 (2006).
Y. Wu, H.L. Tepper and G.A. Voth, Flexible simple point-charge water model with improved liquid-state properties, Journal of Chemical Physics 124, 024503 1--12 (2006).
R.J. Allen, D. Frenkel and P.R. ten Wolde, Forward flux sampling-type schemes for simulating rare events: efficiency analysis, Journal of Chemical Physics 124, 194111 1--17 (2006).
S. Tanase-Nicola, P.B. Warren and P.R. ten Wolde, Signal detection, modularity, and the correlation between extrinsic and intrinsic noise in biochemical networks, Physical Review Letters 97, 068102 1--4 (2006).
P.B. Warren, S. Tanase-Nicola and P.R. ten Wolde, Exact results for noise power spectra in linear biochemical reaction networks, Journal of Chemical Physics 125, 144904 1--11 (2006).
J.S. van Zon, M.J. Morelli, S. Tanase-Nicola and P.R. ten Wolde, Diffusion of transcription factors can drastically enhance the noise in gene expression, Biophys. J. 91, 4350--4367 (2006).
P.R. ten Wolde and S. Tanase-Nicola, Pass on the message, Nature Physics 2, 371--372 (2006).
R. Hermsen, S.J. Tans and P.R. ten Wolde, Transcriptional regulation by competing transcription factor modules, PLoS Computational Biology 2, e164 1-9 (2006).

Article(s) published in 2005

M. Howard and P.R. ten Wolde, Finding the center reliably: robust patterns of developmental gene expression, Physical Review Letters 95, 208103 1--4 (2005).
R.J. Allen, P.B. Warren and P.R. ten Wolde, Sampling rare switching events in biochemical networks, Physical Review Letters 94, 018104 1--4 (2005).
J.S. van Zon and P.R. ten Wolde, Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics, Physical Review Letters 94, 128103 1--4 (2005).
D. Moroni, P.R. ten Wolde and P.G. Bolhuis, Interplay between structure and size in a critical crystal nucleus, Physical Review Letters 94, 235703 1--4 (2005).
J.S. van Zon and P.R. ten Wolde, Green's-function reaction dynamics: a particle-based approach for simulating biochemical networks in time and space, Journal of Chemical Physics 123, 234910 1--16 (2005).
P.B. Warren and P.R. ten Wolde, Chemical models of genetic toggle switches, Journal of Physical Chemistry B 109, 6812--6823 (2005).
R.J. Allen, P.B. Warren and P.R. ten Wolde, Genen als moleculaire (sub)microprocessoren, Nederlands Tijdschrift voor Natuurkunde 71, 188--191 (2005).

Article(s) published in 2004

P.B. Warren and P.R. ten Wolde, Enhancement of the stability of genetic switches by overlapping upstream regulatory domains, Physical Review Letters 92, 128101 1--4 (2004).
P.B. Warren and P.R. ten Wolde, Statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli, Journal of Molecular Biology 342, 1379--1390 (2004).

Article(s) published in 2003

N. Combe, T. Vlugt, P.R. ten Wolde and D. Frenkel, Dynamic pruned-enriched Rosenbluth method., Molecular Physics 101, 1675--1682 (2003).

Article(s) published in 2002

P.R. ten Wolde and D. Chandler, Drying-induced hydrophobic polymer collapse, PNAS 99, 6519--7186 (2002).
S.A. Auer, P.R. ten Wolde and D. Frenkel, Computersimulaties onthullen mechanisme van kristalnucleatie, Nederlands Tijdschrift voor Natuurkunde 68, 50--54 (2002).
P.R. ten Wolde, Hydrophobic interactions: an overview, Journal of Physics: Condensed Matter 14, 9445--9460 (2002).

Article(s) published in 1999

P.R. ten Wolde and D. Frenkel, Enhanced protein crystallization around the metastable critical point, Theoretical Chemistry Accounts 101, 205-208 (1999).
P.R. ten Wolde, D.W. Oxtoby and D. Frenkel, Chain formation in homogeneous gas-liquid nucleation of polar fluids, Journal of Chemical Physics 111, 4762-4773 (1999).
P.R. ten Wolde and D. Frenkel, Homogeneous nucleation and the Ostwald step rule, Physical Chemistry Chemical Physics 1, 2191-2196 (1999).
P.R. ten Wolde, M.J. Ruiz-Montero and D. Frenkel, Numerical calculation of the rate of homogeneous gas-liquid nucleation in a Lennard-Jones system, Journal of Chemical Physics 110, 1591-1599 (1999).

Article(s) published in 1998

P.R. ten Wolde and D. Frenkel, Numerical study of gas-liquid nucleation in partially miscible binary mixtures, Journal of Chemical Physics 109, 9919-9927 (1998).
P.R. ten Wolde and D. Frenkel, Computer simulation study of gas-liquid nucleation in a Lennard-Jones system, Journal of Chemical Physics 109, 9901-9918 (1998).
P.R. ten Wolde, D.W. Oxtoby and D. Frenkel, Coil-globule transition in gas-liquid nucleation of polar fluids, Physical Review Letters 81, 3695-3698 (1998).

Article(s) published in 1997

P.R. ten Wolde and D. Frenkel, Enhancement of protein crystal nucleation by critical density fluctuations, Science 277, 1975-1978 (1997).

Article(s) published in 1996

P.R. ten Wolde, M.J. Ruiz-Montero and D. Frenkel, Simulation of homogeneous crystal nucleation close to coexistence, Faraday Discuss. 104, 93-110 (1996).
P.R. ten Wolde, M.J. Ruiz-Montero and D. Frenkel, Numerical calculation of the rate of crystal nucleation in a Lennard-Jones system at moderate undercooling, Journal of Chemical Physics 104, 9932-9947 (1996).

Article(s) published in 1995

P.R. ten Wolde, M.J. Ruiz-Montero and D. Frenkel, Numerical evidence for bcc ordering at the surface of a critical fcc nucleus, Physical Review Letters 75, 2714-2717 (1995).