Publications Biochemical Networks
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). |