Biochemical Networks

Cellular Information Transmission

1. Malaguti, G. and P. R. ten Wolde, Theory for the Optimal Detection of Time-varying Signals in Cell Sensing Systems, eLife 2021;10:e62574
2. J.M. Poulton, P.R. ten Wolde and T.E. Ouldridge, Nonequilibrium correlations in minimal dynamical models of polymer copying, PNAS 116, 6: 1946-1951 (2019)
3. T.E. Ouldridge and P.R. ten Wolde, Fundamental costs in the production and destruction of persistent polymer copies, Phys.Rev.Lett. 118, Article number: 158103: 1-5 (2017)
4. T.E. Ouldridge, C.C. Govern and P.R. ten Wolde, Thermodynamics of Computational Copying in Biochemical Systems, Phys. Rev. X 7, 2, Article number: 021004: 1-13 (2017)
5. N.B. Becker, A. Mugler and P.R. ten Wolde, Optimal Prediction by Cellular Signaling Networks, Phys.Rev.Lett. 115, 25, Article number: 258103: 1-5 (2015)
6. C.C. Govern and P.R. ten Wolde, Energy Dissipation and Noise Correlations in Biochemical Sensing, Phys.Rev.Lett. 113, 25, Article number: 258102: 1-5 (2014)
7. C.C. Govern and P.R. ten Wolde, Optimal resource allocation in cellular sensing systems, PNAS 111, 49: 17486-17491 (2014)

Circadian Rhythms

1. M. Monti, D.K. Lubensky and P.R. ten Wolde, Robustness of Clocks to Input Noise, Phys.Rev.Lett. 121, (7) 078101: 1-6 (2018)
2. J. Paijmans, D.K. Lubensky and P.R. ten Wolde, A thermodynamically consistent model of the post-translational Kai circadian clock, PLoS Comput. Biol. 13, 3, Article number: e1005415: 1-43 (2017)
3. J. Paijmans, M. Bosman, P.R. ten Wolde and D.K. Lubensky, Discrete gene replication events drive coupling between the cell cycle and circadian clocks, PNAS 113, 15: 4063-4068 (2016)

Force Generation By Cytoskeletal Systems

1. H. Wierenga and P.R. ten Wolde, Diffusible Cross-linkers Cause Superexponential friction Forces, Phys.Rev.Lett. 125, 078101: 1-6 (2020)
2. M. Braun, Z. Lansky, A. Szuba, A. Zelena, F.W. Schwarz, A. Mitra, M. Gao, A. Lüdecke, P.R. ten Wolde and S. Diez, Changes in microtubule Overlap length regulate kinesin-14-driven microtubule sliding, Nature Chem. Biol. 13, 12: 1245-1252 (2017)
3. Z. Lansky, M. Braun, A. Lüdecke, M. Schlierf, P.R. ten Wolde, M.E. Janson and S. Diez, Diffusible Crosslinkers Generate Directed Forces in Microtubule Networks, Cell 160, 6: 1159-1168 (2015)

Development New Computational Techniques

Green’s Function Reaction Dynamics (GFRD)

1. T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker, K. Kaizu, K. Takahashi, M. Dogterom and P.R. ten Wolde, eGFRD in all dimensions, J. Chem. Phys. 150, 5: 054108: 1-24 (2019)
2. A. Vijaykumar, T.E. Ouldridge, P.R. ten Wolde and P.G. Bolhuis, Multiscale simulations of anisotropic particles combining molecular dynamics and Green’s function reaction dynamics, J. Chem. Phys. 146, 11, Article number: 114106: 1-12 (2017)
3. A. Vijaykumar, P.G. Bolhuis and P.R. ten Wolde, Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations, J. Chem. Phys. 143, 21, Article number: 214102: 1-12 (2015)
4. K. Takahashi, S. Tanase-Nicola and P.R. ten Wolde, Spatio-temporal correlations can drastically change the response of a MAPK pathway, PNAS 107, 6: 2473-2478 (2010)
5. 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, Phys.Rev.Lett. 94, Article number: 128103: 1-4 (2005)

Forward Flux Sampling (FFS)

1. S. Hussain and A. Haji-Akbari, Studying rare events using forward flux sampling: Recent breakthroughs and future outlook, J. Chem. Phys. 152, 060901 (2020) (article from the Haji-Akbari group with an excellent overview of FFS applications)
2. Y. Li and P.R. ten Wolde, Shape Transformations of Vesicles Induced by Swim Pressure, Phys.Rev.Lett. 123, 14: 148003: 1-6 (2019)
3. N.B. Becker, R.J. Allen and P.R. ten Wolde, Non-Stationary Forward Flux Sampling, J. Chem. Phys. 136, Article number: 174118: 1-18 (2012)
4. R.J. Allen, C. Valeriani and P.R. ten Wolde, Forward flux sampling for rare event simulations, J. Phys.: Condens. Matter 21, Article number: 463102: 1-21 (2009)
5. R.J. Allen, P.B. Warren and P.R. ten Wolde, Sampling rare switching events in biochemical networks, Phys.Rev.Lett. 94, Article number: 18104: 1-4 (2005)