P. T. Wolde

发表

Dynamic pruned-enriched Rosenbluth method

D. Frenkel, T. Vlugt, N. Combe, 2003 .

Thermodynamics of Computational Copying in Biochemical Systems

Pieter Rein ten Wolde, Thomas E. Ouldridge, T. Ouldridge, 2015, 1503.00909.

Multiplexing oscillatory biochemical signals

W. de Ronde, P. T. Wolde, W. D. Ronde, 2013, Physical biology.

Green's-function reaction dynamics: a particle-based approach for simulating biochemical networks in time and space.

P. R. ten Wolde, P. T. Wolde, J. V. Zon, 2005, The Journal of chemical physics.

Effects of macromolecular crowding on genetic networks.

R. Allen, P. T. Wolde, M. Morelli, 2011, Biophysical journal.

Spatial-Stochastic Simulation of Reaction-Diffusion Systems

T. Sokolowski, P. T. Wolde, 2017, 1705.08669.

The Macroscopic Effects of Microscopic Heterogeneity in Cell Signaling

A. Mugler, P. T. Wolde, 2012, 1210.0104.

Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics.

P. T. Wolde, J. V. Zon, J. S. Zon, 2005 .

Coil-globule transition in gas-liquid nucleation of polar fluids

D. Frenkel, P. T. Wolde, D. Oxtoby, 1998 .

Green's Function Reaction Dynamics: a new approach to simulate biochemical networks at the particle level and in time and space

Pieter Rein ten Wolde, P. T. Wolde, J. V. Zon, 2004, q-bio/0404002.

The accuracy of telling time via oscillatory signals

Michele Monti, P. T. Wolde, Michele Monti, 2016, Physical biology.

Putting Bounds on Biochemical Noise Biochemical

P. T. Wolde, 2016 .

Putting Bounds on Biochemical Noise

P. T. Wolde, 2016 .

Numerical calculation of the rate of crystal nucleation in a Lennard‐Jones system at moderate undercooling

Pieter Rein ten Wolde, Daan Frenkel, M. J. Ruiz-Montero, 1996 .

Robust replication initiation from coupled homeostatic mechanisms

P. R. ten Wolde, P. T. Wolde, M. Berger, 2021, bioRxiv.

Enzyme Localization Can Drastically Affect Signal Amplification in Signal Transduction Pathways

P. T. Wolde, S. V. Albada, 2007, PLoS Comput. Biol..

Hydrophobic interactions: an overview

P. T. Wolde, 2002, cond-mat/0207131.

Numerical study of gas–liquid nucleation in partially miscible binary mixtures

D. Frenkel, P. T. Wolde, 1998 .

Publisher’s Note: “Eliminating fast reactions in stochastic simulations of biochemical networks: A bistable genetic switch” [J. Chem. Phys. 128, 045105 (2008)]

R. Allen, S. Tanase-Nicola, P. T. Wolde, 2008 .

Homogeneous nucleation and the Ostwald step rule

Daan Frenkel, D. Frenkel, P. T. Wolde, 1999 .

Computer simulation study of gas–liquid nucleation in a Lennard-Jones system

Daan Frenkel, D. Frenkel, P. T. Wolde, 1998 .

Transcriptional Regulation by Competing Transcription Factor Modules

Pieter Rein ten Wolde, Rutger Hermsen, Sander Tans, 2006, PLoS Comput. Biol..

Fundamental Limits to Position Determination by Concentration Gradients

Pieter Rein ten Wolde, Martin Howard, Filipe Tostevin, 2007, PLoS Comput. Biol..

Text S 1 : supplementary information for Combinatorial gene regulation using autoregulation

Pieter Rein ten Wolde, Rutger Hermsen, Bas Ursem, 2010 .

How biochemical resources determine fundamental limits in cellular sensing

P. T. Wolde, C. Govern, 2013, 1308.1449.

Molecular clustering digitizes signaling and increases fidelity

A. Mugler, P. T. Wolde, Nicola Trendel, 2015, 1511.00631.

Differential Affinity and Catalytic Activity of CheZ in E. coli Chemotaxis

Pieter Rein ten Wolde, Siebe B. van Albada, P. T. Wolde, 2009, PLoS Comput. Biol..

Synchronous Replication Initiation of Multiple Origins

P. R. ten Wolde, P. T. Wolde, M. Berger, 2023, PRX Life.

Chain formation in homogeneous gas–liquid nucleation of polar fluids

D. Frenkel, P. T. Wolde, D. Oxtoby, 1999 .

Diffusible Cross-linkers Cause Superexponential Friction Forces.

P. T. Wolde, H. Wierenga, 2019, Physical review letters.

Constriction of Actin Rings by Passive Crosslinkers.

P. R. ten Wolde, P. T. Wolde, A. Cumberworth, 2022, Physical review letters.

Diffusible Crosslinkers Generate Directed Forces in Microtubule Networks

S. Diez, P. T. Wolde, M. Schlierf, 2015, Cell.

Regulatory Control and the Costs and Benefits of Biochemical Noise

Pieter Rein ten Wolde, Sorin Tanase-Nicola, S. Tanase-Nicola, 2007, PLoS Comput. Biol..

Simulation of homogeneous crystal nucleation close to coexistence

Daan Frenkel, M. J. Ruiz-Montero, D. Frenkel, 1996 .

The Power of Being Explicit: Demystifying Work, Heat, and Free Energy in the Physics of Computation

Pieter Rein ten Wolde, Thomas E Ouldridge, Rory A. Brittain, 2018, The Energetics of Computing in Life and Machines.

Mutual Repression Enhances the Steepness and Precision of Gene Expression Boundaries

Pieter Rein ten Wolde, Thomas R. Sokolowski, Thorsten Erdmann, 2012, PLoS Comput. Biol..

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

Joris Paijmans, David K. Lubensky, Pieter Rein ten Wolde, 2016, PLoS Comput. Biol..

Numerical calculation of the rate of homogeneous gas–liquid nucleation in a Lennard-Jones system

Daan Frenkel, M. J. Ruiz-Montero, D. Frenkel, 1999 .

Energetic constraints on filament-mediated cell polarization.

P. T. Wolde, H. Wierenga, 2021, Physical review. E.

Diffusible Cross-linkers Cause Superexponential Friction Forces.

P. T. Wolde, H. Wierenga, 2019, Physical review letters.

Statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli.

P. R. ten Wolde, P. B. Warren, P. T. Wolde, 2003, Journal of molecular biology.

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

Pieter Rein ten Wolde, Alireza Mashaghi, Sander J. Tans, 2015, Scientific Reports.

Enhancement of protein crystal nucleation by critical density fluctuations.

D. Frenkel, P. R. ten Wolde, P. T. Wolde, 1997, Science.

Enzyme Localization Can Drastically Affect Signal Amplification in Signal Transduction Pathways

P. T. Wolde, Siebe B. van Albada, 2007, PLoS Comput. Biol..

Combinatorial Gene Regulation Using Auto-Regulation

R. Hermsen, P. T. Wolde, Bas Ursem, 2010, PLoS Comput. Biol..

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

F. Tostevin, P. R. ten Wolde, W. de Ronde, 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories

G. Tkačik, P. T. Wolde, Manuel Reinhardt, 2022, Physical Review X.

Predicting a noisy signal: the costs and benefits of time averaging as a noise mitigation strategy

P. T. Wolde, Age J. Tjalma, Lotte Slim, 2023, 2307.03006.

Quantitative Biology: Theory, Computational Methods, and Models

Terrence J. Sejnowski, Alan S. Perelson, Marco S. Nobile, 2018 .