53 citations · 189 across the 9 of their papers we have counts for
11 papers
Active T1 transitions in cellular networks
Charlie Duclut, Joris Paijmans, Mandar M. Inamdar +2
In amorphous solids as in tissues, neighbor exchanges can relax local stresses and allow the material to flow. In this paper, we use an anisotropic vertex model to study T1 rearran…
Coarse-grained curvature tensor on polygonal surfaces
Charlie Duclut, Aboutaleb Amiri, Joris Paijmans +1
Using concepts from integral geometry, we propose a definition for a local coarse-grained curvature tensor that is well-defined on polygonal surfaces. This coarse-grained curvature…
Nonlinear rheology of cellular networks
Charlie Duclut, Joris Paijmans, Mandar M. Inamdar +2
Morphogenesis depends crucially on the complex rheological properties of cell tissues and on their ability to maintain mechanical integrity while rearranging at long times. In this…
Distinguishing Feedback Mechanisms in Clock Models
Alexander D. Golden, Joris Paijmans, David K. Lubensky
Biological oscillators are very diverse but can be classified based on dynamical motifs such as the types of feedback loops present. The S. Elongatus circadian clock is a remarkabl…
eGFRD in all dimensions
Thomas R. Sokolowski, Joris Paijmans, Laurens Bossen +7
Biochemical reactions typically occur at low copy numbers, but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical…
Robustness of synthetic oscillators in growing and dividing cells
Joris Paijmans, David K Lubensky, Pieter Rein ten Wolde
Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. In 2000, Elowitz and Leibler showed that by r…
A Thermodynamically consistent model of the post-translational Kai circadian clock
Joris Paijmans, David K Lubensky, Pieter Rein ten Wolde
The principal pacemaker of the circadian clock of the cyanobacterium S. elongatus is a protein phosphorylation cycle consisting of three proteins, KaiA, KaiB and KaiC. KaiC forms a…
Period Robustness and Entrainability of the Kai System to Changing Nucleotide Concentrations
Joris Paijmans, David K Lubensky, Pieter Rein ten Wolde
Circadian clocks must be able to entrain to time-varying signals to keep their oscillations in phase with the day-night rhythm. On the other hand, they must also exhibit input comp…
Discrete gene replication events drive coupling between the cell cycle and circadian clocks
Joris Paijmans, Mark Bosman, Pieter Rein ten Wolde +1
Many organisms possess both a cell cycle to control DNA replication and a circadian clock to anticipate changes between day and night. In some cases, these two rhythmic systems are…
The lower bound on the precision of transcriptional regulation
Joris Paijmans, Pieter Rein ten Wolde
The diffusive arrival of transcription factors at the promoter sites on the DNA sets a lower bound on how accurately a cell can regulate its protein levels. Using results from the…
Building a linguistic corpus from bee dance data
J. J. Paijmans
This paper discusses the problems and possibility of collecting bee dance data in a linguistic \textit{corpus} and use linguistic instruments such as Zipf's law and entropy statist…