Related papers: Enzyme localization can drastically affect signal …
This paper considers the capacity of a diffusion-based molecular communication link assuming the receiver uses chemical reactions. The key contribution is we show that enzymatic reaction cycles, which is a class of chemical reactions…
Liquid-liquid phase separation has emerged as a fundamental mechanism underlying intracellular organization, with evidence for it being reported in numerous different systems. However, there is a growing concern regarding the lack of…
Optimizing information transmission across a network is an essential task for controlling and manipulating generic information-processing systems. Here, we show how topological amplification effects in scale-free networks of signaling…
Site-specific transcription factors (TFs) bind to their target sites on the DNA, where they regulate the rate at which genes are transcribed. Bacterial TFs undergo facilitated diffusion (a combination of 3D diffusion around and 1D random…
During cell migration, cells become polarized, change their shape, and move in response to various internal and external cues. Cell polarization is defined through the spatio-temporal organization of molecules such as PI3K or small GTPases,…
Optical tracking in vivo experiments reveal that diffusion of particles in biological cells is strongly enhanced in the presence of ATP and the experimental data for animal cells could previously be reproduced within a phenomenological…
It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a…
We propose a minimal mathematical model to explain long-range coordination of dynamics of multiple cells in epithelial spreading, which may be induced, under different conditions, by a chemical signal, or mechanical stress, or both. The…
T1 transitions, which are localised cell rearrangements, play an important role in the fluidization of epithelial monolayers. Using a multi-phase field model and an active elastic solid model, we show that although each cell undergoes T1…
The simulation of the metabolism in mammalian cells becomes a severe problem if spatial distributions must be taken into account. Especially the cytoplasm has a very complex geometric structure which cannot be handled by standard…
Biological signaling is imagined as a combination of activation and transport. The former is triggered by local molecular interactions and the latter is the result of molecular diffusion. However, other fundamental physical principles of…
The uplink of a wireless network with base stations distributed according to a Poisson Point Process (PPP) is analyzed. The base stations are assumed to have a large number of antennas and use linear minimum-mean-square-error (MMSE) spatial…
A network is called localizable if the positions of all the nodes of the network can be computed uniquely. If a network is localizable and embedded in plane with generic configuration, the positions of the nodes may be computed uniquely in…
Signaling events in eukaryotic cells are often guided by a scaffolding protein. Scaffold proteins assemble multiple proteins in a spatially localized signaling complex and exert numerous physical effects on signaling pathways. To study…
Flow of particles of two different species through a narrow channel with solely two discrete spatial positions is analyzed with respect to the species' capability to cooperate or compete for transport. In contrast to mean field approaches,…
Cells are known to utilize biochemical noise to probabilistically switch between distinct gene expression states. We demonstrate that such noise-driven switching is dominated by tails of probability distributions and is therefore…
Experiments have found that diffusion in metabolically active cells is much faster than in dormant cells, especially for large particles. However, the mechanism of this size-dependent diffusion enhancement in living cells is still unclear.…
Several enzymes exhibit enhanced diffusion in the presence of a substrate. One explanation of this enhancement arises from fluctuating dimer models, which suggest that enzymes have a higher diffusion constant when interacting with…
In a diversity of physiological contexts, eukaryotic cells adhere to an extracellular matrix (ECM), a disordered network with complex nonlinear mechanics. Such cells can perform mechanosensation: using local force probing they can measure…
Enzymes have been recently found to exhibit enhanced diffusion due to their catalytic activities. A recent experiment [C. Riedel et al., Nature 517, 227 (2015)] has found evidence that suggests this phenomenon might be controlled by the…