Phase separation provides a mechanism to reduce noise in cells

A Klosin, F Oltsch, T Harmon, A Honigmann, F Jülicher… - Science, 2020 - science.org
Expression of proteins inside cells is noisy, causing variability in protein concentration
among identical cells. A central problem in cellular control is how cells cope with this …

Geocentrism vs genocentrism: theories without metaphors, metaphors without theories

G Longo, M Mossio - Interdisciplinary Science Reviews, 2020 - journals.sagepub.com
Through the comparison between two major, long-lasting theoretical frameworks–
geocentrism and genocentrism–we discuss the different epistemological role played by …

Accurate dynamics from self-consistent memory in stochastic chemical reactions with small copy numbers

M Harsh, P Sollich - Journal of Physics A: Mathematical and …, 2023 - iopscience.iop.org
We present a method that captures the fluctuations beyond mean field in chemical reactions
in the regime of small copy numbers and hence large fluctuations, using self-consistently …

On the design of a PID bio-controller with set point weighting and filtered derivative action

E Alexis, L Cardelli… - IEEE Control Systems …, 2022 - ieeexplore.ieee.org
Effective and robust regulation of biomolecular processes is crucial for designing reliable
synthetic bio-devices functioning in uncertain and constantly changing biological …

EIciRNA‐mediated gene expression: tunability and bimodality

Q Hu, T Zhou - FEBS letters, 2018 - Wiley Online Library
Biological experiments have verified that EIciRNAs (a class of circRNA) produced from pre‐
mRNA can regulate gene expression, but the effect of regulation remains unexplored. Here …

Syntax-guided optimal synthesis for chemical reaction networks

L Cardelli, M Češka, M Fränzle, M Kwiatkowska… - … Aided Verification: 29th …, 2017 - Springer
We study the problem of optimal syntax-guided synthesis of stochastic Chemical Reaction
Networks (CRNs) that plays a fundamental role in design automation of molecular devices …

Chemical reaction network designs for asynchronous logic circuits

L Cardelli, M Kwiatkowska, M Whitby - Natural computing, 2018 - Springer
Chemical reaction networks (CRNs) are a versatile language for describing the dynamical
behaviour of chemical kinetics, capable of modelling a variety of digital and analogue …

Biomolecular mechanisms for signal differentiation

E Alexis, CCM Schulte, L Cardelli… - Iscience, 2021 - cell.com
Cells can sense temporal changes of molecular signals, allowing them to predict
environmental variations and modulate their behavior. This paper elucidates biomolecular …

Systematic analysis of noise reduction properties of coupled and isolated feed-forward loops

S Chakravarty, A Csikász-Nagy - PLOS Computational Biology, 2021 - journals.plos.org
Cells can maintain their homeostasis in a noisy environment since their signaling pathways
can filter out noise somehow. Several network motifs have been proposed for biological …

Estimating information exchange performance of engineered cell-to-cell molecular communications: a computational approach

C Harper, M Pierobon… - IEEE INFOCOM 2018-IEEE …, 2018 - ieeexplore.ieee.org
Biological cells naturally exchange information for adapting to the environment, or even
influencing other cells. One of the latest frontiers of synthetic biology stands in engineering …