Luca Ciandrini

Documents

Publications

Incoherent feedback from coupled amino acids and ribosome pools generates damped oscillations in growing E. coli

Rossana Droghetti , Philippe Fuchs , Ilaria Iuliani , Valerio Firmano , Giorgio Tallarico et al.

Nature Communications, 2025, 16 (1), pp.3063. ⟨10.1038/s41467-025-57789-4⟩

Article dans une revue hal-05406272v1

How total mRNA influences cell growth

Ludovico Calabrese , Luca Ciandrini , Marco Cosentino Lagomarsino

Proceedings of the National Academy of Sciences of the United States of America, 2024, 121 (21), ⟨10.1073/pnas.2400679121⟩

Article dans une revue hal-04945737v1

Optimal control of ribosome population for gene expression under periodic nutrient intake

Clément Soubrier , Eric Foxall , Luca Ciandrini , Khanh Dao Duc

Journal of the Royal Society Interface, 2024, 21 (212), pp.20230652. ⟨10.1098/rsif.2023.0652⟩

Article dans une revue hal-04789156v1

TASEPy: A Python-based package to iteratively solve the inhomogeneous exclusion process

Luca Ciandrini , Richmond Crisostomo , Juraj Szavits-Nossan

SciPost Physics Codebases, 2023, pp.22. ⟨10.21468/SciPostPhysCodeb.22⟩

Article dans une revue hal-04945758v1

Protein degradation sets the fraction of active ribosomes at vanishing growth

Ludovico Calabrese , Jacopo Grilli , Matteo Osella , Christopher Kempes , Marco Cosentino Lagomarsino et al.

PLoS Computational Biology, 2022, 18 (5), pp.e1010059. ⟨10.1371/journal.pcbi.1010059⟩

Article dans une revue hal-03980452v1

Inferring efficiency of translation initiation and elongation from ribosome profiling

Juraj Szavits-Nossan , Luca Ciandrini

Nucleic Acids Research, 2020, 48, pp.9478 - 9490. ⟨10.1093/nar/gkaa678⟩

Article dans une revue hal-03980481v1

Rational programming of history-dependent logic in cellular populations

Ana Zúñiga , Sarah Guiziou , Pauline Mayonove , Zachary Ben Meriem , Miguel Camacho et al.

Nature Communications, 2020, 11 (1), pp.4758. ⟨10.1038/s41467-020-18455-z⟩

Article dans une revue inserm-02952457v1

Unraveling Molecular Interactions in Liquid–Liquid Phase Separation of Disordered Proteins by Atomistic Simulations

Matteo Paloni , Rémy Bailly , Luca Ciandrini , Alessandro Barducci

Journal of Physical Chemistry B, 2020, 124 (41), pp.9009-9016. ⟨10.1021/acs.jpcb.0c06288⟩

Article dans une revue hal-03334992v1

Driven transport on a flexible polymer with particle recycling: A model inspired by transcription and translation

Lucas Dias Fernandes , Luca Ciandrini

Physical Review E , 2019, 99 (5), pp.052409. ⟨10.1103/PhysRevE.99.052409⟩

Article dans une revue hal-01743450v1

An equilibrium model for ribosome competition

Pascal Rogalla , Timothy Rudge , Luca Ciandrini

Physical Biology, 2019, 17 (1), pp.015002. ⟨10.1088/1478-3975/ab4fbc⟩

Article dans une revue hal-04945783v1

Exclusion process subject to conformational size changes

Yvan Rousset , Luca Ciandrini , Norbert Kern

SciPost Physics, 2019, 6 (6), pp.077. ⟨10.21468/SciPostPhys.6.6.077⟩

Article dans une revue hal-04773708v1

Power series solution of the inhomogeneous exclusion process

Juraj Szavits-Nossan , M. Carmen Romano , Luca Ciandrini

Physical Review E : Statistical, Nonlinear, and Soft Matter Physics [2001-2015], 2018, 97, pp.052139. ⟨10.1103/PhysRevE.97.052139⟩

Article dans une revue hal-01737998v1

Deciphering mRNA Sequence Determinants of Protein Production Rate

Juraj Szavits-Nossan , Luca Ciandrini , M. Carmen Romano

Physical Review Letters, 2018, 120, pp.128101. ⟨10.1103/PhysRevLett.120.128101⟩

Article dans une revue hal-01585251v1

Gene length as a regulator for ribosome recruitment and protein synthesis: theoretical insights

Lucas Dias Fernandes , Alessandro de Moura , Luca Ciandrini

Scientific Reports, 2017, 7, pp.17409. ⟨10.1038/s41598-017-17618-1⟩

Article dans une revue hal-01585262v1

Identification of the mRNA targets of tRNA-specific regulation using genome-wide simulation of translation.

Barbara Gorgoni , Luca Ciandrini , Matthew R Mcfarland , M Carmen Romano , Ian Stansfield

Nucleic Acids Research, 2016, 44 (19), pp.9231-9244. ⟨10.1093/nar/gkw630⟩

Article dans une revue hal-02060317v1

Stepping and crowding of molecular motors: statistical kinetics from an exclusion process perspective

Luca Ciandrini , M. Carmen Romano , Andrea Parmeggiani

Biophysical Journal, 2014, 107 (5), pp.1176-1184. ⟨10.1016/j.bpj.2014.07.012⟩

Article dans une revue hal-01061351v1

Motor proteins traffic regulation by supply-demand balance of resources

Luca Ciandrini , Izaak Neri , Jean-Charles Walter , Olivier Dauloudet , Andrea Parmeggiani

Physical Biology, 2014, 11 (5), pp.056006. ⟨10.1088/1478-3975/11/5/056006⟩

Article dans une revue hal-01063014v1

Transport on a lattice with dynamical defects

Francesco Turci , Andrea Parmeggiani , Estelle Pitard , M. Carmen Romano , Luca Ciandrini

Physical Review E : Statistical, Nonlinear, and Soft Matter Physics [2001-2015], 2013, 87 (1), pp.012705. ⟨10.1103/PhysRevE.87.012705⟩

Article dans une revue hal-00816492v1

Biologically relevant finite-size effects in a driven lattice gas with particle pausing and dynamical defects

Johannes Keisers , Lorenzo Vito Dal Zovo , Norbert Kern , Luca Ciandrini

2024

Pré-publication, Document de travail hal-04945892v1

Ribosome economics: Ribosome usage in translation initiation and elongation

Luca Ciandrini

Reverse mathematical methods for reconstructing molecular dynamics in single cell, Centro di Ricerca Matematica Ennio de Giorgi, Oct 2018, Pisa, Italy

Communication dans un congrès hal-01935528v1

Codon bias and cost of ribosome usage

Luca Ciandrini

Statistical physics of cells and genomes, Marco Cosentino Lagomarsino (CNRS/Sorbonne; Paris and IFOM Milan), May 2018, Alghero, Italy

Communication dans un congrès hal-01938405v1

Driven transport on a polymer: a model inspired by transcription and translation

Luca Ciandrini

Rencontre de Physique Statistique, Jan 2018, Paris, France

Communication dans un congrès hal-01938456v1

Deciphering mRNA sequence determinants of protein production rate

Luca Ciandrini

Biophysics: Today and Beyond, Joint Meeting GRISBI; Labex EpiGenMed; Labex NUMEV, Apr 2018, Montpellier, France

Communication dans un congrès hal-01938431v1

Ribosome Economics: Ribosome usage, translation initiation and elongation

Luca Ciandrini

Integrative Cell Models for Disease Intervention, Banff International Research Station, Jun 2018, Banff, Canada

Communication dans un congrès hal-01938095v1

Gene length as a regulator for ribosome recruitment and protein synthesis: theoretical insights

Luca Ciandrini

Meeting of the International Physics of Living Systems (iPoLS) Network, Jun 2017, Paris, France

Communication dans un congrès hal-01938945v1

A quantitative view on mRNA translation: the relative role of initiation and elongation

Luca Ciandrini

Quantitative Laws II: Physiology, ecology, interaction structures, collective behavior, Jun 2016, Como, Italy

Communication dans un congrès hal-01939004v1

Cellular Tradeoff between Resources and Demand in gene Expression

Luca Ciandrini

Como Pohskrow, Oct 2016, Como, Italy

Communication dans un congrès hal-01939053v1

Molecular Motors with a Stepping Cycle: From Theory to Experiments

Luca Ciandrini

Traffic and Granular Flow '13, Sep 2013, Julich, Germany. pp.619-627, ⟨10.1007/978-3-319-10629-8_70⟩

Communication dans un congrès hal-01103149v1

Transcript length as a main determinant of mRNA translation efficiency

Luca Ciandrini

Quantitative Methods in Gene Regulation III, Dec 2015, Cambridge, United Kingdom

Communication dans un congrès hal-01939067v1

Ribosome recycling as a main determinant of experimental ribosome densities

Luca Ciandrini

EMBO fellows’ meeting, Jun 2015, Heidelberg, Germany

Communication dans un congrès hal-01939095v1

Crowded mRNAs and translation efficiency: from theory to experiments and speculations

Luca Ciandrini

Chromosome Structure and Function: Experiments and Modeling, SISSA, Oct 2013, Trieste, Italy

Communication dans un congrès hal-01939133v1

Stepping and crowding ofmolecular motors: from theory to mRNA translation

Luca Ciandrini

Paris Biological Physics Community Day, Dec 2013, Paris, France

Communication dans un congrès hal-01939123v1

Fluctuations and cooperative properties of molecular motors: from theory to experiments

Luca Ciandrini

Traffic and Granular Flow '13, Sep 2013, Juelich, Germany

Communication dans un congrès hal-01939150v1

Quantifying gene expression at the level of translation

Luca Ciandrini

Quantitative Laws of Genome Evolution, Jun 2013, Como, Italy

Communication dans un congrès hal-01939022v1

Predicting the steady-state rate of mRNA translation in protein biosynthesis

Juraj Szavits-Nossan , Luca Ciandrini , Carmen Maria Romano

19th IUPAB congress and 11th EBSA congress, Jul 2017, Edinburgh, United Kingdom

Poster de conférence hal-01938988v1

Genelength as a regulator for ribosome recruitmentand protein synthesis: theoretical insights

Luca Ciandrini

Protein Synthesis and Translational Control, Sep 2017, Heidelberg, Germany

Poster de conférence hal-01938973v1

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