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Paolo De Los Rios

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Publications associées (89)

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A dynamical study of antibody-antigen encounter reactions

Paolo De Los Rios, Francesco Piazza

The effects of internal dynamics in diffusion-driven encounters between macro-molecules represent a problem of broad relevance in molecular biology. In this view, we investigate a typical antigen-antibody reaction chain, based on a coarse-grained mechanica ...

2007

Existence, cost and robustness of spatial small-world networks

Thomas Petermann, Paolo De Los Rios

Small-world networks embedded in Euclidean space represent useful cartoon models for a number of real systems such as electronic circuits, communication systems, the large-scale brain architecture and others. Since the small-world behavior relies on the pr ...

World Scientific Publishing2007

Spectral coarse graining of complex networks

Paolo De Los Rios, David Gfeller

Reducing the complexity of large systems described as complex networks is key to understanding them and a crucial issue is to know which properties of the initial system are preserved in the reduced one. Here we use random walks to design a coarse graining ...

American Physical Society2007

ScienceWISE: Topic Modeling over Scientific Literature Networks

Paolo De Los Rios, Andrea Martini, Alessio Vincenzo Cardillo

We provide an up-to-date view on the knowledge management system ScienceWISE (SW) and address issues related to the automatic assignment of articles to research topics. So far, SW has been proven to be an effective platform for managing large volumes of te ...

2017

Explaining the length threshold of polyglutamine aggregation

Marc Hafner, Paolo De Los Rios

The existence of a length threshold, of about 35 residues, above which polyglutamine repeats can give rise to aggregation and to pathologies, is one of the hallmarks of polyglutamine neurodegenerative diseases such as Huntington's disease. The reason why s ...

2012

On the origin of the boson peak in globular proteins

Paolo De Los Rios, Francesco Piazza

We study the boson peak phenomenology experimentally observed in globular proteins by means of elastic network models. These models are suitable for an analytic treatment in the framework of Euclidean random matrix theory, whose predictions can be numerica ...

Taylor & Francis2007

Spectral coarse graining and synchronization in oscillator networks

Paolo De Los Rios, David Gfeller

Coarse graining techniques offer a promising alternative to large-scale simulations of complex dynamical systems, as long as the coarse-grained system is truly representative of the initial one. Here, we investigate how the dynamical properties of oscillat ...

American Physical Society2008

Minimal Model for Carnot Efficiency at Maximum Power

Paolo De Los Rios, Shiling Liang

Carnot efficiency sets a fundamental upper bound on the heat engine efficiency, attainable in the quasistatic limit, albeit at the cost of completely sacrificing power output. Here, we present a minimal heat engine model that can attain Carnot efficiency w ...

2025

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

Paolo De Los Rios, Alessandro Barducci

Cells possess remarkable control of the folding and entanglement topology of long and flexible chromosomal DNA molecules. It is thought that structural maintenance of chromosome (SMC) protein complexes play a crucial role in this, by organizing long DNAs i ...

2019

Relief of ParB autoinhibition by parS DNA catalysis and recycling of ParB by CTP hydrolysis promote bacterial centromere assembly

Paolo De Los Rios, Stefano Zamuner

Three-component ParABS systems are widely distributed factors for plasmid partitioning and chromosome segregation in bacteria. ParB acts as adaptor protein between the 16-base pair centromeric parS DNA sequences and the DNA segregation proteins ParA and Sm ...

AMER ASSOC ADVANCEMENT SCIENCE2021

CERT1 mutations perturb human development by disrupting sphingolipid homeostasis

Paolo De Los Rios, Bruno Lemaitre, Evelyne Ruchti, Sylvia Ho, Anthony Vocat, Marine Van Campenhoudt, Samuel Rommelaere, Greta Limoni, Stefano Zamuner, Giovanni D'Angelo, Laura Capolupo, Charlotte Julie Caroline Gehin, Samuel Sagar Kumar, Huixin Guo

Neural differentiation, synaptic transmission, and action potential propagation depend on membrane sphingolipids, whose metabolism is tightly regulated. Mutations in the ceramide transporter CERT (CERT1), which is involved in sphingolipid biosynthesis, are ...

American Society for Clinical Investigation2023

Ant behavioral maturation is mediated by a stochastic transition between two fundamental states

Paolo De Los Rios, Matthias Rüegg

The remarkable ecological success of social insects is often attributed to their advanced division of labor, which is closely associated with temporal polyethism in which workers transition between different tasks as they age. Young nurses are typically fo ...

CELL PRESS2021

The kinetic parameters and energy cost of the Hsp70 chaperone as a polypeptide unfoldase

Paolo De Los Rios

Hsp70-Hsp40-NEF and possibly Hsp100 are the only known molecular chaperones that can use the energy of ATP to convert stably pre-aggregated polypeptides into natively refolded proteins. However, the kinetic parameters and ATP costs have remained elusive be ...

Nature Publishing Group2010

Dissipation-driven selection of states in non-equilibrium chemical networks

Paolo De Los Rios, Francesco Piazza, Shiling Liang, Daniel Maria Busiello

Life has most likely originated as a consequence of processes taking place in non-equilibrium conditions (e.g. in the proximity of deep-sea thermal vents) selecting states of matter that would have been otherwise unfavorable at equilibrium. Here we present ...

2021

Phase boundaries promote chemical reactions through localized fluxes

Paolo De Los Rios, Alexandra Shelest, Hugo Camille Valentin Le Roy

One of the hypothesized functions of biomolecular condensates is to act as chemical reactors, where chemical reactions can be modulated, i.e., accelerated or slowed down, while substrate molecules enter and products exit from the condensate. Similarly, the ...

2025

ABC transporters are billion-year-old Maxwell Demons

Paolo De Los Rios, Solange Marie Flatt, Stefano Zamuner, Daniel Maria Busiello

ATP-Binding Cassette (ABC) transporters are a broad family of biological machines, found in most prokaryotic and eukaryotic cells, performing the crucial import or export of substrates through both plasma and organellar membranes, and maintaining a steady ...

NATURE PORTFOLIO2023

Vibrational entropy and the structural organization of proteins

Paolo De Los Rios, Francesco Piazza

In this paper we analyze the vibrational spectra of a large ensemble of non-homologous protein structures by means of a novel tool, that we coin Hierarchical Network Model (HNM). Our coarse-grained scheme accounts for the intrinsic heterogeneity of force c ...

2010

Hyperplectonemes: A Higher Order Compact and Dynamic DNA Self-Organization

Giovanni Dietler, Paolo De Los Rios, Fabrizio Benedetti, Giovanni Longo, Aleksandre Japaridze

Bacterial chromosome has a compact structure that dynamically changes its shape in response to bacterial growth rate and growth phase. Determining how chromatin remains accessible to DNA binding proteins, and transcription machinery is crucial to understan ...

American Chemical Society2017

Self-organization of parS centromeres by the ParB CTP hydrolase

Paolo De Los Rios, Stefano Zamuner

ParABS systems facilitate chromosome segregation and plasmid partitioning in bacteria and archaea. ParB protein binds centromeric parS DNA sequences and spreads to flanking DNA. We show that ParB is an enzyme that hydrolyzes cytidine triphosphate (CTP) to ...

American Association for the Advancement of Science2019

Molecular dissection of amyloid disaggregation by human HSP70

Paolo De Los Rios, Alessandro Barducci

The molecular steps that lead to the disaggregation of amyloid fibrils are shown to involve the synergistic action of HSP70 and its co-chaperones DNAJB1 and HSP110. ...

NATURE RESEARCH2020