Publications

2024

Journal Articles

Valence can control the nonexponential viscoelastic relaxation of multivalent reversible gels

H. C. V. Le Roy; J. Song; D. Lundberg; A. V. Zhukhovitskiy; J. A. Johnson et al. 

Science Advances. 2024-05-15. Vol. 10, num. 20, p. eadl5056. DOI : 10.1126/sciadv.adl5056.

Autorepression of yeast Hsp70 cochaperones by intramolecular interactions involving their J-domains

M. E. Rebeaud; S. Tiwari; B. Fauvet; A. Mohr; P. Goloubinoff et al. 

Cell Stress & Chaperones. 2024-04-01. Vol. 29, num. 2, p. 338-348. DOI : 10.1016/j.cstres.2024.03.008.

2023

Journal Articles

Thermodynamic bounds on time-reversal asymmetry

S. Liang; S. Pigolotti 

Physical Review E. 2023-12-12. Vol. 108, num. 6, p. L062101. DOI : 10.1103/PhysRevE.108.L062101.

Individual and combined benefits of different nonequilibrium proofreading mechanisms

A. A. Mohr; D. M. Busiello; S. Zamuner; P. De Los Rios 

Physical Review Research. 2023-11-13. Vol. 5, num. 4, p. 043145. DOI : 10.1103/PhysRevResearch.5.043145.

Modulation of Pulsatile Left Ventricular Afterload by Renal Denervation in Heart Failure With Preserved Ejection Fraction

K-P. Rommel; S. Z. Pagoulatou; K-P. Kresoja; S. Rosch; A. R. Schoeber et al. 

Circulation-Heart Failure. 2023-10-01. Vol. 16, num. 10, p. e010543. DOI : 10.1161/CIRCHEARTFAILURE.123.010543.

ABC transporters are billion-year-old Maxwell Demons

S. Flatt; D. M. Busiello; S. Zamuner; P. de los Rios 

Communications Physics. 2023-08-08. Vol. 6, num. 1, p. 205. DOI : 10.1038/s42005-023-01320-y.

Ricca’s factors as mobile proteinaceous effectors of electrical signaling

Y-Q. Gao; P. Jimenez-Sandoval; S. Tiwari; S. Stolz; J. Wang et al. 

Cell. 2023-03-30. Vol. 186, num. 7, p. 1337-+. DOI : 10.1016/j.cell.2023.02.006.

Design of an Arabidopsis thaliana reporter line to detect heat-sensing and signaling mutants

A. Guihur; B. Bourgine; M. E. Rebeaud; P. Goloubinoff 

Plant Methods. 2023-06-08. Vol. 19, num. 1, p. 56. DOI : 10.1186/s13007-023-01033-x.

Fluctuations of entropy production of a run-and-tumble particle

P. Padmanabha; D. M. Busiello; A. Maritan; D. Gupta 

Physical Review E. 2023-01-18. Vol. 107, num. 1, p. 014129. DOI : 10.1103/PhysRevE.107.014129.

Reviews

Second Virtual International Symposium on Cellular and Organismal Stress Responses, September 8-9, 2022

P. van Oosten-Hawle; S. J. Backe; A. Ben-Zvi; D. Bourboulia; M. Brancaccio et al. 

Cell Stress & Chaperones. 2023-01-05. Vol. 28, num. 1, p. 1-9. DOI : 10.1007/s12192-022-01318-5.

Theses

Why do we need so many proteins? A physical insight into the collaboration of Hsp70 and DnaJ

A. A. Mohr / P. De Los Rios (Dir.)  

Lausanne, EPFL, 2023. 

Information Theory in Transmembrane Transport

S. M. Flatt / P. De Los Rios (Dir.)  

Lausanne, EPFL, 2023. 

2022

Journal Articles

Emergent thermophoretic behavior in chemical reaction systems

S. Liang; D. M. Busiello; P. De Los Rios 

New Journal Of Physics. 2022-12-01. Vol. 24, num. 12, p. 123006. DOI : 10.1088/1367-2630/aca556.

A fluorescent multi-domain protein reveals the unfolding mechanism of Hsp70

S. Tiwari; B. Fauvet; S. Assenza; P. De Los Rios; P. Goloubinoff 

Nature Chemical Biology. 2022-10-20. DOI : 10.1038/s41589-022-01162-9.

Mutual information in changing environments: Nonlinear interactions, out-of-equilibrium systems, and continuously varying diffusivities

G. Nicoletti; D. M. Busiello 

Physical Review E. 2022-07-29. Vol. 106, num. 1, p. 014153. DOI : 10.1103/PhysRevE.106.014153.

Information-driven transitions in projections of underdamped dynamics

G. Nicoletti; A. Maritan; D. M. Busiello 

Physical Review E. 2022-07-18. Vol. 106, num. 1, p. 014118. DOI : 10.1103/PhysRevE.106.014118.

Emergence of synergistic and competitive pathogens in a coevolutionary spreading model

F. Ghanbarnejad; K. Seegers; A. Cardillo; P. Hovel 

Physical Review E. 2022-03-21. Vol. 105, num. 3, p. 034308. DOI : 10.1103/PhysRevE.105.034308.

Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules

S. Zamuner; F. Seno; A. Trovato 

Plos One. 2022-01-27. Vol. 17, num. 1, p. e0254969. DOI : 10.1371/journal.pone.0254969.

An Efficient Signal-to-noise Approximation for Eccentric Inspiraling Binaries

L. Randall; A. Shelest; Z-Z. Xianyu 

Astrophysical Journal. 2022-01-01. Vol. 924, num. 2, p. 102. DOI : 10.3847/1538-4357/ac36c5.

Reviews

J-domain protein chaperone circuits in proteostasis and disease

R. Zhang; D. Malinverni; D. M. Cyr; P. De Los Rios; N. B. Nillegoda 

Trends In Cell Biology. 2022-12-22. Vol. 33, num. 1, p. 30-47. DOI : 10.1016/j.tcb.2022.05.004.

2021

Journal Articles

Mutual Information Disentangles Interactions from Changing Environments

G. Nicoletti; D. M. Busiello 

Physical Review Letters. 2021-11-22. Vol. 127, num. 22, p. 228301. DOI : 10.1103/PhysRevLett.127.228301.

Inducing and optimizing Markovian Mpemba effect with stochastic reset

D. M. Busiello; D. Gupta; A. Maritan 

New Journal Of Physics. 2021-10-01. Vol. 23, num. 10, p. 103012. DOI : 10.1088/1367-2630/ac2922.

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

H. Antar; Y-M. Soh; S. Zamuner; F. P. Bock; A. Anchimiuk et al. 

Science Advances. 2021-10-01. Vol. 7, num. 41, p. eabj2854. DOI : 10.1126/sciadv.abj2854.

Dissipation-Driven Selection under Finite Diffusion: Hints from Equilibrium and Separation of Time Scales

S. Liang; P. De los Rios; D. M. Busiello 

Entropy. 2021-08-01. Vol. 23, num. 8, p. 1068. DOI : 10.3390/e23081068.

Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network

A. V. Dass; T. Georgelin; F. Westall; F. Foucher; P. De los Rios et al. 

Nature Communications. 2021-05-12. Vol. 12, num. 1, p. 2749. DOI : 10.1038/s41467-021-22818-5.

Bidirectional propagation of low frequency oscillations over the human hippocampal surface

A. V. Dass; T. Georgelin; F. Westall; F. Foucher; P. De Los Rios et al. 

Nature Communications. 2021-05-12. Vol. 12, num. 1, p. 2764. DOI : 10.1038/s41467-021-22850-5.

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

T. O. Richardson; T. Kay; R. Braunschweig; O. A. Journeau; M. Ruegg et al. 

Current Biology. 2021-05-24. Vol. 31, num. 10, p. 2253-2260.e3. DOI : 10.1016/j.cub.2020.05.038.

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

D. M. Busiello; S. Liang; F. Piazza; P. De Los Rios 

Communications Chemistry. 2021-02-15. Vol. 4, num. 1, p. 16. DOI : 10.1038/s42004-021-00454-w.

Reviews

Repair or Degrade: the Thermodynamic Dilemma of Cellular Protein Quality-Control

B. Fauvet; M. E. Rebeaud; S. Tiwari; P. De Los Rios; P. Goloubinoff 

Frontiers In Molecular Biosciences. 2021-10-27. Vol. 8, p. 768888. DOI : 10.3389/fmolb.2021.768888.

2020

Journal Articles

Coarse-grained entropy production with multiple reservoirs: Unraveling the role of time scales and detailed balance in biology-inspired systems

D. M. Busiello; D. Gupta; A. Maritan 

Physical Review Research. 2020-11-19. Vol. 2, num. 4, p. 043257. DOI : 10.1103/PhysRevResearch.2.043257.

Entropy production in systems with unidirectional transitions

D. M. Busiello; D. Gupta; A. Maritan 

Physical Review Research. 2020-04-07. Vol. 2, num. 2, p. 023011. DOI : 10.1103/PhysRevResearch.2.023011.

Tighter thermodynamic bound on the speed limit in systems with unidirectional transitions

D. Gupta; D. M. Busiello 

Physical Review E. 2020-12-10. Vol. 102, num. 6, p. 062121. DOI : 10.1103/PhysRevE.102.062121.

Molecular dissection of amyloid disaggregation by human HSP70

A. S. Wentink; N. B. Nillegoda; J. Feufel; G. Ubartaite; C. P. Schneider et al. 

Nature. 2020-11-11. Vol. 587, p. 483–488. DOI : 10.1038/s41586-020-2904-6.

Computational pipeline to probe NaV1.7 gain-of-function variants in neuropathic painful syndromes

A. A. Toffano; G. Chiarot; S. Zamuner; M. Marchi; E. Salvi et al. 

Scientific Reports. 2020-10-21. Vol. 10, num. 1, p. 17930. DOI : 10.1038/s41598-020-74591-y.

Thermodynamics and kinetics of protonated merocyanine photoacids in water

C. Berton; D. M. Busiello; S. Zamuner; E. Solari; R. Scopelliti et al. 

Chemical Science. 2020. Vol. 11, num. 32, p. 8457-8468. DOI : 10.1039/D0SC03152F.

Protein Structural Information and Evolutionary Landscape by In Vitro Evolution

M. Fantini; S. Lisi; P. De Los Rios; A. Cattaneo; A. Pastore 

Molecular Biology And Evolution. 2020-04-01. Vol. 37, num. 4, p. 1179-1192. DOI : 10.1093/molbev/msz256.

Conference Papers

How Complex Molecules Could Possibly be Stable at the Dawn of Life: Out of Equilibrium Dissipation Shapes Selection

D. M. Busiello; S. Liang; P. De Los Rios 

2020-02-07. 64th Annual Meeting of the Biophysical-Society, San Diego, CA, Feb 15-19, 2020. p. 611A-611A. DOI : 10.1016/j.bpj.2019.11.3301.

Reviews

Membraneless organelles: phasing out of equilibrium

M. Hondele; S. Heinrich; P. De Los Rios; K. Weis 

Emerging Topics In Life Sciences. 2020-12-01. Vol. 4, num. 3, p. 331-342. DOI : 10.1042/ETLS20190190.

2019

Journal Articles

Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones

S. Assenza; A. S. Sassi; R. Kellner; B. Schuler; P. De Los Rios et al. 

Elife. 2019-12-17. Vol. 8, p. e48491. DOI : 10.7554/eLife.48491.

Hyperaccurate currents in stochastic thermodynamics

D. M. Busiello; S. Pigolotti 

Physical Review E. 2019-12-16. Vol. 100, num. 6, p. 060102. DOI : 10.1103/PhysRevE.100.060102.

Self-organization of parS centromeres by the ParB CTP hydrolase

Y-M. Soh; I. F. Davidson; S. Zamuner; J. Basquin; F. P. Bock et al. 

Science. 2019. Vol. 366, num. 6469, p. 1129-1133. DOI : 10.1126/science.aay3965.

Mechanics of Allostery: Contrasting the Induced Fit and Population Shift Scenarios

R. Ravasio; S. M. Flatt; L. Yan; S. Zamuner; C. Brito et al. 

Biophysical Journal. 2019-11-19. Vol. 117, num. 10, p. 1954-1962. DOI : 10.1016/j.bpj.2019.10.002.

Entropy production in master equations and Fokker-Planck equations: facing the coarse-graining and recovering the information loss

D. M. Busiello; A. Maritan 

Journal of Statistical Mechanics-Theory and Experiment. 2019-10-01. Vol. 2019, num. 10, p. 104013. DOI : 10.1088/1742-5468/ab363e.

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

J. F. Marko; P. De Los Rios; A. Barducci; S. Gruber 

Nucleic Acids Research. 2019-07-26. Vol. 47, num. 13, p. 6956-6972. DOI : 10.1093/nar/gkz497.

Entropy production for coarse-grained dynamics

D. M. Busiello; J. Hidalgo; A. Maritan 

New Journal Of Physics. 2019-07-01. Vol. 21, p. 073004. DOI : 10.1088/1367-2630/ab29c0.

Detailed experiments on weakly deformed cavitation bubbles

O. Supponen; D. Obreschkow; P. Kobel; N. Dorsaz; M. Farhat 

Experiments In Fluids. 2019-02-01. Vol. 60, num. 2, p. 33. DOI : 10.1007/s00348-019-2679-4.

Reviews

Function, evolution, and structure of J-domain proteins

H. H. Kampinga; C. Andreasson; A. Barducci; M. E. Cheetham; D. Cyr et al. 

Cell Stress and Chaperones. 2019. Vol. 24, num. 1, p. 7-15. DOI : 10.1007/s12192-018-0948-4.

2018

Journal Articles

Vibrational entropy estimation can improve binding affinity prediction for non-obligatory protein complexes

T. Skrbic; S. Zamuner; R. Hong; F. Seno; A. Laio et al. 

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2018. Vol. 86, num. 4, p. 393-404. DOI : 10.1002/prot.25454.

Toward a unified scoring function for native state discrimination and drug-binding pocket recognition

A. Battisti; S. Zamuner; E. Sartic; A. Laio 

Physical Chemistry Chemical Physics. 2018-05-30. Vol. 20, num. 25, p. 17148-17155. DOI : 10.1039/C7CP08170G.

Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins

P. Goloubinoff; A. S. Sassi; B. Fauvet; A. Barducci; P. De Los Rios 

Nature Chemical Biology. 2018-03-05. Vol. 14, num. 4, p. 388-395. DOI : 10.1038/s41589-018-0013-8.

The cold denaturation of IscU highlights structure–function dualism in marginally stable proteins

R. Yan; P. De Los Rios; A. Pastore; P. A. Temisso 

Communications Chemistry. 2018-04-05. Vol. 1, num. 1, p. 13. DOI : 10.1038/s42004-018-0015-1.

Interplay between cost and benefits triggers nontrivial vaccination uptake

B. Steinegger; A. Cardillo; P. De Los Rios; J. Gómez-Gardeñes; A. Arenas 

Physical Review E. 2018-02-02. Vol. 97, num. 3, p. 032308. DOI : 10.1103/PhysRevE.97.032308.

Theses

Non equilibrium thermodynamics of protein organization

A. S. Sassi / P. De Los Rios (Dir.)  

Lausanne, EPFL, 2018. 

Unleashing the power of semantic text analysis: a complex systems approach

A. Martini / P. De Los Rios (Dir.)  

Lausanne, EPFL, 2018. 

Statistical Analysis of Protein Sequences: A Coevolutionary Study of Molecular Chaperones

D. Malinverni / P. De Los Rios; A. Barducci (Dir.)  

Lausanne, EPFL, 2018. 

2017

Journal Articles

Molecular chaperones inject energy from ATP hydrolysis into the non-equilibrium stabilisation of native proteins

P. Goloubinoff; A. S. Sassi; B. Fauvet; A. Barducci; P. De Los Rios 

bioRxiv. 2017. DOI : 10.1101/146852.

Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes

N. B. Nillegoda; A. Stank; D. Malinverni; N. Alberts; A. Szlachcic et al. 

eLife. 2017. Vol. 6, p. e24560. DOI : 10.7554/eLife.24560.

Irreducible network backbones: unbiased graph filtering via maximum entropy

V. Gemmetto; A. Cardillo; D. Garlaschelli 

arXiv. 2017. 

Coevolution of Synchronization and Cooperation in Costly Networked Interactions

A. Antonioni; A. Cardillo 

Physical Review Letters. 2017. Vol. 118, num. 23, p. 238301. DOI : 10.1103/PhysRevLett.118.238301.

The Shape of a Stretched Polymer

S. Assenza; P. De Los Rios; A. S. Sassi 

Physical Review Letters. 2017. Vol. 119, num. 3, p. 037801. DOI : 10.1103/PhysRevLett.119.037801.

Thermodynamic bounds on the ultra- and infra-affinity of Hsp70 for its substrates

B. Nguyen; D. Hartich; U. Seifert; P. De Los Rios 

Biophysical Journal. 2017. Vol. 34, num. 4, p. 362-370. DOI : 10.1016/j.bpj.2017.06.010.

New Techniques for Ancient Proteins: Direct Coupling Analysis Applied on Proteins Involved in Iron Sulfur Cluster Biogenesis

M. Fantini; D. Malinverni; P. De Los Rios; A. Pastore 

Frontiers in Molecular Biosciences. 2017. Vol. 4, p. 40. DOI : 10.3389/fmolb.2017.00040.

Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis

D. Malinverni; A. Jost Lopez; P. De Los Rios; G. Hummer; A. Barducci 

eLife. 2017. Vol. 6, p. e23471. DOI : 10.7554/eLife.23471.

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

A. Japaridze; G. Muskhelishvili; F. Benedetti; A. F. M. Gavriilidou; R. Zenobi et al. 

Nano Letters. 2017. Vol. 17, num. 3, p. 1938-1948. DOI : 10.1021/acs.nanolett.6b05294.

ScienceWISE: Topic Modeling over Scientific Literature Networks

A. Cardillo; P. De Los Rios; A. Martini 

arXiv. 2017. 

2016

Journal Articles

Hsp70 chaperones use ATP to remodel native protein oligomers and stable aggregates by entropic pulling

P. De Los Rios; P. Goloubinoff 

Nature Structural & Molecular Biology. 2016. Vol. 23, num. 9, p. 766-769. DOI : 10.1038/nsmb.3283.

Book Chapters

Experimental Milestones in the Discovery of Molecular Chaperones as Polypeptide Unfolding Enzymes

A. Finka; R. U. H. Mattoo; P. Goloubinoff 

Annual Review Of Biochemistry; Palo Alto: Annual Reviews, 2016. p. 715-742.

2015

Journal Articles

Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones

D. Malinverni; S. Marsili; A. Barducci; P. De Los Rios 

Plos Computational Biology. 2015. Vol. 11, num. 6, p. e1004262. DOI : 10.1371/journal.pcbi.1004262.

Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States

F. Palazzesi; M. K. Prakash; M. Bonomi; A. Barducci 

Journal Of Chemical Theory And Computation. 2015. Vol. 11, num. 1, p. 2-7. DOI : 10.1021/ct500718s.

Theoretical and Experimental Characterization of Amino-PEG-Phosphonate-Terminated Polyphosphorhydrazone Dendrimers: Influence of Size and PEG Capping on Cytotoxicity Profiles

A. Hameau; S. Fruchon; C. Bijani; A. Barducci; M. Blanzat et al. 

Journal Of Polymer Science Part A-Polymer Chemistry. 2015. Vol. 53, num. 6, p. 761-774. DOI : 10.1002/pola.27501.

Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs

A. Finka; V. Sood; M. Quadroni; P. De Los Rios; P. Goloubinoff 

Cell Stress and Chaperones. 2015. Vol. 20, num. 4, p. 605-620. DOI : 10.1007/s12192-015-0583-2.

Quantifying the role of chaperones in protein translocation by computational modeling

S. Assenza; P. De Los Rios; A. Barducci 

Frontiers in Molecular Biosciences. 2015. Vol. 2, p. 8. DOI : 10.3389/fmolb.2015.00008.

Reviews

Non-equilibrium conformational dynamics in the function of molecular chaperones

A. Barducci; P. De Los Rios 

Current Opinion in Structural Biology. 2015. Vol. 30, p. 161-169. DOI : 10.1016/j.sbi.2015.02.008.

Theses

Polymer-theory insights into biomolecular systems

S. Assenza / P. De Los Rios; A. Barducci (Dir.)  

Lausanne, EPFL, 2015. 

2014

Journal Articles

Universal Behavior in the Mesoscale Properties of Amyloid Fibrils

S. Assenza; J. Adamcik; R. Mezzenga; P. De Los Rios 

Physical Review Letters. 2014. Vol. 113, num. 26, p. 268103. DOI : 10.1103/PhysRevLett.113.268103.

Real-Time Monitoring of Protein Conformational Changes Using a Nano-Mechanical Sensor

L. Alonso-Sarduy; P. De Los Rios; F. Benedetti; D. Vobornik; G. Dietler et al. 

Plos One. 2014. Vol. 9, num. 7, p. e103674. DOI : 10.1371/journal.pone.0103674.

Single-molecule spectroscopy reveals chaperone-mediated expansion of substrate protein

R. Kellner; H. Hofmann; A. Barducci; B. Wunderlich; D. Nettels et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2014. Vol. 111, num. 37, p. 13355-13360. DOI : 10.1073/pnas.1407086111.

Hsp70 chaperones are non-equilibrium machines that achieve ultra-affinity by energy consumption

P. De Los Rios; A. Barducci 

Elife. 2014. Vol. 3, p. e02218. DOI : 10.7554/eLife.02218.

Addressing Conditioning Data in Multiple-Point Statistics Simulation Algorithms Based on a Multiple Grid Approach

J. Straubhaar; D. Malinverni 

Mathematical Geosciences. 2014. Vol. 46, num. 2, p. 187-204. DOI : 10.1007/s11004-013-9479-9.

Hydrophobic hydration of poly-N-isopropyl acrylamide: a matter of the mean energetic state of water

I. Bischofberger; D. C. E. Calzolari; P. De Los Rios; I. Jelezarov; V. Trappe 

Scientific Reports. 2014. Vol. 4, p. 4377. DOI : 10.1038/srep04377.

Reviews

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

F. Sterpone; S. Melchionna; P. Tuffery; S. Pasquali; N. Mousseau et al. 

Chemical Society Reviews. 2014. Vol. 43, num. 13, p. 4871-4893. DOI : 10.1039/c4cs00048j.

Theses

Topics in Community Detection

L. Floretta / P. De Los Rios (Dir.)  

Lausanne, EPFL, 2014. 

Book Chapters

Several Multiplexes in the same City: The role of wealth differences in urban mobility

L. Lotero; A. Cardillo; R. Hurtado; J. Gómez-Gardeñes 

Interconnected Networks; Springer, 2014. p. 149–164.

2013

Journal Articles

Stochastic fluctuations and the detectability limit of network communities

L. Floretta; J. Liechti; A. Flammini; P. De Los Rios 

Physical Review E. 2013. Vol. 88, num. 6, p. 060801(R). DOI : 10.1103/PhysRevE.88.060801.

Free-energy landscape of protein oligomerization from atomistic simulations

A. Barducci; M. Bonomi; M. K. Prakash; M. Parrinello 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2013. Vol. 110, num. 49, p. E4708-E4713. DOI : 10.1073/pnas.1320077110.

Structural and energetic basis for hybridization limits in high-density DNA monolayers

G. Doni; M. D. N. Ngavouka; A. Barducci; P. Parisse; A. De Vita et al. 

Nanoscale. 2013. Vol. 5, num. 20, p. 9988-9993. DOI : 10.1039/c3nr01799k.

The allosteric communication pathways in KIX domain of CBP

F. Palazzesi; A. Barducci; M. Tollinger; M. Parrinello 

Proceedings of the National Academy of Sciences. 2013. Vol. 110, p. 14237-14242. DOI : 10.1073/pnas.1313548110.

The effect of crowding and confinement: a comparison of Yfh1 stability in different environments

D. Sanfelice; A. Politou; S. R. Martin; P. De Los Rios; P. Temussi et al. 

Physical Biology. 2013. Vol. 10, p. 045002. DOI : 10.1088/1478-3975/10/4/045002.

GroEL and CCT are catalytic unfoldases mediating out-of-cage polypeptide refolding without ATP

S. Priya; S. K. Sharma; V. Sood; R. U. H. Mattoo; A. Finka et al. 

Proceedings of the National Academy of Sciences. 2013. Vol. 110, p. 7199-7204. DOI : 10.1073/pnas.1219867110.

Diffusion-limited reactions in crowded environments: a local density approximation

F. Piazza; N. Dorsaz; C. De Michele; P. De Los Rios; G. Foffi 

Journal of Physics: Condensed Matter. 2013. Vol. 25, num. 37, p. 375104. DOI : 10.1088/0953-8984/25/37/375104.

2012

Journal Articles

First-order coil-globule transition driven by vibrational entropy

C. Maffi; M. Baiesi; L. Casetti; F. Piazza; P. De Los Rios 

Nature Communications. 2012. Vol. 3, p. 1065. DOI : 10.1038/ncomms2055.

Explaining the length threshold of polyglutamine aggregation

P. De Los Rios; M. Hafner; A. Pastore 

Journal of Physics: Condensed Matter. 2012. Vol. 24, p. 244105. DOI : 10.1088/0953-8984/24/24/244105.

Protein folding: Chaperoning protein evolution

P. De Los Rios; P. Goloubinoff 

Nature Chemical Biology. 2012. Vol. 8, p. 226-228. DOI : 10.1038/nchembio.791.

Theses

Entropy in the Coil-to-Globule Transition of Macromolecules

C. Maffi / P. De Los Rios (Dir.)  

Lausanne, EPFL, 2012. 

Modern Portfolio Theory Revisited

D. Morton de Lachapelle / P. De Los Rios; M. Marsili (Dir.)  

Lausanne, EPFL, 2012. 

2011

Journal Articles

Probing the different chaperone activities of the bacterial HSP70-HSP40 system using a thermolabile luciferase substrate

S. K. Sharma; P. De Los Rios; P. Goloubinoff 

Proteins. 2011. Vol. 79, p. 1991-1998. DOI : 10.1002/prot.23024.

Emerging Meso- and Macroscales from Synchronization of Adaptive Networks

R. Gutierrez; A. Amann; S. Assenza; J. Gomez-Gardenes; V. Latora et al. 

Physical Review Letters. 2011. Vol. 107, p. 234103. DOI : 10.1103/PhysRevLett.107.234103.

2010

Journal Articles

On inconsistent entities. A reply to Colyvan

T. Piazza; F. Piazza 

Philosophical Studies. 2010. Vol. 150, num. 2, p. 301-311. DOI : 10.1007/s11098-009-9410-x.

A facile strategy for the modification of polyethylene substrates with non-fouling, bioactive poly(poly(ethylene glycol) methacrylate) brushes

L. Lavanant; B. Pullin; J. A. Hubbell; H-A. Klok 

Macromolecular bioscience. 2010. Vol. 10, num. 1, p. 101-8. DOI : 10.1002/mabi.200900205.

Diffusion-Limited Reactions in Crowded Environments

N. Dorsaz; C. De Michele; F. Piazza; P. De Los Rios; G. Foffi 

Physical Review Letters. 2010. Vol. 105, num. 12, p. 120601. DOI : 10.1103/PhysRevLett.105.120601.

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

S. K. Sharma; P. De Los Rios; P. Christen; A. Lustig; P. Goloubinoff 

Nature Chemical Biology. 2010. Vol. 6, num. 12, p. 914-920. DOI : 10.1038/nchembio.455.

Simple Monte Carlo model for crowd dynamics

F. Piazza 

Physical Review E. 2010. Vol. 82, p. 026111. DOI : 10.1103/PhysRevE.82.026111.

Vibrational entropy and the structural organization of proteins

L. Bongini; F. Piazza; L. Casetti; P. De Los Rios 

The European Physical Journal E – Soft Matter & Biological Physics. 2010. Vol. 33, p. 89-96. DOI : 10.1140/epje/i2010-10653-8.

Turnover, account value and diversification of real traders: evidence of collective portfolio optimizing behavior

D. Morton de Lachapelle; D. Challet 

New Journal of Physics. 2010. Vol. 12, p. 075039. DOI : 10.1088/1367-2630/12/7/075039.

Understanding amyloid aggregation by statistical analysis of atomic force microscopy images

J. Adamcik; J-M. Jung; J. Flakowski; P. De Los Rios; G. Dietler et al. 

Nature Nanotechnology. 2010. Vol. 5, num. 6, p. 423-428. DOI : 10.1038/nnano.2010.59.

Inertial effects in diffusion-limited reactions

N. Dorsaz; C. De Michele; F. Piazza; G. Foffi 

Journal Of Physics-Condensed Matter. 2010. Vol. 22, p. 104116. DOI : 10.1088/0953-8984/22/10/104116.

Preparation and characterization of toxic Abeta aggregates for structural and functional studies in Alzheimer’s disease research

A. Jan; D. M. Hartley; H. A. Lashuel 

Nature protocols. 2010. Vol. 5, num. 6, p. 1186-209. DOI : 10.1038/nprot.2010.72.

Fonction sportive de la ruelle: une ethnologie du basket dans le monde des gangs et des barrios

Y. Pedrazzini 

Ethnographiques.org. 2010. Vol. “Aux frontières du sport: regards socio-anthropologiques sur les pratiques ludiques et informelles, num. 20.

Conference Papers

In contextual modulation, bigger is not better for low luminance stimuli

M. Manassi; B. Sayim; M. H. Herzog 

2010. 33rd European Conference on Visual Perception , Lausanne, Switzerland, August 22-26, 2010. p. 28.

Improving API Documentation for Java-like Languages

G. Dubochet; D. Malayeri 

2010. Evaluation and Usability of Programming Languages and Tools, Reno, Nevada, USA, October 18, 2010.

Fault Prediction in Distributed Systems Gone Wild

M. Canini; D. Novakovic; V. Jovanovic; D. Kostic 

2010. LADIS 2010: The 4th ACM SIGOPS/SIGACT Workshop on Large Scale Distributed Systems and Middleware, Zurich, Switzerland, July 2010. p. 7–11. DOI : 10.1145/1859184.1859187.

Books

Networks in Cell Biology

 

Cambridge: Cambridge University Press, 2010.

Student Projects

Monitoring bone fetal cells seeded in PLA scaffolds using bioluminescence imaging

A. Roshan Ghias 

2010.

Back-calculation of mechanical properties of bone scaffolds using micro- finite element analysis and compression test (Semester project)

E. Denstaad; A. Roshan Ghias 

2010.

2009

Journal Articles

Feedback topology and XOR-dynamics in Boolean networks with varying input structure

L. Ciandrini; C. Maffi; A. Motta; B. Bassetti; M. Cosentino Lagomarsino 

Physical Review E. 2009. Vol. 80, num. 2, p. 026122. DOI : 10.1103/PhysRevE.80.026122.

Heat wave propagation in a nonlinear chain

F. Piazza; S. Lepri 

Physical Review B. 2009. Vol. 79, p. 094306. DOI : 10.1103/PhysRevB.79.094306.

Long-range energy transfer in proteins

F. Piazza; Y-H. Sanejouand 

Physical Biology. 2009. Vol. 6, p. 046014. DOI : 10.1088/1478-3975/6/4/046014.

Energy transfer in nonlinear network models of proteins

F. Piazza; Y-H. Sanejouand 

Europhysics Letters. 2009. Vol. 88, p. 68001. DOI : 10.1209/0295-5075/88/68001.

Temperature Dependence of Normal Mode Reconstructions of Protein Dynamics

F. Piazza; P. De Los Rios; F. Cecconi 

Physical Review Letters. 2009. Vol. 102, p. 218104. DOI : 10.1103/PhysRevLett.102.218104.

Extended Navigability of Small World Networks: Exact Results and New Insights

C. C. Cartozo; P. De Los Rios 

Physical Review Letters. 2009. Vol. 102, p. 238703. DOI : 10.1103/PhysRevLett.102.238703.

Theses

Complex networks

C. Caretta Cartozo / P. De Los Rios (Dir.)  

Lausanne, EPFL, 2009. 

2008

Journal Articles

Self-similarity of complex networks and hidden metric spaces

M. A. Serrano; D. Krioukov; M. Boguna 

Physical Review Letters. 2008. Vol. 100, num. 7, p. 078701. DOI : 10.1103/PhysRevLett.100.078701.

Elastic membrane heterogeneity of living cells revealed by stiff nanoscale membrane domains

C. Roduit; F. G. van der Goot; P. De Los Rios; A. Yersin; P. Steiner et al. 

Biophysical Journal. 2008. Vol. 94, p. 1521-1532. DOI : 10.1529/biophysj.107.112862.

Spectral coarse graining and synchronization in oscillator networks

D. Gfeller; P. De Los Rios 

Physical Review Letters. 2008. Vol. 100, p. 174104. DOI : 10.1103/PhysRevLett.100.174104.

Cold denaturation of yeast frataxin offers the clue to understand the effect of alcohols on protein stability

S. R. Martin; V. Esposito; P. De Los Rios; A. Pastore; P. A. Temussi 

Journal Of The American Chemical Society. 2008. Vol. 130, p. 9963-9970. DOI : 10.1021/ja803280e.

Structural Efficiency of Percolated Landscapes in Flow Networks

M. A. Serrano; P. De Los Rios 

Plos One. 2008. Vol. 3, p. e3654. DOI : 10.1371/journal.pone.0003654.

Discrete breathers in protein structures

F. Piazza; Y-H. Sanejouand 

Physical Biology. 2008. Vol. 5, p. 026001. DOI : 10.1088/1478-3975/5/2/026001.

Conference Papers

Quantifying the taxonomic diversity in real species communities

C. C. Cartozo; D. Garlaschelli; C. Ricotta; M. Barthelemy; G. Caldarelli 

2008. Workshop on Complex Networks – from Biology to Information Technology, Pula, ITALY, Jul, 2007. p. 224012. DOI : 10.1088/1751-8113/41/22/224012.

How TMS and (light) masks modulate feature integration

J. Rüter; F. Scharnowski; T. Kammer; M. H. Herzog 

2008. 6th FENS: Forum of European Neuroscience, Genève, Switzerland, July 12-16, 2008. p. 220.13.

2007

Journal Articles

Existence, cost and robustness of spatial small-world networks

P. De Los Rios; T. Petermann 

International Journal Of Bifurcation And Chaos. 2007. Vol. 17, p. 2331-2342. DOI : 10.1142/S0218127407018427.

Patterns of dominant flows in the world trade web

M. Angeles Serrano; M. Boguna; A. Vespignani 

Journal of Economic Interaction and Coordination. 2007. Vol. 2, p. 111. DOI : 10.1007/s11403-007-0026-y.

Complex network analysis of free-energy landscapes

D. Gfeller; P. De Los Rios; A. Caflisch; F. Rao 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2007. Vol. 104, p. 1817-1822. DOI : 10.1073/pnas.0608099104.

Fractal dimension and localization of DNA knots

E. Ercolini; F. Valle; J. Adamcik; G. Witz; R. Metzler et al. 

Physical Review Letters. 2007. Vol. 98, p. 058102. DOI : 10.1103/PhysRevLett.98.058102.

On the origin of the boson peak in globular proteins

S. Ciliberti; P. De Los Rios; F. Piazza 

Philosophical Magazine. 2007. Vol. 87, p. 631-641. DOI : 10.1080/14786430601042369.

Bottleneck genes and community structure in the cell cycle network of S-pombe

C. Caretta-Cartozo; P. De Los Rios; F. Piazza; P. Lio 

Plos Computational Biology. 2007. Vol. 3, p. 968-976. DOI : 10.1371/journal.pcbi.0030103.

Spectral coarse graining of complex networks

D. Gfeller; P. De Los Rios 

Physical Review Letters. 2007. Vol. 99, p. 038701. DOI : 10.1103/PhysRevLett.99.038701.

Resolving the geometry of biomolecules imaged by cryo electron tomography

L. Bongini; D. Fanelli; S. Svensson; M. Gedda; F. Piazza et al. 

Journal Of Microscopy-Oxford. 2007. Vol. 228, p. 174-184. DOI : 10.1111/j.1365-2818.2007.01839.x.

Diffusion-limited unbinding of small peptides from PDZ domains

F. Cecconi; P. D. L. Rios; F. Piazza 

Journal Of Physical Chemistry B. 2007. Vol. 111, p. 11057-11063. DOI : 10.1021/jp0730390.

Uncovering the topology of configuration space networks

D. Gfeller; D. M. de Lachapelle; P. D. L. Rios; G. Caldarelli; F. Rao 

Physical Review E. 2007. Vol. 76, p. 026113. DOI : 10.1103/PhysRevE.76.026113.

A dynamical study of antibody-antigen encounter reactions

L. Bongini; D. Fanelli; F. Piazza; P. De Los Rios; M. Sanner et al. 

Physical Biology. 2007. Vol. 4, p. 172-180. DOI : 10.1088/1478-3975/4/3/004.

Interfaces and the edge percolation map of random directed networks

M. A. Serrano; P. D. L. Rios 

Physical Review E. 2007. Vol. 76, p. 056121. DOI : 10.1103/PhysRevE.76.056121.

Discrete Breathers in Nonlinear Network Models of Proteins

B. Juanico; Y-H. Sanejouand; F. Piazza; P. De Los Rios 

Physical Review Letters. 2007. Vol. 99, num. 23, p. 8104. DOI : 10.1103/PhysRevLett.99.238104.

Mechanisms of Quantum Dot Energy Engineering by Metalorganic Vapor Phase Epitaxy on Patterned Nonplanar Substrates

E. Pelucchi; S. Watanabe; K. Leifer; Q. Zhu; B. Dwir et al. 

Nano Letters. 2007. Vol. 7, num. 5, p. 1282-1285. DOI : 10.1021/nl0702012.

Size and microstructure effects on the mechanical behavior of FCC bicrystals by quasicontinuum method

F. Sansoz; J. F. Molinari 

Thin Solid Films. 2007. Vol. 515, num. 6, p. 3158-3163. DOI : 10.1016/j.tsf.2006.01.012.

Reviews

The mechanism of Hsp70 chaperones: (entropic) pulling the models together

P. Goloubinoff; P. De Los Rios 

Trends in Biochemical Sciences. 2007. Vol. 32, num. 8, p. 372-380. DOI : 10.1016/j.tibs.2007.06.008.

Theses

Simplifying complex networks

D. Gfeller / P. De Los Rios (Dir.)  

Lausanne, EPFL, 2007. 

Posters

Real Time Analysis of Myogenesis in Behaving Myoblasts

E. Thomasson; B. Städler; T. Blättler; L. Jacot-Descombes; J. Vörös et al. 

JPK SPM Workshop, Berlin, Germany, October 9, 2007.

2006

Journal Articles

Physical realizability of small-world networks

P. De Los Rios; T. Petermann 

Physical Review E. 2006. Vol. 73, p. 026114. DOI : 10.1103/PhysRevE.73.026114.

Hsp70 chaperones accelerate protein translocation and the unfolding of stable protein aggregates by entropic pulling

P. De Los Rios; A. Ben-Zvi; O. Slutski; A. Azem; P. Goloubinoff 

Proceedings of the National Academy of Sciences. 2006. Vol. 103, num. 16, p. 6166-6171. DOI : 10.1073/pnas.0510496103.

Glasslike structure of globular proteins and the boson peak

P. De Los Rios; F. Piazza; S. Ciliberti 

Physical Review Letters. 2006. Vol. 96, p. 198103. DOI : 10.1103/PhysRevLett.96.198103.

Numerical simulation of gel electrophoresis of DNA knots in weak and strong electric fields

C. Weber; A. Stasiak; P. De los Rios; G. Dietler 

Biophysical Journal. 2006. Vol. 90, num. 9, p. 3100-3105. DOI : 10.1529/biophysj.105.070128.

Simulations of electrophoretic collisions of DNA knots with gel obstacles

C. Weber; P. D. L. Rios; G. Dietler; A. Stasiak 

Journal of Physics-Condensed Matter. 2006. Vol. 18, num. 14, p. S161-S171. DOI : 10.1088/0953-8984/18/14/S02.

2005

Journal Articles

Statistical analysis of simple repeats in the human genome

F. Piazza; P. Lio 

Physica A: Statistical Mechanics and its Applications. 2005. Vol. 347, p. 472-488. DOI : 10.1016/j.physa.2004.08.038.

Dynamics of antibodies from cryo-electron tomography

D. Fanelli; F. Piazza; P. D. Rios; S. Sandin; U. Skoglund et al. 

Biophysical Chemistry. 2005. Vol. 115, p. 235-240. DOI : 10.1016/j.bpc.2004.12.037.

Anti-cooperativity in diffusion-controlled reactions with pairs of anisotropic domains: a model for the antigen-antibody encounter

F. Piazza; P. D. L. Rios; D. Fanelli; L. Bongini; U. Skoglund 

European biophysics journal : EBJ. 2005. Vol. 34, num. 7, p. 899-911. DOI : 10.1007/s00249-005-0460-5.

Effective interactions between chaotropic agents and proteins

P. De los Rios; M. Vendruscolo; G. Salvi 

Proteins-Structure Function And Bioinformatics. 2005. Vol. 61, p. 492-499. DOI : 10.1002/prot.20626.

Slow Energy Relaxation of Macromolecules and Nanoclusters in Solution

F. Piazza; P. De Los Rios; Y-H. Sanejouand 

Physical Review Letters. 2005. Vol. 94, num. 14, p. 5502. DOI : 10.1103/PhysRevLett.94.145502.

Functional dynamics of PDZ binding domains: A normal-mode analysis

P. De Los Rios; F. Cecconi; A. Pretre; G. Dietler; O. Michielin et al. 

Biophysical Journal. 2005. Vol. 89, num. 1, p. 14-21. DOI : 10.1529/biophysj.104.055004.

Scaling exponents and probability distributions of DNA end-to-end distance

F. Valle; M. Favre; P. De Los Rios; A. Rosa; G. Dietler 

Physical Review Letters. 2005. Vol. 95, num. 15, p. 158105. DOI : 10.1103/PhysRevLett.95.158105.

Finding instabilities in the community structure of complex networks

D. Gfeller; J-C. Chappelier; P. De Los Rios 

Physical Review E. 2005. Vol. 72, num. 5, p. 056135. DOI : 10.1103/PhysRevE.72.056135.

Theses

A statistical physics perspective of complex networks

T. Petermann / P. De Los Rios (Dir.)  

Lausanne, EPFL, 2005. 

2004

Journal Articles

Preferential exchange: Strengthening connections in complex networks

G. Caldarelli; F. Coccetti; P. De Los Rios 

Physical Review E. 2004. Vol. 70, num. 2, p. 7102. DOI : 10.1103/PhysRevE.70.027102.

Active solubilization and refolding of stable protein aggregates by cooperative unfolding action of individual hsp70 chaperones

A. Ben-Zvi; P. De Los Rios; G. Dietler; P. Goloubinoff 

The Journal of biological chemistry. 2004. Vol. 279, num. 36, p. 37298-303. DOI : 10.1074/jbc.M405627200.

Solvent-induced micelle formation in a hydrophobic interaction model

S. Moelbert; B. Normand; P. Rios 

Physical Review E. 2004. Vol. 69, num. 6, p. 1924. DOI : 10.1103/PhysRevE.69.061924.

Scale-free behavior and universality in random fragmentation and aggregation

J. R. Banavar; P. De Los Rios; A. Flammini; N. S. Holter; A. Maritan 

Physical Review E – Statistical, Nonlinear, and Soft Matter Physics. 2004. Vol. 69, num. 3 2, p. 036123-1-036123-4. DOI : 10.1103/PhysRevE.69.036123.

Role of clustering and gridlike ordering in epidemic spreading

T. Petermann; P. De Los Rios 

Physical Review E. 2004. Vol. 69, num. 6, p. 6116. DOI : 10.1103/PhysRevE.69.066116.

Freezing immunoglobulins to see them move

D. Fanelli; F. Piazza; P. De los Rios; S. Sandin; U. Skoglund et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2004. Vol. 101, p. 6466-6471. DOI : 10.1073/pnas.0400119101.

Cluster approximations for epidemic processes: a systematic description of correlations beyond the pair level

T. Petermann; P. De Los Rios 

Journal of Theoretical Biology. 2004. Vol. 229, num. 1, p. 1-11. DOI : 10.1016/j.jtbi.2004.02.017.

Statistical features of drainage basins in mars channel networks – Can one guess from the landscape the past presence of water?

P. De los Rios; M. Montuori; V. D. P. Servedio; G. Caldarelli 

European Physical Journal B. 2004. Vol. 38, p. 387-391. DOI : 10.1140/epjb/e2004-00132-y.

Virtual Round Table on ten leading questions for network research

A. Barrat; A. L. Barabasi; G. Caldarelli; P. De los Rios; A. Erzan et al. 

European Physical Journal B. 2004. Vol. 38, p. 143-145. DOI : 10.1140/epjb/e2004-00109-x.

Exploration of scale-free networks

T. Petermann; P. De Los Rios 

The European Physical Journal B – Condensed Matter. 2004. Vol. 38, num. 2, p. 201-204. DOI : 10.1140/epjb/e2004-00021-5.

Widespread occurrence of the inverse square distribution in social sciences and taxonomy

G. Caldarelli; C. C. Cartozo; P. D. L. Rios; V. D. P. Servedio 

Physical Review E – Statistical, Nonlinear, and Soft Matter Physics. 2004. Vol. 69, num. 3 2, p. 035101-1-035101-3. DOI : 10.1103/PhysRevE.69.035101.

Oscillation modes of microtubules

S. Kasas; C. Cibert; A. Kis; P. De Los Rios; B. M. Riederer et al. 

Biology of the Cell. 2004. Vol. 96, num. 9, p. 697-700. DOI : 10.1016/j.biolcel.2004.09.002.

Theses

Explicit solvent effects on protein physics – modeling lattice proteins in aqueous environments

G. Salvi / P. De Los Rios (Dir.)  

Lausanne, EPFL, 2004. 

2003

Journal Articles

Orientational order of the lamellipodial actin network as demonstrated in living motile cells

A. B. Verkhovsky; O. Y. Chaga; S. Schaub; T. M. Svitkina; J-J. Meister et al. 

Molecular biology of the cell. 2003. Vol. 14, num. 11, p. 4667-4675. DOI : 10.1091/mbc.E02-10-0630.

Chaotropic effect and preferential binding in a hydrophobic interaction model

S. Moelbert; P. De Los Rios 

The Journal of Chemical Physics. 2003. Vol. 119, num. 15, p. 7988. DOI : 10.1063/1.1609982.

Quantitative description and modeling of real networks

G. Caldarelli; P. De Los Rios; A. Capocci 

Physical Review E. 2003. Vol. 68, p. 047101. DOI : 10.1103/PhysRevE.68.047101.

Hydrophobic Interaction Model for Upper and Lower Critical Solution Temperatures

S. Moelbert; P. De Los Rios 

Macromolecules. 2003. Vol. 36, num. 15, p. 5845-5853. DOI : 10.1021/ma025890c.

Effective Interactions Cannot Replace Solvent Effects in a Lattice Model of Proteins

G. Salvi; P. De Los Rios 

Physical Review Letters. 2003. Vol. 91, num. 25, p. 8102. DOI : 10.1103/PhysRevLett.91.258102.

Interactions between synaptic vesicle fusion proteins explored by atomic force microscopy

A. Yersin; H. Hirling; P. Steiner; S. Magnin; R. Regazzi et al. 

Proceedings of the National Academy of Sciences of the United States of America. 2003. Vol. 100, num. 15, p. 8736-8741. DOI : 10.1073/pnas.1533137100.

Conference Papers

Superresolution images reconstructed from aliased images

P. Vandewalle; S. Süsstrunk; M. Vetterli 

2003.  p. 1398-1405. DOI : 10.1117/12.506874.

2002

Journal Articles

Scale-free networks from varying vertex intrinsic fitness

A. Capocci; P. De Los Rios; M. A. Munoz; G. Caldarelli 

Physical Review Letters. 2002. Vol. 89, p. 258702. DOI : 10.1103/PhysRevLett.89.258702.

Design of lattice proteins with explicit solvent

S. Molbert; P. De Los Rios; G. Salvi 

Physical Review E. 2002. Vol. 66, p. 061911. DOI : 10.1103/PhysRevE.66.061911.

The local minority game

P. De Los Rios; S. Moelbert 

Physica A-Statistical Mechanics And Its Applications. 2002. Vol. 303, p. 217-225. DOI : 10.1016/S0378-4371(01)00480-0.

Conference Papers

Modeling of Texture Movies for Video Coding

S. Valaeys; G. Menegaz; J. Reichel; F. Ziliani 

2002. ECCV First International Workshop on Generative-Model-Based Vision. p. 43-51.

Optimization for Hue Constant RGB Sensors

G. D. Finlayson; S. Süsstrunk 

2002. IS&T/SID 10th Color Imaging Conference, Scottsdale, November 2002. p. 343-348.

Color Demosaicing by Estimating Luminance and Opponent Chromatic Signals in the Fourier Domain

D. Alleysson; S. Süsstrunk; J. Hérault 

2002. IS&T/SID 10th Color Imaging Conference, Scottsdale, AZ, Nov. 2002. p. 331-336.

2001

Journal Articles

Power law size distribution of supercritical random trees

P. De Los Rios 

Europhysics Letters. 2001. Vol. 56, p. 898-903. DOI : 10.1209/epl/i2001-00604-2.

Cold and warm denaturation of proteins

P. De Los Rios; G. Caldarelli 

Journal Of Biological Physics. 2001. Vol. 27, p. 229-241. DOI : 10.1023/A:1013145009949.

Cold and warm swelling of hydrophobic polymers

P. De Los Rios; G. Caldarelli 

Physical Review E – Statistical, Nonlinear, and Soft Matter Physics. 2001. Vol. 63, p. 0318021-03180205. DOI : 10.1103/PhysRevE.63.031802.

Bethe approximation for self-interacting lattice trees

S. Lise; A. Pelizzola; P. De los Rios 

Europhysics Letters. 2001. Vol. 53, p. 176-182. DOI : 10.1209/epl/i2001-00133-6.

2000

Journal Articles

Discretized diffusion processes

G. Caldarelli; P. De los Rios; L. Pietronero; Y. C. Zhang; S. Ciliberti 

Physical Review Letters. 2000. Vol. 85, p. 4848-4851. DOI : 10.1103/PhysRevLett.85.4848.

Putting proteins back into water

G. Caldarelli; P. De Los Rios 

Physical Review E. 2000. Vol. 62, p. 8449-8452. DOI : 10.1103/PhysRevE.62.8449.

Statistical analysis of genealogical trees for polygamic species

O. Pla; P. De los Rios 

Physical Review E. 2000. Vol. 61, p. 5620-5623. DOI : 10.1103/PhysRevE.61.5620.

Berry phase and ground-state symmetry in H circle times h dynamical Jahn-Teller systems

P. De los Rios; N. Manini 

Physical Review B. 2000. Vol. 62, p. 29-32. DOI : 10.1103/PhysRevB.62.29.

Conference Papers

Digital Photography – How Long Will It Last

F. Frey; S. Süsstrunk 

2000. IEEE International Symposium on Circuits and Systems. p. 113-116. DOI : 10.1109/ISCAS.2000.857376.

1999

Journal Articles

Polymers with a bimodal disorder distribution and directed percolation

P. D. L. Rios; A. Maritan; F. Seno 

Journal of Physics A: Mathematical and General. 1999. Vol. 30, num. 18, p. L617-L621. DOI : 10.1088/0305-4470/30/18/002.

The role of the Berry phase in dynamical Jahn-Teller systems

N. Manini; P. D. L. Rios 

Journal of Physics: Condensed Matter. 1999. Vol. 10, num. 38, p. 8485-8495. DOI : 10.1088/0953-8984/10/38/009.

Levy-nearest-neighbors Bak-Sneppen model

R. Cafiero; P. De Los Rios; A. Valleriani; J. Vega 

Physical Review E. 1999. Vol. 60, num. 2, p. R1111-R1114. DOI : 10.1103/PhysRevE.60.R1111.

Universality and Crossover of Directed Polymers and Growing Surfaces

P. De Los Rios 

Physical Review Letters. 1999. Vol. 82, num. 21, p. 4236-4239. DOI : 10.1103/PhysRevLett.82.4236.

Universal 1/f Noise from Dissipative Self-Organized Criticality Models

P. De Los Rios; Y-C. Zhang 

Physical Review Letters. 1999. Vol. 82, num. 3, p. 472-475. DOI : 10.1103/PhysRevLett.82.472.

1998

Journal Articles

Critical exponents of the anisotropic Bak-Sneppen model

S. Maslov; P. De Los Rios; M. Marsili; Y-C. Zhang 

Physical Review E. 1998. Vol. 58, num. 6, p. 7141-7145. DOI : 10.1103/PhysRevE.58.7141.

Directed Polymers on a Factorized Disorder Landscape

P. De Los Rios; Y-C. Zhang 

Physical Review Letters. 1998. Vol. 81, num. 5, p. 1023-1026. DOI : 10.1103/PhysRevLett.81.1023.

Power-law behavior in a nonextremal Bak-Sneppen model

R. Cafiero; P. De Los Rios; F-M. Dittes; A. Valleriani; J. Vega 

Physical Review E. 1998. Vol. 58, num. 3, p. 3993-3996. DOI : 10.1103/PhysRevE.58.3993.

High-Dimensional Bak-Sneppen Model

P. De Los Rios; M. Marsili; M. Vendruscolo 

Physical Review Letters. 1998. Vol. 80, num. 26, p. 5746-5749. DOI : 10.1103/PhysRevLett.80.5746.

Self-organized criticality in deterministic systems with disorder

P. De Los Rios; A. Valleriani; J. Luis Vega 

Physical Review E. 1998. Vol. 57, num. 6, p. 6451-6459. DOI : 10.1103/PhysRevE.57.6451.

Expansion Around the Mean-Field Solution of the Bak-Sneppen Model

M. Marsili; P. De Los Rios; S. Maslov 

Physical Review Letters. 1998. Vol. 80, num. 7, p. 1457-1460. DOI : 10.1103/PhysRevLett.80.1457.

1997

Journal Articles

Self-organized criticality driven by deterministic rules

P. De Los Rios; A. Valleriani; J. Vega 

Physical Review E. 1997. Vol. 56, num. 4, p. 4876-4879. DOI : 10.1103/PhysRevE.56.4876.

1996

Journal Articles

Model of correlated evolution

M. Vendruscolo; P. De Los Rios; L. Bonesi 

Physical Review E. 1996. Vol. 54, num. 6, p. 6053-6057. DOI : 10.1103/PhysRevE.54.6053.

Optimal path and directed percolation

P. Rios; G. Caldarelli; A. Maritan; F. Seno 

Physical Review E. 1996. Vol. 53, num. 3, p. R2029-R2032. DOI : 10.1103/PhysRevE.53.R2029.

Dynamical Jahn-Teller effect and Berry phase in positively charged fullerenes: Basic considerations

P. De Los Rios; N. Manini; E. Tosatti 

Physical Review B. 1996. Vol. 54, num. 10, p. 7157-7167. DOI : 10.1103/PhysRevB.54.7157.

1994

Journal Articles

Reentrant behaviour in a highly anisotropic system

C. Buzano; P. De Los Rios 

Physica A: Statistical and Theoretical Physics. 1994. Vol. 203, num. 3-4, p. 640-654. DOI : 10.1016/0378-4371(94)90019-1.