Publications

2018

Journal Articles

A. Battisti; S. Zamuner; E. Sartic; A. Laio : Toward a unified scoring function for native state discrimination and drug-binding pocket recognition; Physical Chemistry Chemical Physics. 2018-05-30. Vol. 20, num. 25, p. 17148-17155. DOI : 10.1039/C7CP08170G.
R. Yan; P. De Los Rios; A. Pastore; P. A. Temisso : The cold denaturation of IscU highlights structure–function dualism in marginally stable proteins; Communications Chemistry. 2018-04-05. Vol. 1, num. 1, p. 13. DOI : 10.1038/s42004-018-0015-1.
P. Goloubinoff; A. S. Sassi; B. Fauvet; A. Barducci; P. De Los Rios : Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins; Nature Chemical Biology. 2018-03-05. Vol. 14, num. 4, p. 388-395. DOI : 10.1038/s41589-018-0013-8.
B. Steinegger; A. Cardillo; P. De Los Rios; J. Gómez-Gardeñes; A. Arenas : Interplay between cost and benefits triggers nontrivial vaccination uptake; Physical Review. 2018-02-02. Vol. E97, num. 3. DOI : 10.1103/PhysRevE.97.032308.
T. Skrbic; S. Zamuner; R. Hong; F. Seno; A. Laio et al. : Vibrational entropy estimation can improve binding affinity prediction for non-obligatory protein complexes; PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2018. Vol. 86, num. 4, p. 393-404. DOI : 10.1002/prot.25454.

Theses

A. S. Sassi : Non equilibrium thermodynamics of protein organization. Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8507.
A. Martini : Unleashing the power of semantic text analysis: a complex systems approach. Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8473.
D. Malinverni : Statistical Analysis of Protein Sequences: A Coevolutionary Study of Molecular Chaperones. Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8463.

2017

Journal Articles

A. S. Sassi; S. Assenza; P. De Los Rios : Shape of a Stretched Polymer; Physical Review Letters. 2017. Vol. 119, num. 3, p. 037801. DOI : 10.1103/PhysRevLett.119.037801.
P. Goloubinoff; A. S. Sassi; B. Fauvet; A. Barducci; P. De Los Rios : Molecular chaperones inject energy from ATP hydrolysis into the non-equilibrium stabilisation of native proteins; bioRxiv. 2017. DOI : 10.1101/146852.
N. B. Nillegoda; A. Stank; D. Malinverni; N. Alberts; A. Szlachcic et al. : Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes; eLife. 2017. Vol. 6. DOI : 10.7554/eLife.24560.
V. Gemmetto; A. Cardillo; D. Garlaschelli : Irreducible network backbones: unbiased graph filtering via maximum entropy; arxiv.org. 2017.
A. Antonioni; A. Cardillo : Coevolution of Synchronization and Cooperation in Costly Networked Interactions; Physical Review Letters. 2017. Vol. 118, num. 23, p. 238301. DOI : 10.1103/PhysRevLett.118.238301.
B. Nguyen; D. Hartich; U. Seifert; P. De Los Rios : Thermodynamic bounds on the ultra- and infra-affinity of Hsp70 for its substrates; Biophysical Journal. 2017. Vol. 34, num. 4, p. 362-370. DOI : 10.1016/j.bpj.2017.06.010.
M. Fantini; D. Malinverni; P. De Los Rios; A. Pastore : New Techniques for Ancient Proteins: Direct Coupling Analysis Applied on Proteins Involved in Iron Sulfur Cluster Biogenesis; Frontiers in Molecular Biosciences. 2017. Vol. 4. DOI : 10.3389/fmolb.2017.00040.
D. Malinverni; A. Jost Lopez; P. De Los Rios; G. Hummer; A. Barducci : Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis; eLife. 2017. Vol. 6. DOI : 10.7554/eLife.23471.
A. Japaridze; G. Muskhelishvili; F. Benedetti; A. F. M. Gavriilidou; R. Zenobi et al. : Hyperplectonemes: A Higher Order Compact and Dynamic DNA Self-Organization; Nano Letters. 2017. Vol. 17, num. 3, p. 1938-1948. DOI : 10.1021/acs.nanolett.6b05294.
A. Cardillo; P. De Los Rios; A. Martini : ScienceWISE: Topic Modeling over Scientific Literature Networks; arxiv.org. 2017.

2016

Journal Articles

P. De Los Rios; P. Goloubinoff : Hsp70 chaperones use ATP to remodel native protein oligomers and stable aggregates by entropic pulling; Nature Structural & Molecular Biology. 2016. Vol. 23, num. 9, p. 766-769. DOI : 10.1038/nsmb.3283.

Book Chapters

A. Finka; R. U. H. Mattoo; P. Goloubinoff : Experimental Milestones in the Discovery of Molecular Chaperones as Polypeptide Unfolding Enzymes; Annual Review Of Biochemistry, Vol 85; Palo Alto: Annual Reviews, 2016. p. 715-742.

2015

Journal Articles

S. Assenza; P. De Los Rios; A. S. Sassi : The Shape of a Stretched Polymer; arxiv. 2015.
D. Malinverni; S. Marsili; A. Barducci; P. De Los Rios : Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones; Plos Computational Biology. 2015. Vol. 11, num. 6, p. e1004262. DOI : 10.1371/journal.pcbi.1004262.
F. Palazzesi; M. K. Prakash; M. Bonomi; A. Barducci : Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States; Journal Of Chemical Theory And Computation. 2015. Vol. 11, num. 1, p. 2-7. DOI : 10.1021/ct500718s.
A. Hameau; S. Fruchon; C. Bijani; A. Barducci; M. Blanzat et al. : Theoretical and Experimental Characterization of Amino-PEG-Phosphonate-Terminated Polyphosphorhydrazone Dendrimers: Influence of Size and PEG Capping on Cytotoxicity Profiles; Journal Of Polymer Science Part A-Polymer Chemistry. 2015. Vol. 53, num. 6, p. 761-774. DOI : 10.1002/pola.27501.
A. Finka; V. Sood; M. Quadroni; P. De Los Rios; P. Goloubinoff : Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs; Cell Stress and Chaperones. 2015. Vol. 20, num. 4, p. 605–620. DOI : 10.1007/s12192-015-0583-2.
S. Assenza; P. De Los Rios; A. Barducci : Quantifying the role of chaperones in protein translocation by computational modeling; Frontiers in Molecular Biosciences. 2015. Vol. 2. DOI : 10.3389/fmolb.2015.00008.

Reviews

A. Barducci; P. De Los Rios : Non-equilibrium conformational dynamics in the function of molecular chaperones; Current Opinion in Structural Biology. 2015. Vol. 30, p. 161-169. DOI : 10.1016/j.sbi.2015.02.008.

Theses

S. Assenza : Polymer-theory insights into biomolecular systems. Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6585.

2014

Journal Articles

S. Assenza; J. Adamcik; R. Mezzenga; P. De Los Rios : Universal Behavior in the Mesoscale Properties of Amyloid Fibrils; Physical Review Letters. 2014. Vol. 113, num. 26, p. 268103. DOI : 10.1103/PhysRevLett.113.268103.
L. Alonso-Sarduy; P. De Los Rios; F. Benedetti; D. Vobornik; G. Dietler et al. : Real-Time Monitoring of Protein Conformational Changes Using a Nano-Mechanical Sensor; Plos One. 2014. Vol. 9, num. 7, p. e103674. DOI : 10.1371/journal.pone.0103674.
R. Kellner; H. Hofmann; A. Barducci; B. Wunderlich; D. Nettels et al. : Single-molecule spectroscopy reveals chaperone-mediated expansion of substrate protein; 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.
P. De Los Rios; A. Barducci : Hsp70 chaperones are non-equilibrium machines that achieve ultra-affinity by energy consumption; Elife. 2014. Vol. 3. DOI : 10.7554/eLife.02218.
J. Straubhaar; D. Malinverni : Addressing Conditioning Data in Multiple-Point Statistics Simulation Algorithms Based on a Multiple Grid Approach; Mathematical Geosciences. 2014. Vol. 46, num. 2, p. 187-204. DOI : 10.1007/s11004-013-9479-9.
I. Bischofberger; D. C. E. Calzolari; P. De Los Rios; I. Jelezarov; V. Trappe : Hydrophobic hydration of poly-N-isopropyl acrylamide: a matter of the mean energetic state of water; Scientific Reports. 2014. Vol. 4. DOI : 10.1038/srep04377.

Reviews

F. Sterpone; S. Melchionna; P. Tuffery; S. Pasquali; N. Mousseau et al. : The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems; Chemical Society Reviews. 2014. Vol. 43, num. 13, p. 4871-4893. DOI : 10.1039/c4cs00048j.

Theses

L. Floretta : Topics in Community Detection. Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6140.

Book Chapters

L. Lotero; A. Cardillo; R. Hurtado; J. Gómez-Gardeñes : Several Multiplexes in the same City: The role of wealth differences in urban mobility; Interconnected Networks; Springer, 2014.

2013

Journal Articles

L. Floretta; J. Liechti; A. Flammini; P. De Los Rios : Stochastic fluctuations and the detectability limit of network communities; Physical Review E. 2013. Vol. 88, num. 6. DOI : 10.1103/PhysRevE.88.060801.
A. Barducci; M. Bonomi; M. K. Prakash; M. Parrinello : Free-energy landscape of protein oligomerization from atomistic simulations; 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.
G. Doni; M. D. N. Ngavouka; A. Barducci; P. Parisse; A. De Vita et al. : Structural and energetic basis for hybridization limits in high-density DNA monolayers; Nanoscale. 2013. Vol. 5, num. 20, p. 9988-9993. DOI : 10.1039/c3nr01799k.
F. Palazzesi; A. Barducci; M. Tollinger; M. Parrinello : The allosteric communication pathways in KIX domain of CBP; Proceedings of the National Academy of Sciences. 2013. Vol. 110, p. 14237-14242. DOI : 10.1073/pnas.1313548110.
D. Sanfelice; A. Politou; S. R. Martin; P. De Los Rios; P. Temussi et al. : The effect of crowding and confinement: a comparison of Yfh1 stability in different environments; Physical Biology. 2013. Vol. 10, p. 045002. DOI : 10.1088/1478-3975/10/4/045002.
S. Priya; S. K. Sharma; V. Sood; R. U. H. Mattoo; A. Finka et al. : GroEL and CCT are catalytic unfoldases mediating out-of-cage polypeptide refolding without ATP; Proceedings of the National Academy of Sciences. 2013. Vol. 110, p. 7199-7204. DOI : 10.1073/pnas.1219867110.
F. Piazza; N. Dorsaz; C. De Michele; P. De Los Rios; G. Foffi : Diffusion-limited reactions in crowded environments: a local density approximation; Journal of Physics: Condensed Matter. 2013. Vol. 25, num. 37, p. 375104. DOI : 10.1088/0953-8984/25/37/375104.

2012

Journal Articles

C. Maffi; M. Baiesi; L. Casetti; F. Piazza; P. De Los Rios : First-order coil-globule transition driven by vibrational entropy; Nature Communications. 2012. Vol. 3. DOI : 10.1038/ncomms2055.
P. De Los Rios; M. Hafner; A. Pastore : Explaining the length threshold of polyglutamine aggregation; Journal of Physics: Condensed Matter. 2012. Vol. 24, p. 244105. DOI : 10.1088/0953-8984/24/24/244105.
P. De Los Rios; P. Goloubinoff : Protein folding: Chaperoning protein evolution; Nature Chemical Biology. 2012. Vol. 8, p. 226-228. DOI : 10.1038/nchembio.791.

Theses

C. Maffi : Entropy in the Coil-to-Globule Transition of Macromolecules. Lausanne, EPFL, 2012. DOI : 10.5075/epfl-thesis-5256.
D. Morton de Lachapelle : Modern Portfolio Theory Revisited. Lausanne, EPFL, 2012. DOI : 10.5075/epfl-thesis-5255.

2011

Journal Articles

S. K. Sharma; P. De Los Rios; P. Goloubinoff : Probing the different chaperone activities of the bacterial HSP70-HSP40 system using a thermolabile luciferase substrate; Proteins. 2011. Vol. 79, p. 1991-1998. DOI : 10.1002/prot.23024.
R. Gutierrez; A. Amann; S. Assenza; J. Gomez-Gardenes; V. Latora et al. : Emerging Meso- and Macroscales from Synchronization of Adaptive Networks; Physical Review Letters. 2011. Vol. 107, p. 234103. DOI : 10.1103/PhysRevLett.107.234103.

2010

Journal Articles

T. Piazza; F. Piazza : On inconsistent entities. A reply to Colyvan; Philosophical Studies. 2010. Vol. 150, num. 2, p. 301-311. DOI : 10.1007/s11098-009-9410-x.
L. Lavanant; B. Pullin; J. A. Hubbell; H.-A. Klok : A facile strategy for the modification of polyethylene substrates with non-fouling, bioactive poly(poly(ethylene glycol) methacrylate) brushes; Macromolecular bioscience. 2010. Vol. 10, num. 1, p. 101-8. DOI : 10.1002/mabi.200900205.
N. Dorsaz; C. De Michele; F. Piazza; P. De Los Rios; G. Foffi : Diffusion-Limited Reactions in Crowded Environments; Physical Review Letters. 2010. Vol. 105, num. 12. DOI : 10.1103/PhysRevLett.105.120601.
S. K. Sharma; P. De Los Rios; P. Christen; A. Lustig; P. Goloubinoff : The kinetic parameters and energy cost of the Hsp70 chaperone as a polypeptide unfoldase; Nature Chemical Biology. 2010. Vol. 6, num. 12, p. 914-920. DOI : 10.1038/nchembio.455.
F. Piazza : Simple Monte Carlo model for crowd dynamics; Physical Review E. 2010. Vol. 82, p. 026111. DOI : 10.1103/PhysRevE.82.026111.
L. Bongini; F. Piazza; L. Casetti; P. De Los Rios : Vibrational entropy and the structural organization of proteins; The European Physical Journal E - Soft Matter & Biological Physics. 2010. Vol. 33, p. 89-96. DOI : 10.1140/epje/i2010-10653-8.
D. Morton de Lachapelle; D. Challet : Turnover, account value and diversification of real traders: evidence of collective portfolio optimizing behavior; New Journal of Physics. 2010. Vol. 12, p. 075039. DOI : 10.1088/1367-2630/12/7/075039.
J. Adamcik; J.-M. Jung; J. Flakowski; P. De Los Rios; G. Dietler et al. : Understanding amyloid aggregation by statistical analysis of atomic force microscopy images; Nature Nanotechnology. 2010. Vol. 5, num. 6, p. 423-428. DOI : 10.1038/nnano.2010.59.
N. Dorsaz; C. De Michele; F. Piazza; G. Foffi : Inertial effects in diffusion-limited reactions; Journal Of Physics-Condensed Matter. 2010. Vol. 22, p. 104116. DOI : 10.1088/0953-8984/22/10/104116.
A. Jan; D. M. Hartley; H. A. Lashuel : Preparation and characterization of toxic Abeta aggregates for structural and functional studies in Alzheimer's disease research; Nature protocols. 2010. Vol. 5, num. 6, p. 1186-209. DOI : 10.1038/nprot.2010.72.
Y. Pedrazzini : Fonction sportive de la ruelle: une ethnologie du basket dans le monde des gangs et des barrios; Ethnographiques.org. 2010. Vol. "Aux frontières du sport: regards socio-anthropologiques sur les pratiques ludiques et informelles, num. 20.

Conference Papers

M. Manassi; B. Sayim; M. H. Herzog : In contextual modulation, bigger is not better for low luminance stimuli ; Perception. 2010. 33rd European Conference on Visual Perception , Lausanne, Switzerland, August 22-26, 2010. p. 28.
G. Dubochet; D. Malayeri : Improving API Documentation for Java-like Languages. 2010. Evaluation and Usability of Programming Languages and Tools, Reno, Nevada, USA, October 18, 2010.
M. Canini; D. Novakovic; V. Jovanovic; D. Kostic : Fault Prediction in Distributed Systems Gone Wild ; Proceedings of The 4th ACM SIGOPS/SIGACT Workshop on Large Scale Distributed Systems and Middleware. 2010. LADIS 2010: The 4th ACM SIGOPS/SIGACT Workshop on Large Scale Distributed Systems and Middleware, Zurich, Switzerland, July 2010.

Books

Networks in Cell Biology ; Cambridge: Cambridge University Press.

Student Projects

A. Roshan Ghias : Monitoring bone fetal cells seeded in PLA scaffolds using bioluminescence imaging ; 2010.
E. Denstaad; A. Roshan Ghias : Back-calculation of mechanical properties of bone scaffolds using micro- finite element analysis and compression test (Semester project) ; 2010.

2009

Journal Articles

L. Ciandrini; C. Maffi; A. Motta; B. Bassetti; M. Cosentino Lagomarsino : Feedback topology and XOR-dynamics in Boolean networks with varying input structure; Physical Review E. 2009. Vol. 80, num. 2. DOI : 10.1103/PhysRevE.80.026122.
F. Piazza; S. Lepri : Heat wave propagation in a nonlinear chain; Physical Review B. 2009. Vol. 79, p. 094306. DOI : 10.1103/PhysRevB.79.094306.
F. Piazza; Y.-H. Sanejouand : Long-range energy transfer in proteins; Physical Biology. 2009. Vol. 6, p. 046014. DOI : 10.1088/1478-3975/6/4/046014.
F. Piazza; Y.-H. Sanejouand : Energy transfer in nonlinear network models of proteins; Europhysics Letters. 2009. Vol. 88, p. 68001. DOI : 10.1209/0295-5075/88/68001.
F. Piazza; P. De Los Rios; F. Cecconi : Temperature Dependence of Normal Mode Reconstructions of Protein Dynamics; Physical Review Letters. 2009. Vol. 102, p. 218104. DOI : 10.1103/PhysRevLett.102.218104.
C. C. Cartozo; P. De Los Rios : Extended Navigability of Small World Networks: Exact Results and New Insights; Physical Review Letters. 2009. Vol. 102, p. 238703. DOI : 10.1103/PhysRevLett.102.238703.

Theses

C. Caretta Cartozo : Complex networks. Lausanne, EPFL, 2009. DOI : 10.5075/epfl-thesis-4462.

2008

Journal Articles

M. A. Serrano; D. Krioukov; M. Boguna : Self-similarity of complex networks and hidden metric spaces; Physical Review Letters. 2008. Vol. 100, p. -. DOI : 10.1103/PhysRevLett.100.078701.
C. Roduit; F. G. van der Goot; P. De Los Rios; A. Yersin; P. Steiner et al. : Elastic membrane heterogeneity of living cells revealed by stiff nanoscale membrane domains; Biophysical Journal. 2008. Vol. 94, p. 1521-1532. DOI : 10.1529/biophysj.107.112862.
D. Gfeller; P. De Los Rios : Spectral coarse graining and synchronization in oscillator networks; Physical Review Letters. 2008. Vol. 100, p. 174104. DOI : 10.1103/PhysRevLett.100.174104.
S. R. Martin; V. Esposito; P. De Los Rios; A. Pastore; P. A. Temussi : Cold denaturation of yeast frataxin offers the clue to understand the effect of alcohols on protein stability; Journal Of The American Chemical Society. 2008. Vol. 130, p. 9963-9970. DOI : 10.1021/ja803280e.
M. A. Serrano; P. De Los Rios : Structural Efficiency of Percolated Landscapes in Flow Networks; Plos One. 2008. Vol. 3, p. e3654. DOI : 10.1371/journal.pone.0003654.
F. Piazza; Y.-H. Sanejouand : Discrete breathers in protein structures; Physical Biology. 2008. Vol. 5, p. 026001. DOI : 10.1088/1478-3975/5/2/026001.

Conference Papers

C. C. Cartozo; D. Garlaschelli; C. Ricotta; M. Barthelemy; G. Caldarelli : Quantifying the taxonomic diversity in real species communities ; Journal Of Physics A-Mathematical And Theoretical. 2008. Workshop on Complex Networks - from Biology to Information Technology, Pula, ITALY, Jul, 2007. p. -. DOI : 10.1088/1751-8113/41/22/224012.
J. Rüter; F. Scharnowski; T. Kammer; M. H. Herzog : How TMS and (light) masks modulate feature integration ; FENS Abstr.. 2008. 6th FENS: Forum of European Neuroscience, Genève, Switzerland, July 12-16, 2008. p. 220.13.

2007

Journal Articles

P. De Los Rios; T. Petermann : Existence, cost and robustness of spatial small-world networks; International Journal Of Bifurcation And Chaos. 2007. Vol. 17, p. 2331-2342. DOI : 10.1142/S0218127407018427.
M. Angeles Serrano; M. Boguna; A. Vespignani : Patterns of dominant flows in the world trade web; J. Econ. Interac. Coor.. 2007. Vol. 2, p. 111. DOI : 10.1007/s11403-007-0026-y.
D. Gfeller; P. De Los Rios; A. Caflisch; F. Rao : Complex network analysis of free-energy landscapes; Proceedings Of The National Academy Of Sciences Of The United States Of America. 2007. Vol. 104, p. 1817-1822. DOI : 10.1073/pnas.0608099104.
E. Ercolini; F. Valle; J. Adamcik; G. Witz; R. Metzler et al. : Fractal dimension and localization of DNA knots; Physical Review Letters. 2007. Vol. 98, p. 058102. DOI : 10.1103/PhysRevLett.98.058102.
S. Ciliberti; P. De Los Rios; F. Piazza : On the origin of the boson peak in globular proteins; Philosophical Magazine. 2007. Vol. 87, p. 631-641. DOI : 10.1080/14786430601042369.
C. Caretta-Cartozo; P. De Los Rios; F. Piazza; P. Lio : Bottleneck genes and community structure in the cell cycle network of S-pombe; Plos Computational Biology. 2007. Vol. 3, p. 968-976. DOI : 10.1371/journal.pcbi.0030103.
D. Gfeller; P. De Los Rios : Spectral coarse graining of complex networks; Physical Review Letters. 2007. Vol. 99, p. 038701. DOI : 10.1103/PhysRevLett.99.038701.
L. Bongini; D. Fanelli; S. Svensson; M. Gedda; F. Piazza et al. : Resolving the geometry of biomolecules imaged by cryo electron tomography; Journal Of Microscopy-Oxford. 2007. Vol. 228, p. 174-184. DOI : 10.1111/j.1365-2818.2007.01839.x.
F. Cecconi; P. D. L. Rios; F. Piazza : Diffusion-limited unbinding of small peptides from PDZ domains; Journal Of Physical Chemistry B. 2007. Vol. 111, p. 11057-11063. DOI : 10.1021/jp0730390.
D. Gfeller; D. M. de Lachapelle; P. D. L. Rios; G. Caldarelli; F. Rao : Uncovering the topology of configuration space networks; Physical Review E. 2007. Vol. 76, p. 026113. DOI : 10.1103/PhysRevE.76.026113.
L. Bongini; D. Fanelli; F. Piazza; P. De Los Rios; M. Sanner et al. : A dynamical study of antibody-antigen encounter reactions; Physical Biology. 2007. Vol. 4, p. 172-180. DOI : 10.1088/1478-3975/4/3/004.
M. A. Serrano; P. D. L. Rios : Interfaces and the edge percolation map of random directed networks; Physical Review E. 2007. Vol. 76, p. 056121. DOI : 10.1103/PhysRevE.76.056121.
B. Juanico; Y.-H. Sanejouand; F. Piazza; P. De Los Rios : Discrete Breathers in Nonlinear Network Models of Proteins; Physical Review Letters. 2007. Vol. 99, num. 23, p. 8104. DOI : 10.1103/PhysRevLett.99.238104.
E. Pelucchi; S. Watanabe; K. Leifer; Q. Zhu; B. Dwir et al. : Mechanisms of Quantum Dot Energy Engineering by Metalorganic Vapor Phase Epitaxy on Patterned Nonplanar Substrates; Nano Letters. 2007. Vol. 7, num. 5, p. 1282-1285. DOI : 10.1021/nl0702012.
F. Sansoz; J. F. Molinari : Size and microstructure effects on the mechanical behavior of FCC bicrystals by quasicontinuum method; Thin Solid Films. 2007. Vol. 515, num. 6, p. 3158-3163. DOI : 10.1016/j.tsf.2006.01.012.

Reviews

P. Goloubinoff; P. De Los Rios : The mechanism of Hsp70 chaperones: (entropic) pulling the models together; Trends in Biochemical Sciences. 2007. Vol. 32, num. 8, p. 372-380. DOI : 10.1016/j.tibs.2007.06.008.

Theses

D. Gfeller : Simplifying complex networks. Lausanne, EPFL, 2007. DOI : 10.5075/epfl-thesis-3888.

Posters

E. Thomasson; B. Städler; T. Blättler; L. Jacot-Descombes; J. Vörös et al. : Real Time Analysis of Myogenesis in Behaving Myoblasts ; JPK SPM Workshop, Berlin, Germany, October 9, 2007.

2006

Journal Articles

P. De Los Rios; T. Petermann : Physical realizability of small-world networks; Physical Review E. 2006. Vol. 73, p. 026114. DOI : 10.1103/PhysRevE.73.026114.
P. De Los Rios; A. Ben-Zvi; O. Slutski; A. Azem; P. Goloubinoff : Hsp70 chaperones accelerate protein translocation and the unfolding of stable protein aggregates by entropic pulling; Proceedings of the National Academy of Sciences. 2006. Vol. 103, num. 16, p. 6166-6171. DOI : 10.1073/pnas.0510496103.
P. De Los Rios; F. Piazza; S. Ciliberti : Glasslike structure of globular proteins and the boson peak; Physical Review Letters. 2006. Vol. 96, p. 198103. DOI : 10.1103/PhysRevLett.96.198103.
C. Weber; A. Stasiak; P. De los Rios; G. Dietler : Numerical simulation of gel electrophoresis of DNA knots in weak and strong electric fields; Biophysical Journal. 2006. Vol. 90, num. 9, p. 3100-3105. DOI : 10.1529/biophysj.105.070128.
C. Weber; P. D. L. Rios; G. Dietler; A. Stasiak : Simulations of electrophoretic collisions of DNA knots with gel obstacles; Journal of Physics-Condensed Matter. 2006. Vol. 18, num. 14, p. S161-S171. DOI : 10.1088/0953-8984/18/14/S02.

2005

Journal Articles

F. Piazza; P. Lio : Statistical analysis of simple repeats in the human genome; Physica A: Statistical Mechanics and its Applications. 2005. Vol. 347, p. 472-488. DOI : 10.1016/j.physa.2004.08.038.
D. Fanelli; F. Piazza; P. D. Rios; S. Sandin; U. Skoglund et al. : Dynamics of antibodies from cryo-electron tomography; Biophysical Chemistry. 2005. Vol. 115, p. 235-240. DOI : 10.1016/j.bpc.2004.12.037.
F. Piazza; P. D. L. Rios; D. Fanelli; L. Bongini; U. Skoglund : Anti-cooperativity in diffusion-controlled reactions with pairs of anisotropic domains: a model for the antigen-antibody encounter; European biophysics journal : EBJ. 2005. Vol. 34, num. 7, p. 899-911. DOI : 10.1007/s00249-005-0460-5.
P. De los Rios; M. Vendruscolo; G. Salvi : Effective interactions between chaotropic agents and proteins; Proteins-Structure Function And Bioinformatics. 2005. Vol. 61, p. 492-499. DOI : 10.1002/prot.20626.
F. Piazza; P. De Los Rios; Y.-H. Sanejouand : Slow Energy Relaxation of Macromolecules and Nanoclusters in Solution; Physical Review Letters. 2005. Vol. 94, num. 14, p. 5502. DOI : 10.1103/PhysRevLett.94.145502.
P. De Los Rios; F. Cecconi; A. Pretre; G. Dietler; O. Michielin et al. : Functional dynamics of PDZ binding domains: A normal-mode analysis; Biophysical Journal. 2005. Vol. 89, num. 1, p. 14-21. DOI : 10.1529/biophysj.104.055004.
F. Valle; M. Favre; P. De Los Rios; A. Rosa; G. Dietler : Scaling exponents and probability distributions of DNA end-to-end distance; Physical Review Letters. 2005. Vol. 95, num. 15, p. 158105. DOI : 10.1103/PhysRevLett.95.158105.
D. Gfeller; J.-C. Chappelier; P. De Los Rios : Finding instabilities in the community structure of complex networks; Physical Review E. 2005. Vol. 72, num. 5, p. 056135. DOI : 10.1103/PhysRevE.72.056135.

Theses

T. Petermann : A statistical physics perspective of complex networks. Lausanne, EPFL, 2005. DOI : 10.5075/epfl-thesis-3270.

2004

Journal Articles

G. Caldarelli; F. Coccetti; P. De Los Rios : Preferential exchange: Strengthening connections in complex networks; Physical Review E. 2004. Vol. 70, num. 2, p. 7102. DOI : 10.1103/PhysRevE.70.027102.
A. Ben-Zvi; P. De Los Rios; G. Dietler; P. Goloubinoff : Active solubilization and refolding of stable protein aggregates by cooperative unfolding action of individual hsp70 chaperones; The Journal of biological chemistry. 2004. Vol. 279, num. 36, p. 37298-303. DOI : 10.1074/jbc.M405627200.
S. Moelbert; B. Normand; P. Rios : Solvent-induced micelle formation in a hydrophobic interaction model; Physical Review E. 2004. Vol. 69, num. 6, p. 1924. DOI : 10.1103/PhysRevE.69.061924.
J. R. Banavar; P. De Los Rios; A. Flammini; N. S. Holter; A. Maritan : Scale-free behavior and universality in random fragmentation and aggregation; 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.
T. Petermann; P. De Los Rios : Role of clustering and gridlike ordering in epidemic spreading; Physical Review E. 2004. Vol. 69, num. 6, p. 6116. DOI : 10.1103/PhysRevE.69.066116.
D. Fanelli; F. Piazza; P. De los Rios; S. Sandin; U. Skoglund et al. : Freezing immunoglobulins to see them move; Proceedings Of The National Academy Of Sciences Of The United States Of America. 2004. Vol. 101, p. 6466-6471. DOI : 10.1073/pnas.0400119101.
T. Petermann; P. De Los Rios : Cluster approximations for epidemic processes: a systematic description of correlations beyond the pair level; Journal of Theoretical Biology. 2004. Vol. 229, num. 1, p. 1-11. DOI : 10.1016/j.jtbi.2004.02.017.
P. De los Rios; M. Montuori; V. D. P. Servedio; G. Caldarelli : Statistical features of drainage basins in mars channel networks - Can one guess from the landscape the past presence of water?; European Physical Journal B. 2004. Vol. 38, p. 387-391. DOI : 10.1140/epjb/e2004-00132-y.
A. Barrat; A. L. Barabasi; G. Caldarelli; P. De los Rios; A. Erzan et al. : Virtual Round Table on ten leading questions for network research; European Physical Journal B. 2004. Vol. 38, p. 143-145. DOI : 10.1140/epjb/e2004-00109-x.
T. Petermann; P. De Los Rios : Exploration of scale-free networks; The European Physical Journal B - Condensed Matter. 2004. Vol. 38, num. 2, p. 201-204. DOI : 10.1140/epjb/e2004-00021-5.
G. Caldarelli; C. C. Cartozo; P. D. L. Rios; V. D. P. Servedio : Widespread occurrence of the inverse square distribution in social sciences and taxonomy; 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.
S. Kasas; C. Cibert; A. Kis; P. De Los Rios; B. M. Riederer et al. : Oscillation modes of microtubules; Biology of the Cell. 2004. Vol. 96, num. 9, p. 697-700. DOI : 10.1016/j.biolcel.2004.09.002.

Theses

G. Salvi : Explicit solvent effects on protein physics - modeling lattice proteins in aqueous environments. Lausanne, EPFL, 2004. DOI : 10.5075/epfl-thesis-3070.

2003

Journal Articles

A. B. Verkhovsky; O. Y. Chaga; S. Schaub; T. M. Svitkina; J.-J. Meister et al. : Orientational order of the lamellipodial actin network as demonstrated in living motile cells; Molecular biology of the cell. 2003. Vol. 14, num. 11, p. 4667-4675. DOI : 10.1091/mbc.E02-10-0630.
S. Moelbert; P. De Los Rios : Chaotropic effect and preferential binding in a hydrophobic interaction model; The Journal of Chemical Physics. 2003. Vol. 119, num. 15, p. 7988. DOI : 10.1063/1.1609982.
G. Caldarelli; P. De Los Rios; A. Capocci : Quantitative description and modeling of real networks; Physical Review E. 2003. Vol. 68, p. 047101. DOI : 10.1103/PhysRevE.68.047101.
S. Moelbert; P. De Los Rios : Hydrophobic Interaction Model for Upper and Lower Critical Solution Temperatures; Macromolecules. 2003. Vol. 36, num. 15, p. 5845-5853. DOI : 10.1021/ma025890c.
G. Salvi; P. De Los Rios : Effective Interactions Cannot Replace Solvent Effects in a Lattice Model of Proteins; Physical Review Letters. 2003. Vol. 91, num. 25, p. 8102. DOI : 10.1103/PhysRevLett.91.258102.
A. Yersin; H. Hirling; P. Steiner; S. Magnin; R. Regazzi et al. : Interactions between synaptic vesicle fusion proteins explored by atomic force microscopy; 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

P. Vandewalle; S. Süsstrunk; M. Vetterli : Superresolution images reconstructed from aliased images ; Proc. SPIE/IS&T Visual Communications and Image Processing Conference. 2003. p. 1398-1405. DOI : 10.1117/12.506874.

2002

Journal Articles

A. Capocci; P. De Los Rios; M. A. Munoz; G. Caldarelli : Scale-free networks from varying vertex intrinsic fitness; Physical Review Letters. 2002. Vol. 89, p. 258702. DOI : 10.1103/PhysRevLett.89.258702.
S. Molbert; P. De Los Rios; G. Salvi : Design of lattice proteins with explicit solvent; Physical Review E. 2002. Vol. 66, p. 061911. DOI : 10.1103/PhysRevE.66.061911.
P. De Los Rios; S. Moelbert : The local minority game; Physica A-Statistical Mechanics And Its Applications. 2002. Vol. 303, p. 217-225. DOI : 10.1016/S0378-4371(01)00480-0.

Conference Papers

S. Valaeys; G. Menegaz; J. Reichel; F. Ziliani : Modeling of Texture Movies for Video Coding ; Proc. ECCV First International Workshop on Generative-Model-Based Vision. 2002. ECCV First International Workshop on Generative-Model-Based Vision. p. 43-51.
G. D. Finlayson; S. Süsstrunk : Optimization for Hue Constant RGB Sensors ; Proc. IS&T/SID 10th Color Imaging Conference. 2002. IS&T/SID 10th Color Imaging Conference, Scottsdale, November 2002. p. 343-348.
D. Alleysson; S. Süsstrunk; J. Hérault : Color Demosaicing by Estimating Luminance and Opponent Chromatic Signals in the Fourier Domain ; Proc. IS&T/SID 10th Color Imaging Conference. 2002. IS&T/SID 10th Color Imaging Conference, Scottsdale, AZ, Nov. 2002. p. 331-336.

2001

Journal Articles

P. De Los Rios : Power law size distribution of supercritical random trees; Europhysics Letters. 2001. Vol. 56, p. 898-903. DOI : 10.1209/epl/i2001-00604-2.
P. De Los Rios; G. Caldarelli : Cold and warm denaturation of proteins; Journal Of Biological Physics. 2001. Vol. 27, p. 229-241. DOI : 10.1023/A:1013145009949.
P. De Los Rios; G. Caldarelli : Cold and warm swelling of hydrophobic polymers; Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 2001. Vol. 63, p. 0318021-03180205. DOI : 10.1103/PhysRevE.63.031802.
S. Lise; A. Pelizzola; P. De los Rios : Bethe approximation for self-interacting lattice trees; Europhysics Letters. 2001. Vol. 53, p. 176-182. DOI : 10.1209/epl/i2001-00133-6.

2000

Journal Articles

G. Caldarelli; P. De los Rios; L. Pietronero; Y. C. Zhang; S. Ciliberti : Discretized diffusion processes; Physical Review Letters. 2000. Vol. 85, p. 4848-4851. DOI : 10.1103/PhysRevLett.85.4848.
G. Caldarelli; P. De Los Rios : Putting proteins back into water; Physical Review E. 2000. Vol. 62, p. 8449-8452. DOI : 10.1103/PhysRevE.62.8449.
O. Pla; P. De los Rios : Statistical analysis of genealogical trees for polygamic species; Physical Review E. 2000. Vol. 61, p. 5620-5623. DOI : 10.1103/PhysRevE.61.5620.
P. De los Rios; N. Manini : Berry phase and ground-state symmetry in H circle times h dynamical Jahn-Teller systems; Physical Review B. 2000. Vol. 62, p. 29-32. DOI : 10.1103/PhysRevB.62.29.

Conference Papers

F. Frey; S. Süsstrunk : Digital Photography - How Long Will It Last ; Proc. IEEE International Symposium on Circuits and Systems. 2000. IEEE International Symposium on Circuits and Systems. p. 113-116. DOI : 10.1109/ISCAS.2000.857376.

1999

Journal Articles

P. D. L. Rios; A. Maritan; F. Seno : Polymers with a bimodal disorder distribution and directed percolation; Journal of Physics A: Mathematical and General. 1999. Vol. 30, num. 18, p. L617-L621. DOI : 10.1088/0305-4470/30/18/002.
N. Manini; P. D. L. Rios : The role of the Berry phase in dynamical Jahn-Teller systems; Journal of Physics: Condensed Matter. 1999. Vol. 10, num. 38, p. 8485-8495. DOI : 10.1088/0953-8984/10/38/009.
R. Cafiero; P. De Los Rios; A. Valleriani; J. Vega : Levy-nearest-neighbors Bak-Sneppen model; Physical Review E. 1999. Vol. 60, num. 2, p. R1111-R1114. DOI : 10.1103/PhysRevE.60.R1111.
P. De Los Rios : Universality and Crossover of Directed Polymers and Growing Surfaces; Physical Review Letters. 1999. Vol. 82, num. 21, p. 4236-4239. DOI : 10.1103/PhysRevLett.82.4236.
P. De Los Rios; Y.-C. Zhang : Universal 1/f Noise from Dissipative Self-Organized Criticality Models; Physical Review Letters. 1999. Vol. 82, num. 3, p. 472-475. DOI : 10.1103/PhysRevLett.82.472.

1998

Journal Articles

S. Maslov; P. De Los Rios; M. Marsili; Y.-C. Zhang : Critical exponents of the anisotropic Bak-Sneppen model; Physical Review E. 1998. Vol. 58, num. 6, p. 7141-7145. DOI : 10.1103/PhysRevE.58.7141.
P. De Los Rios; Y.-C. Zhang : Directed Polymers on a Factorized Disorder Landscape; Physical Review Letters. 1998. Vol. 81, num. 5, p. 1023-1026. DOI : 10.1103/PhysRevLett.81.1023.
R. Cafiero; P. De Los Rios; F.-M. Dittes; A. Valleriani; J. Vega : Power-law behavior in a nonextremal Bak-Sneppen model; Physical Review E. 1998. Vol. 58, num. 3, p. 3993-3996. DOI : 10.1103/PhysRevE.58.3993.
P. De Los Rios; M. Marsili; M. Vendruscolo : High-Dimensional Bak-Sneppen Model; Physical Review Letters. 1998. Vol. 80, num. 26, p. 5746-5749. DOI : 10.1103/PhysRevLett.80.5746.
P. De Los Rios; A. Valleriani; J. Luis Vega : Self-organized criticality in deterministic systems with disorder; Physical Review E. 1998. Vol. 57, num. 6, p. 6451-6459. DOI : 10.1103/PhysRevE.57.6451.
M. Marsili; P. De Los Rios; S. Maslov : Expansion Around the Mean-Field Solution of the Bak-Sneppen Model; Physical Review Letters. 1998. Vol. 80, num. 7, p. 1457-1460. DOI : 10.1103/PhysRevLett.80.1457.

1997

Journal Articles

P. De Los Rios; A. Valleriani; J. Vega : Self-organized criticality driven by deterministic rules; Physical Review E. 1997. Vol. 56, num. 4, p. 4876-4879. DOI : 10.1103/PhysRevE.56.4876.

1996

Journal Articles

M. Vendruscolo; P. De Los Rios; L. Bonesi : Model of correlated evolution; Physical Review E. 1996. Vol. 54, num. 6, p. 6053-6057. DOI : 10.1103/PhysRevE.54.6053.
P. Rios; G. Caldarelli; A. Maritan; F. Seno : Optimal path and directed percolation; Physical Review E. 1996. Vol. 53, num. 3, p. R2029-R2032. DOI : 10.1103/PhysRevE.53.R2029.
P. De Los Rios; N. Manini; E. Tosatti : Dynamical Jahn-Teller effect and Berry phase in positively charged fullerenes: Basic considerations; Physical Review B. 1996. Vol. 54, num. 10, p. 7157-7167. DOI : 10.1103/PhysRevB.54.7157.

1994

Journal Articles

C. Buzano; P. De Los Rios : Reentrant behaviour in a highly anisotropic system; Physica A: Statistical and Theoretical Physics. 1994. Vol. 203, num. 3-4, p. 640-654. DOI : 10.1016/0378-4371(94)90019-1.