Distribution and evolutionary significance of the DnaK-DnaJ-GrpE (KJE) chaperone system in archaea

M. E. Rebeaud 

J-domain Proteins: From Molecular Mechanisms to Diseases

J. Kirstein; R. Rosenzweig; P. De Los Rios; P. Genevaux; C. Adang et al. 

Subtle variations in a client protein determine bacterial Hsp90 dependence

M. Corteggiani; A. Ali-Chaouche; M. Bahun; F. A. Honoré; D. Byrne et al. 

Hsp110 Nucleotide Exchange Factors may amplify Hsp70-disaggregation by enhanced entropic pulling

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

Physics of Protein Aggregation in Normal and Accelerated Brain Aging

A. J. Espay; A. Sturchio; A. Imarisio; E. J. Hill; B. J. Williamson et al. 

Collective Deformation Modes Promote Fibrous Self-Assembly in Deformable Particles

H. Le Roy; M. M. Terzi; M. Lenz 

Minimal Model for Carnot Efficiency at Maximum Power

S. Liang; Y. H. Ma; D. M. Busiello; P. De Los Rios 

Phase boundaries promote chemical reactions through localized fluxes

A. Shelest; H. Le Roy; D. M. Busiello; P. De Los Rios 

Stochastic thermodynamics for biological functions

Y. Cao; S. Liang 

Clearing the protein clutter in human cells: the role of protein disaggregases

N. Alberts-Visscher; P. De Los Rios; H. H. Kampinga; N. B. Nillegoda 

Non-equilibrium control of biomolecular condensates

Protein Organisation at Different Scales: Amyloid Disaggregation, Chaperone Networks and Engineered Allostery

Protein chaperones and the protein unfolding problem

P. De Los Rios 

Native, full-length, refolding-assisted purification of TDP-43 compatible with BSL-2 safety regulations

P. De Los Rios; S. Dehury; S. Tiwari 

Conserved intrinsically disordered region of DNAJB6 dictates its surveillance of FG-Nup condensates

T. Bergsma; M. K. Musskopf; P. Gallardo; M. E. Rebeaud; J. Feenstra et al. 

Controllable Protein Design via Autoregressive Direct Coupling Analysis Conditioned on Principal Components

F. Caredda; A. Pagnani; P. De Los Rios; L. Gennai 

On adaptation to a mesophilic environment and the chaperone network in Archaea

M. E. Rebeaud 

Discovery of a DNA-based Optical Nanotube Sensor for Glucose Using Clustering and Deep Learning Algorithms

Y. Rabbani; J. Bregy; B. Rousseau; S. H. Sajjadi; L. De Benedittis et al. 

Is Hsp110 boosting the basal disaggregation activity Hsp70 by enhanced entropic pulling strokes?

M. Rebeaud; B. Fauvet; P. De Los Rios; P. Goloubinoff 

An outmoded in vitro-inferred mechanism for chaperonin-accelerated protein refolding is confirmed in cells by cryo-electron tomography

P. De Los Rios; M. Rebeaud; P. Goloubinoff 

Single-molecule evidence of Entropic Pulling by Hsp70 chaperones

V. Rukes; M. Rebeaud; L. W. Perrin; P. De Los Rios; C. Cao 

Thermodynamic Bounds on Symmetry Breaking in Linear and Catalytic Biochemical Systems

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

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. 

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. 

J-domain proteins: From molecular mechanisms to diseases

J. Marszalek; P. De Los Rios; D. Cyr; M. P. Mayer; V. Adupa et al. 

Fundamental Thermodynamic Constraints on Symmetry Breaking in Biochemical Systems

Thermodynamic bounds on time-reversal asymmetry

S. Liang; S. Pigolotti 

Individual and combined benefits of different nonequilibrium proofreading mechanisms

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

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. 

ABC transporters are billion-year-old Maxwell Demons

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

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

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

Ricca’s factors as mobile proteinaceous effectors of electrical signaling

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

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

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

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. 

Information Theory in Transmembrane Transport

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

Emergent thermophoretic behavior in chemical reaction systems

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

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

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

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

G. Nicoletti; D. M. Busiello 

Information-driven transitions in projections of underdamped dynamics

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

Emergence of synergistic and competitive pathogens in a coevolutionary spreading model

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

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

S. Zamuner; F. Seno; A. Trovato 

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

L. Randall; A. Shelest; Z-Z. Xianyu 

J-domain protein chaperone circuits in proteostasis and disease

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

Mutual Information Disentangles Interactions from Changing Environments

G. Nicoletti; D. M. Busiello 

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. 

Inducing and optimizing Markovian Mpemba effect with stochastic reset

D. M. Busiello; D. Gupta; A. Maritan 

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

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

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. 

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. 

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. 

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

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

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

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

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

D. Gupta; D. M. Busiello 

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 

Molecular dissection of amyloid disaggregation by human HSP70

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

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. 

Entropy production in systems with unidirectional transitions

D. M. Busiello; D. Gupta; A. Maritan 

Protein Structural Information and Evolutionary Landscape by In Vitro Evolution

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

Thermodynamics and kinetics of protonated merocyanine photoacids in water

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

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 

Membraneless organelles: phasing out of equilibrium

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

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. 

Hyperaccurate currents in stochastic thermodynamics

D. M. Busiello; S. Pigolotti 

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

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

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

D. M. Busiello; A. Maritan 

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 

Entropy production for coarse-grained dynamics

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

Detailed experiments on weakly deformed cavitation bubbles

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

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. 

Function, evolution, and structure of J-domain proteins

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

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

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

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

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

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 

Interplay between cost and benefits triggers nontrivial vaccination uptake

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

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. 

Non equilibrium thermodynamics of protein organization

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

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

Coevolution of Synchronization and Cooperation in Costly Networked Interactions

A. Antonioni; A. Cardillo 

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

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

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 

The Shape of a Stretched Polymer

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

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. 

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

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

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 

Irreducible network backbones: unbiased graph filtering via maximum entropy

V. Gemmetto; A. Cardillo; D. Garlaschelli 

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 

ScienceWISE: Topic Modeling over Scientific Literature Networks

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

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

P. De Los Rios; P. Goloubinoff 

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

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

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. 

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 

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

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

Quantifying the role of chaperones in protein translocation by computational modeling

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

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 

Non-equilibrium conformational dynamics in the function of molecular chaperones

A. Barducci; P. De Los Rios 

Polymer-theory insights into biomolecular systems

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

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

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

J. Straubhaar; D. Malinverni 

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. 

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 

Universal Behavior in the Mesoscale Properties of Amyloid Fibrils

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

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

P. De Los Rios; A. Barducci 

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. 

Topics in Community Detection

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

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

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. 

Stochastic fluctuations and the detectability limit of network communities

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

Free-energy landscape of protein oligomerization from atomistic simulations

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

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. 

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. 

The allosteric communication pathways in KIX domain of CBP

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

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

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

Explaining the length threshold of polyglutamine aggregation

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

First-order coil-globule transition driven by vibrational entropy

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

Protein folding: Chaperoning protein evolution

P. De Los Rios; P. Goloubinoff 

Entropy in the Coil-to-Globule Transition of Macromolecules : Insights from Simple Models

Modern Portfolio Theory Revisited : from Real Traders to New Methods

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 

Emerging Meso- and Macroscales from Synchronization of Adaptive Networks

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

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 

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 

Simple Monte Carlo model for crowd dynamics

F. Piazza 

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

D. Morton de Lachapelle; D. Challet 

Inertial effects in diffusion-limited reactions

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

Vibrational entropy and the structural organization of proteins

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

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

Y. Pedrazzini 

Diffusion-Limited Reactions in Crowded Environments

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

On inconsistent entities. A reply to Colyvan

T. Piazza; F. Piazza 

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 

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. 

Fault Prediction in Distributed Systems Gone Wild

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

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

M. Manassi; B. Sayim; M. H. Herzog 

Improving API Documentation for Java-like Languages

G. Dubochet; D. Malayeri 

Networks in Cell Biology

Monitoring bone fetal cells seeded in PLA scaffolds using bioluminescence imaging

A. Roshan Ghias 

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

E. Denstaad; A. Roshan Ghias 

Energy transfer in nonlinear network models of proteins

F. Piazza; Y-H. Sanejouand 

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

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

Heat wave propagation in a nonlinear chain

F. Piazza; S. Lepri 

Temperature Dependence of Normal Mode Reconstructions of Protein Dynamics

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

Long-range energy transfer in proteins

F. Piazza; Y-H. Sanejouand 

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

C. C. Cartozo; P. De Los Rios 

Complex networks : from biological applications to exact theoretical solutions

Self-similarity of complex networks and hidden metric spaces

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

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. 

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 

Structural Efficiency of Percolated Landscapes in Flow Networks

M. A. Serrano; P. De Los Rios 

Spectral coarse graining and synchronization in oscillator networks

D. Gfeller; P. De Los Rios 

Discrete breathers in protein structures

F. Piazza; Y-H. Sanejouand 

How TMS and (light) masks modulate feature integration

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

Quantifying the taxonomic diversity in real species communities

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

Fractal dimension and localization of DNA knots

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

Discrete Breathers in Nonlinear Network Models of Proteins

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

On the origin of the boson peak in globular proteins

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

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

F. Sansoz; J. F. Molinari 

Resolving the geometry of biomolecules imaged by cryo electron tomography

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

Complex network analysis of free-energy landscapes

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

Uncovering the topology of configuration space networks

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

Existence, cost and robustness of spatial small-world networks

P. De Los Rios; T. Petermann 

Spectral coarse graining of complex networks

D. Gfeller; P. De Los Rios 

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

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

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. 

Diffusion-limited unbinding of small peptides from PDZ domains

F. Cecconi; P. D. L. Rios; F. Piazza 

A dynamical study of antibody-antigen encounter reactions

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

Interfaces and the edge percolation map of random directed networks

M. A. Serrano; P. D. L. Rios 

Patterns of dominant flows in the world trade web

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

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

P. Goloubinoff; P. De Los Rios 

Simplifying complex networks : from a clustering to a coarse graining strategy

Real Time Analysis of Myogenesis in Behaving Myoblasts

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

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 

Physical realizability of small-world networks

P. De Los Rios; T. Petermann 

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

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

Simulations of electrophoretic collisions of DNA knots with gel obstacles

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

Glasslike structure of globular proteins and the boson peak

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

Finding instabilities in the community structure of complex networks

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

Dynamics of antibodies from cryo-electron tomography

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

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 

Effective interactions between chaotropic agents and proteins

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

Statistical analysis of simple repeats in the human genome

F. Piazza; P. Lio 

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

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

Slow Energy Relaxation of Macromolecules and Nanoclusters in Solution

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

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

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

A statistical physics perspective of complex networks : from the architecture of the Internet and the brain to the spreading of an epidemic

Solvent-induced micelle formation in a hydrophobic interaction model

S. Moelbert; B. Normand; P. Rios 

Preferential exchange: Strengthening connections in complex networks

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

Exploration of scale-free networks

T. Petermann; P. De Los Rios 

Scale-free behavior and universality in random fragmentation and aggregation

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

Oscillation modes of microtubules

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

Freezing immunoglobulins to see them move

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

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

T. Petermann; P. De Los Rios 

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 

Role of clustering and gridlike ordering in epidemic spreading

T. Petermann; P. De Los Rios 

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. 

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 

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 

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

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. 

Quantitative description and modeling of real networks

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

Interactions between synaptic vesicle fusion proteins explored by atomic force microscopy

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

Hydrophobic Interaction Model for Upper and Lower Critical Solution Temperatures

S. Moelbert; P. De Los Rios 

Chaotropic effect and preferential binding in a hydrophobic interaction model

S. Moelbert; P. De Los Rios 

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

G. Salvi; P. De Los Rios 

Superresolution images reconstructed from aliased images

P. Vandewalle; S. Süsstrunk; M. Vetterli 

The local minority game

P. De Los Rios; S. Moelbert 

Scale-free networks from varying vertex intrinsic fitness

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

Design of lattice proteins with explicit solvent

S. Molbert; P. De Los Rios; G. Salvi 

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

D. Alleysson; S. Süsstrunk; J. Hérault 

Optimization for Hue Constant RGB Sensors

G. D. Finlayson; S. Süsstrunk 

Modeling of Texture Movies for Video Coding

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

Cold and warm denaturation of proteins

P. De Los Rios; G. Caldarelli 

Cold and warm swelling of hydrophobic polymers

P. De Los Rios; G. Caldarelli 

Power law size distribution of supercritical random trees

P. De Los Rios 

Bethe approximation for self-interacting lattice trees

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

Discretized diffusion processes

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

Putting proteins back into water

G. Caldarelli; P. De Los Rios 

Statistical analysis of genealogical trees for polygamic species

O. Pla; P. De los Rios 

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

P. De los Rios; N. Manini 

Digital Photography – How Long Will It Last

F. Frey; S. Süsstrunk 

Levy-nearest-neighbors Bak-Sneppen model

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

Polymers with a bimodal disorder distribution and directed percolation

P. D. L. Rios; A. Maritan; F. Seno 

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

P. De Los Rios; Y-C. Zhang 

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

N. Manini; P. D. L. Rios 

Universality and Crossover of Directed Polymers and Growing Surfaces

P. De Los Rios 

Self-organized criticality in deterministic systems with disorder

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

Power-law behavior in a nonextremal Bak-Sneppen model

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

High-Dimensional Bak-Sneppen Model

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

Directed Polymers on a Factorized Disorder Landscape

P. De Los Rios; Y-C. Zhang 

Critical exponents of the anisotropic Bak-Sneppen model

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

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

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

Self-organized criticality driven by deterministic rules

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

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

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

Optimal path and directed percolation

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

Model of correlated evolution

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

Reentrant behaviour in a highly anisotropic system

C. Buzano; P. De Los Rios