Paolo De Los Rios

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Publications associées (93)

Existence, cost and robustness of spatial small-world networks

Thomas Petermann, Paolo De Los Rios

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

World Scientific Publishing2007

Spectral coarse graining of complex networks

Paolo De Los Rios, David Gfeller

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

American Physical Society2007

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

Cédric Weber, Giovanni Dietler, Andrzej Stasiak, Paolo De Los Rios

2006

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

Paolo De Los Rios, Pierre Goloubinoff

National Academy of Sciences2006

Simulations of electrophoretic collisions of DNA knots with gel obstacles

Cédric Weber, Giovanni Dietler, Andrzej Stasiak, Paolo De Los Rios

Gel electrophoresis can be used to separate nicked circular DNA molecules of equal length but forming different knot types. At low electric fields, complex knots drift faster than simpler knots. However, at high electric field the opposite is the case and ...

Institute of Physics2006

Physical realizability of small-world networks

Thomas Petermann, Paolo De Los Rios

Supplementing a lattice with long-range connections effectively models small-world networks characterized by a high local and global interconnectedness observed in systems ranging from society to the brain. If the links have a wiring cost associated with t ...

2006

Glasslike structure of globular proteins and the boson peak

Paolo De Los Rios, Francesco Piazza

Vibrational spectra of proteins and topologically disordered solids display a common anomaly at low frequencies, known as boson peak. We show that such feature in globular proteins can be deciphered in terms of an energy landscape picture, as it is for gla ...

American Physical Society2006

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

Paolo De Los Rios, Francesco Piazza

The encounter between anisotropic agents in diffusion-controlled reactions is a topic of very general relevance in chemistry and biology. Here we introduce a simplified model of encounter of an isotropic molecule with a pair of partially reacting agents an ...

Springer-Verlag2005

Effective interactions between chaotropic agents and proteins

Paolo De Los Rios

Chaotropic agents are cosolutes that can disrupt the hydrogen bonding network between water molecules and reduce the stability of the native state of proteins by weakening the hydrophobic effect. In this work, we represent the chaotropic agent as a factor ...

2005

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Paolo De Los Rios

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Existence, cost and robustness of spatial small-world networks

Spectral coarse graining of complex networks

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

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

Simulations of electrophoretic collisions of DNA knots with gel obstacles

Physical realizability of small-world networks

Glasslike structure of globular proteins and the boson peak

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

Effective interactions between chaotropic agents and proteins

Slow Energy Relaxation of Macromolecules and Nanoclusters in Solution

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

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

Finding instabilities in the community structure of complex networks