Should we use early less invasive hemodynamic monitoring in unstable ICU patients?

In the previous issue of Critical Care, Takala and colleagues presented the results of a multicenter study to investigate whether the early presence of less invasive hemodynamic monitoring improves outcome in patients admitted with hemodynamic instability to the intensive care unit. The authors' results suggest that it makes no difference. We discuss these findings and compare them to the literature on early goal-directed therapy in which monitors are used early but with a protocol

Topological thermal instability and length of proteins

We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the Gaussian Network Model (GNM) and determined the spectral dimension, a parameter describing the low frequency behaviour of the density of modes. We find a surprisingly strong correlation between the spectral dimension and the number of amino acids of the protein. Considering that larger spectral dimension value relate to more topologically compact folded state, our results indicate that for a given temperature and length of the protein, the folded structure corresponds to the less compact folding compatible with thermodynamic stability.Comment: 15 pages, 6 eps figures, 2 table

Macroscopic evidence of microscopic dynamics in the Fermi-Pasta-Ulam oscillator chain from nonlinear time series analysis

The problem of detecting specific features of microscopic dynamics in the macroscopic behavior of a many-degrees-of-freedom system is investigated by analyzing the position and momentum time series of a heavy impurity embedded in a chain of nearest-neighbor anharmonic Fermi-Pasta-Ulam oscillators. Results obtained in a previous work [M. Romero-Bastida, Phys. Rev. E {\bf69}, 056204 (2004)] suggest that the impurity does not contribute significantly to the dynamics of the chain and can be considered as a probe for the dynamics of the system to which the impurity is coupled. The ($r,\tau$) entropy, which measures the amount of information generated by unit time at different scales $\tau$ of time and $r$ of the observable, is numerically computed by methods of nonlinear time-series analysis using the position and momentum signals of the heavy impurity for various values of the energy density $\epsilon$ (energy per degree of freedom) of the system and some values of the impurity mass $M$. Results obtained from these two time series are compared and discussed.Comment: 7 pages, 5 figures, RevTeX4 PRE format; to be published in Phys. Rev.

Refolding dynamics of stretched biopolymers upon force quench

Single molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse of RNA and proteins upon force quench, using simulations of an RNA hairpin and theory based on the de Gennes model for homopolymer collapse. The folding time, $\tau_F$, depends asymmetrically on $\delta f_S = f_S - f_m$ and $\delta f_Q = f_m - f_Q$ where $f_S$ ($f_Q$) is the stretch (quench) force, and $f_m$ is the transition mid-force of the RNA hairpin. In accord with experiments, the relaxation kinetics of the molecular extension, $R(t)$, occurs in three stages: a rapid initial decrease in the extension is followed by a plateau, and finally an abrupt reduction in $R(t)$ that occurs as the native state is approached. The duration of the plateau increases as $\lambda =\tau_Q/\tau_F$ decreases (where $\tau_Q$ is the time in which the force is reduced from $f_S$ to $f_Q$). Variations in the mechanisms of force quench relaxation as $\lambda$ is altered are reflected in the experimentally measurable time-dependent entropy, which is computed directly from the folding trajectories. An analytical solution of the de Gennes model under tension reproduces the multistage stage kinetics in $R(t)$. The prediction that the initial stages of collapse should also be a generic feature of polymers is validated by simulation of the kinetics of toroid (globule) formation in semiflexible (flexible) homopolymers in poor solvents upon quenching the force from a fully stretched state. Our findings give a unified explanation for multiple disparate experimental observations of protein folding.Comment: 31 pages 11 figure

Defining and identifying communities in networks

The investigation of community structures in networks is an important issue in many domains and disciplines. This problem is relevant for social tasks (objective analysis of relationships on the web), biological inquiries (functional studies in metabolic, cellular or protein networks) or technological problems (optimization of large infrastructures). Several types of algorithm exist for revealing the community structure in networks, but a general and quantitative definition of community is still lacking, leading to an intrinsic difficulty in the interpretation of the results of the algorithms without any additional non-topological information. In this paper we face this problem by introducing two quantitative definitions of community and by showing how they are implemented in practice in the existing algorithms. In this way the algorithms for the identification of the community structure become fully self-contained. Furthermore, we propose a new local algorithm to detect communities which outperforms the existing algorithms with respect to the computational cost, keeping the same level of reliability. The new algorithm is tested on artificial and real-world graphs. In particular we show the application of the new algorithm to a network of scientific collaborations, which, for its size, can not be attacked with the usual methods. This new class of local algorithms could open the way to applications to large-scale technological and biological applications.Comment: Revtex, final form, 14 pages, 6 figure

Short period attractors and non-ergodic behavior in the deterministic fixed energy sandpile model

We study the asymptotic behaviour of the Bak, Tang, Wiesenfeld sandpile automata as a closed system with fixed energy. We explore the full range of energies characterizing the active phase. The model exhibits strong non-ergodic features by settling into limit-cycles whose period depends on the energy and initial conditions. The asymptotic activity $\rho_a$ (topplings density) shows, as a function of energy density $\zeta$, a devil's staircase behaviour defining a symmetric energy interval-set over which also the period lengths remain constant. The properties of $\zeta$-$\rho_a$ phase diagram can be traced back to the basic symmetries underlying the model's dynamics.Comment: EPL-style, 7 pages, 3 eps figures, revised versio

Diffusion, super-diffusion and coalescence from single step

From the exact single step evolution equation of the two-point correlation function of a particle distribution subjected to a stochastic displacement field \bu(\bx), we derive different dynamical regimes when \bu(\bx) is iterated to build a velocity field. First we show that spatially uncorrelated fields \bu(\bx) lead to both standard and anomalous diffusion equation. When the field \bu(\bx) is spatially correlated each particle performs a simple free Brownian motion, but the trajectories of different particles result to be mutually correlated. The two-point statistical properties of the field \bu(\bx) induce two-point spatial correlations in the particle distribution satisfying a simple but non-trivial diffusion-like equation. These displacement-displacement correlations lead the system to three possible regimes: coalescence, simple clustering and a combination of the two. The existence of these different regimes, in the one-dimensional system, is shown through computer simulations and a simple theoretical argument.Comment: RevTeX (iopstyle) 19 pages, 5 eps-figure

Thermodynamic formalism for the Lorentz gas with open boundaries in dd dimensions

A Lorentz gas may be defined as a system of fixed dispersing scatterers, with a single light particle moving among these and making specular collisions on encounters with the scatterers. For a dilute Lorentz gas with open boundaries in $d$ dimensions we relate the thermodynamic formalism to a random flight problem. Using this representation we analytically calculate the central quantity within this formalism, the topological pressure, as a function of system size and a temperature-like parameter \ba. The topological pressure is given as the sum of the topological pressure for the closed system and a diffusion term with a \ba-dependent diffusion coefficient. From the topological pressure we obtain the Kolmogorov-Sinai entropy on the repeller, the topological entropy, and the partial information dimension.Comment: 7 pages, 5 figure