Protein accumulation in the endoplasmic reticulum as a non-equilibrium phase transition

Several neurological disorders are associated with the aggregation of aberrant proteins, often localized in intracellular organelles such as the endoplasmic reticulum. Here we study protein aggregation kinetics by mean-field reactions and three dimensional Monte carlo simulations of diffusion-limited aggregation of linear polymers in a confined space, representing the endoplasmic reticulum. By tuning the rates of protein production and degradation, we show that the system undergoes a non-equilibrium phase transition from a physiological phase with little or no polymer accumulation to a pathological phase characterized by persistent polymerization. A combination of external factors accumulating during the lifetime of a patient can thus slightly modify the phase transition control parameters, tipping the balance from a long symptomless lag phase to an accelerated pathological development. The model can be successfully used to interpret experimental data on amyloid-\b{eta} clearance from the central nervous system

Universal distribution of threshold forces at the depinning transition

We study the distribution of threshold forces at the depinning transition for an elastic system of finite size, driven by an external force in a disordered medium at zero temperature. Using the functional renormalization group (FRG) technique, we compute the distribution of pinning forces in the quasi-static limit. This distribution is universal up to two parameters, the average critical force, and its width. We discuss possible definitions for threshold forces in finite-size samples. We show how our results compare to the distribution of the latter computed recently within a numerical simulation of the so-called critical configuration.Comment: 12 pages, 7 figures, revtex

Discrete Fracture Model with Anisotropic Load Sharing

A two-dimensional fracture model where the interaction among elements is modeled by an anisotropic stress-transfer function is presented. The influence of anisotropy on the macroscopic properties of the samples is clarified, by interpolating between several limiting cases of load sharing. Furthermore, the critical stress and the distribution of failure avalanches are obtained numerically for different values of the anisotropy parameter $\alpha$ and as a function of the interaction exponent $\gamma$. From numerical results, one can certainly conclude that the anisotropy does not change the crossover point $\gamma_c=2$ in 2D. Hence, in the limit of infinite system size, the crossover value $\gamma_c=2$ between local and global load sharing is the same as the one obtained in the isotropic case. In the case of finite systems, however, for $\gamma\le2$, the global load sharing behavior is approached very slowly

Elementary plastic events in amorphous silica

Plastic instabilities in amorphous materials are often studied using idealized models of binary mixtures that do not capture accurately molecular interactions and bonding present in real glasses. Here we study atomic-scale plastic instabilities in a three-dimensional molecular dynamics model of silica glass under quasistatic shear. We identify two distinct types of elementary plastic events, one is a standard quasilocalized atomic rearrangement while the second is a bond-breaking event that is absent in simplified models of fragile glass formers. Our results show that both plastic events can be predicted by a drop of the lowest nonzero eigenvalue of the Hessian matrix that vanishes at a critical strain. Remarkably, we find very high correlation between the associated eigenvectors and the nonaffine displacement fields accompanying the bond-breaking event, predicting the locus of structural failure. Both eigenvectors and nonaffine displacement fields display an Eshelby-like quadrupolar structure for both failure modes, rearrangement, and bond breaking Our results thus clarify the nature of atomic-scale plastic instabilities in silica glasses, providing useful information for the development of mesoscale models of amorphous plasticity

Force fluctuation in a driven elastic chain

We study the dynamics of an elastic chain driven on a disordered substrate and analyze numerically the statistics of force fluctuations at the depinning transition. The probability distribution function of the amplitude of the slip events for small velocities is a power law with an exponent $+AFw-tau$ depending on the driving velocity. This result is in qualitative agreement with experimental measurements performed on sliding elastic surfaces with macroscopic asperities. We explore the properties of the depinning transition as a function of the driving mode (i.e. constant force or constant velocity) and compute the force-velocity diagram using finite size scaling methods. The scaling exponents are in excellent agreement with the values expected in interface models and, contrary to previous studies, we found no difference in the exponents for periodic and disordered chains.Comment: 8 page

Resistance and Resistance Fluctuations in Random Resistor Networks Under Biased Percolation

We consider a two-dimensional random resistor network (RRN) in the presence of two competing biased percolations consisting of the breaking and recovering of elementary resistors. These two processes are driven by the joint effects of an electrical bias and of the heat exchange with a thermal bath. The electrical bias is set up by applying a constant voltage or, alternatively, a constant current. Monte Carlo simulations are performed to analyze the network evolution in the full range of bias values. Depending on the bias strength, electrical failure or steady state are achieved. Here we investigate the steady-state of the RRN focusing on the properties of the non-Ohmic regime. In constant voltage conditions, a scaling relation is found between $/_0$ and $V/V_0$, where $$ is the average network resistance, $_0$ the linear regime resistance and $V_0$ the threshold value for the onset of nonlinearity. A similar relation is found in constant current conditions. The relative variance of resistance fluctuations also exhibits a strong nonlinearity whose properties are investigated. The power spectral density of resistance fluctuations presents a Lorentzian spectrum and the amplitude of fluctuations shows a significant non-Gaussian behavior in the pre-breakdown region. These results compare well with electrical breakdown measurements in thin films of composites and of other conducting materials.Comment: 15 figures, 23 page

Modeling relaxation and jamming in granular media

We introduce a stochastic microscopic model to investigate the jamming and reorganization of grains induced by an object moving through a granular medium. The model reproduces the experimentally observed periodic sawtooth fluctuations in the jamming force and predicts the period and the power spectrum in terms of the controllable physical parameters. It also predicts that the avalanche sizes, defined as the number of displaced grains during a single advance of the object, follow a power-law, $P(s)\sim s^{-\tau}$, where the exponent is independent of the physical parameters

Mean-field behavior of the sandpile model below the upper critical dimension

We present results of large scale numerical simulations of the Bak, Tang and Wiesenfeld sandpile model. We analyze the critical behavior of the model in Euclidean dimensions $2\leq d\leq 6$. We consider a dissipative generalization of the model and study the avalanche size and duration distributions for different values of the lattice size and dissipation. We find that the scaling exponents in $d=4$ significantly differ from mean-field predictions, thus suggesting an upper critical dimension $d_c\geq 5$. Using the relations among the dissipation rate $\epsilon$ and the finite lattice size $L$, we find that a subset of the exponents displays mean-field values below the upper critical dimensions. This behavior is explained in terms of conservation laws.Comment: 4 RevTex pages, 2 eps figures embedde