Glassy behavior of a homopolymer from molecular dynamics simulations

We study at- and out-of-equilibrium dynamics of a single homopolymer chain at low temperature using molecular dynamics simulations. The main quantities of interest are the average root mean square displacement of the monomers below the theta point, and the structure factor, as a function of time. The observation of these quantities show a close resemblance to those measured in structural glasses and suggest that the polymer chain in its low temperature phase is in a glassy phase, with its dynamics dominated by traps. In equilibrium, at low temperature, we observe the trapping of the monomers and a slowing down of the overall motion of the polymer as well as non-exponential relaxation of the structure factor. In out-of-equilibrium, at low temperatures, we compute the two-time quantities and observe breaking of ergodicity in a range of waiting times, with the onset of aging.Comment: 11 pages, 4 figure

Correlated percolation models of structured habitat in ecology

Percolation offers acknowledged models of random media when the relevant medium characteristics can be described as a binary feature. However, when considering habitat modeling in ecology, a natural constraint comes from nearest-neighbor correlations between the suitable/unsuitable states of the spatial units forming the habitat. Such constraints are also relevant in the physics of aggregation where underlying processes may lead to a form of correlated percolation. However, in ecology, the processes leading to habitat correlations are in general not known or very complex. As proposed by Hiebeler [Ecology {\bf 81}, 1629 (2000)], these correlations can be captured in a lattice model by an observable aggregation parameter $q$, supplementing the density $p$ of suitable sites. We investigate this model as an instance of correlated percolation. We analyze the phase diagram of the percolation transition and compute the cluster size distribution, the pair-connectedness function $C(r)$ and the correlation function $g(r)$. We find that while $g(r)$ displays a power-law decrease associated with long-range correlations in a wide domain of parameter values, critical properties are compatible with the universality class of uncorrelated percolation. We contrast the correlation structures obtained respectively for the correlated percolation model and for the Ising model, and show that the diversity of habitat configurations generated by the Hiebeler model is richer than the archetypal Ising model. We also find that emergent structural properties are peculiar to the implemented algorithm, leading to questioning the notion of a well-defined model of aggregated habitat. We conclude that the choice of model and algorithm have strong consequences on what insights ecological studies can get using such models of species habitat

Collapse Dynamics of a Homopolymer: Theory and Simulation

We present a scaling theory describing the collapse of a homopolymer chain in poor solvent. At time t after the beginning of the collapse, the original Gaussian chain of length N is streamlined to form N/g segments of length R(t), each containing g ~ t monomers. These segments are statistical quantities representing cylinders of length R ~ t^{1/2} and diameter d ~ t^{1/4}, but structured out of stretched arrays of spherical globules. This prescription incorporates the capillary instability. We compare the time-dependent structure factor derived for our theory with that obtained from ultra-large-scale molecular dynamics simulation with explicit solvent. This is the first time such a detailed comparison of theoretical and simulation predictions of collapsing chain structure has been attempted. The favorable agreement between the theoretical and computed structure factors supports the picture of the coarse-graining process during polymer collapse.Comment: 4 pages, 3 figure

Finite-size effects and intermittency in a simple aging system

We study the intermittent dynamics and the fluctuations of the dynamic correlation function of a simple aging system. Given its size $L$ and its coherence length $\xi$, the system can be divided into $N$ independent subsystems, where $N=(\frac{L}{\xi})^d$, and $d$ is the dimension of space. Each of them is considered as an aging subsystem which evolves according to an activated dynamics between energy levels. We compute analytically the distribution of trapping times for the global system, which can take power-law, stretched-exponential or exponential forms according to the values of $N$ and the regime of times considered. An effective number of subsystems at age $t_w$, $N_{eff}(t_w)$, can be defined, which decreases as $t_w$ increases, as well as an effective coherence length, $\xi(t_w) \sim t_w^{(1-\mu)/d}$, where $\mu <1$ characterizes the trapping times distribution of a single subsystem. We also compute the probability distribution functions of the time intervals between large decorrelations, which exhibit different power-law behaviours as $t_w$ increases (or $N$ decreases), and which should be accessible experimentally. Finally, we calculate the probability distribution function of the two-time correlator. We show that in a phenomenological approach, where $N$ is replaced by the effective number of subsystems $N_{eff}(t_w)$, the same qualitative behaviour as in experiments and simulations of several glassy systems can be obtained.Comment: 15 pages, 6 figures, published versio

Spatial correlations in the relaxation of the Kob-Andersen model

We describe spatio-temporal correlations and heterogeneities in a kinetically constrained glassy model, the Kob-Andersen model. The kinetic constraints of the model alone induce the existence of dynamic correlation lengths, that increase as the density $\rho$ increases, in a way compatible with a double-exponential law. We characterize in detail the trapping time correlation length, the cooperativity length, and the distribution of persistent clusters of particles. This last quantity is related to the typical size of blocked clusters that slow down the dynamics for a given density.Comment: 7 pages, 6 figures, published version (title has changed

Dynamic first-order phase transition in kinetically constrained models of glasses

We show that the dynamics of kinetically constrained models of glass formers takes place at a first-order coexistence line between active and inactive dynamical phases. We prove this by computing the large-deviation functions of suitable space-time observables, such as the number of configuration changes in a trajectory. We present analytic results for dynamic facilitated models in a mean-field approximation, and numerical results for the Fredrickson-Andersen model, the East model, and constrained lattice gases, in various dimensions. This dynamical first-order transition is generic in kinetically constrained models, and we expect it to be present in systems with fully jammed states.Comment: 4.1 pages, 3 figure

Seleção de estirpes de rizóbios para as leguminosas Arachis pintoi e Cratylia argentea.

Efeito das estirpes de rizóbio na nodulação e desenvolvimento da Arachis pinto (médias de 4 repetições. Efeito das estirpes de rizóbio na nodulação e desenvolvimento da cratylia argentea. Fotos.bitstream/CNPAB-2010/27245/1/doc053.pd

CCL5 Neutralization Restricts Cancer Growth and Potentiates the Targeting of PDGFRβ in Colorectal Carcinoma

Increased CCL5 levels are markers of an unfavourable outcome in patients with melanoma, breast, cervical, prostate, gastric or pancreatic cancer. Here, we have assessed the role played by CCL5/CCR5 interactions in the development of colon cancer. To do so, we have examined a number of human colorectal carcinoma clinical specimens and found CCL5 and its receptors over-expressed within primary as well as liver and pulmonary metastases of patients compared to healthy tissues. In vitro, CCL5 increased the growth and migratory responses of colon cancer cells from both human and mouse origins. In addition, systemic treatment of mice with CCL5-directed antibodies reduced the extent of development of subcutaneous colon tumors, of liver metastases and of peritoneal carcinosis. Consistently, we found increased numbers of CD45-immunoreactive cells within the stroma of the remaining lesions as well as at the interface with the healthy tissue. In contrast, selective targeting of CCR5 through administration of TAK-779, a CCR5 antagonist, only partially compromised colon cancer progression. Furthermore, CCL5 neutralization rendered the tumors more sensitive to a PDGFRβ-directed strategy in mice, this combination regimen offering the greatest protection against liver metastases and suppressing macroscopic peritoneal carcinosis. Collectively, our data demonstrate the involvement of CCL5 in the pathogenesis of colorectal carcinoma and point to its potential value as a therapeutic target