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Coarsening systems under uniform shear display a long time regime characterized by the presence of highly stretched and thin domains. The question then arises whether thermal fluctuations may actually destroy this layered structure. To address this problem in the case of non-conserved dynamics we study an anisotropic version of the Burgers equation, constructed to describe thermal fluctuations of an interface in the presence of a uniform shear flow. As a result, we find that stretched domains are only marginally stable against thermal fluctuations in $d=2$, whereas they are stable in $d=3$., Comment: 3 pages, shorter version, additional references

We analytically study coarsening dynamics in a system with nonconserved scalar order parameter, when a uniform time-independent shear flow is present. We use an anisotropic version of the Ohta-Jasnow-Kawasaki approximation to calculate the growth exponents in two and three dimensions: for d=3 the exponents we find are the same as expected on the basis of simple scaling arguments, that is 3/2 in the flow direction and 1/2 in all the other directions, while for d=2 we find an unusual behavior, in that the domains experience an unlimited narrowing for very large times and a nontrivial dynamical scaling appears. In addition, we consider the case where an oscillatory shear is applied to a two-dimensional system, finding in this case a standard t^1/2 growth, modulated by periodic oscillations. We support our two-dimensional results by means of numerical simulations and we propose to test our predictions by experiments on twisted nematic liquid crystals., Comment: 25 RevTeX pages, 7 EPS figures. To be published in Phys. Rev. E

We carry out systematic Monte Carlo simulations of Gō lattice proteins to investigate and compare the folding processes of two model proteins whose native structures differ from each other due to the presence of a trefoil knot located near the terminus of one of the protein chains. We show that the folding time of the knotted fold is larger than that of the unknotted protein and that this difference in folding time is particularly striking in the temperature region below the optimal folding temperature. Both proteins display similar folding transition temperatures, which is indicative of similar thermal stabilities. By using the folding probability reaction coordinate as an estimator of folding progression we have found out that the formation of the knot is mainly a late folding event in our shallow knot system.

For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation mechanism for protein folding whose basic premise is the idea that after completion of a specific set of contacts forming the so-called folding nucleus the native state is achieved promptly. Here we propose a methodology to identify folding nuclei in small lattice polymers and apply it to the study of protein molecules with chain length N=48. To investigate the extent to which protein topology is a robust determinant of the nucleation mechanism we compare the nucleation scenario of a native-centric model with that of a sequence specific model sharing the same native fold. To evaluate the impact of the sequence's finner details in the nucleation mechanism we consider the folding of two non- homologous sequences. We conclude that in a sequence-specific model the folding nucleus is, to some extent, formed by the most stable contacts in the protein and that the less stable linkages in the folding nucleus are solely determined by the fold's topology. We have also found that independently of protein sequence the folding nucleus performs the same `topological' function. This unifying feature of the nucleation mechanism results from the residues forming the folding nucleus being distributed along the protein chain in a similar and well-defined manner that is determined by the fold's topological features., 10 Figures. J. Physics: Condensed Matter (to appear)

Glioblastoma multiforme (GBM) is the most aggressive and invasive malignant brain cancer. GBM is characterized by a dramatic metabolic imbalance leading to increased secretion of the pro-angiogenic factor VEGF and subsequent abnormal tumor vascularization. In 2009, FDA approved the intravenous administration of bevacizumab, an anti-VEGF monoclonal antibody, as a therapeutic agent for patients with GBM. However, the number of systemic side effects and reduced accessibility of bevacizumab to the central nervous system and consequently to the GBM tumor mass limited its effectiveness in improving patient survival. In this study, we combined experimental and computational modelling to quantitatively characterize the dynamics of VEGF secretion and turnover in GBM and in normal brain cells and simultaneous monitoring of vessel growth. We showed that sequestration of VEGF inside GBM cells, can be used as a novel target for improved bevacizumab-based therapy. We have engineered the VEGF nanotrapper, a cargo system that allows cellular uptake of bevacizumab and inhibits VEGF secretion required for angiogenesis activation and development. Here, we show the therapeutic efficacy of this nanocargo in reducing vascularization and tumor cell mass of GBM in vitro and in vivo cancer models.