Interface Fluctuations, Burgers Equations, and Coarsening under Shear

We consider the interplay of thermal fluctuations and shear on the surface of the domains in various systems coarsening under an imposed shear flow. These include systems with nonconserved and conserved dynamics, and a conserved order parameter advected by a fluid whose velocity field satisfies the Navier-Stokes equation. In each case the equation of motion for the interface height reduces to an anisotropic Burgers equation. The scaling exponents that describe the growth and coarsening of the interface are calculated exactly in any dimension in the case of conserved and nonconserved dynamics. For a fluid-advected conserved order parameter we determine the exponents, but we are unable to build a consistent perturbative expansion to support their validity.Comment: 10 RevTeX pages, 2 eps figure

The folding of knotted proteins: insights from lattice simulations

We carry out systematic Monte Carlo simulations of Go 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

The Mechanics of Blood Vessel Growth

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Dynamics and delocalisation transition for an interface driven by a uniform shear flow

We study the effect of a uniform shear flow on an interface separating the two broken-symmetry ordered phases of a two-dimensional system with nonconserved scalar order parameter. The interface, initially flat and perpendicular to the flow, is distorted by the shear flow. We show that there is a critical shear rate, \gamma_c, proportional to 1/L^2, (where L is the system width perpendicular to the flow) below which the interface can sustain the shear. In this regime the countermotion of the interface under its curvature balances the shear flow, and the stretched interface stabilizes into a time-independent shape whose form we determine analytically. For \gamma > \gamma_c, the interface acquires a non-zero velocity, whose profile is shown to reach a time-independent limit which we determine exactly. The analytical results are checked by numerical integration of the equations of motion.Comment: 5 page

Pathways to folding, nucleation events and native geometry

We perform extensive Monte Carlo simulations of a lattice model and the Go potential to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries. Our analysis of folding pathways revealed a common underlying folding mechanism, based on nucleation phenomena, for both protein models. However, folding to the more complex geometry (i.e. that with more non-local contacts) is driven by a folding nucleus whose geometric traits more closely resemble those of the native fold. For this geometry folding is clearly a more cooperative process.Comment: Accepted in J. Chem. Phy

Novel glassy behavior in a ferromagnetic p-spin model

Recent work has suggested the existence of glassy behavior in a ferromagnetic model with a four-spin interaction. Motivated by these findings, we have studied the dynamics of this model using Monte Carlo simulations with particular attention being paid to two-time quantities. We find that the system shares many features in common with glass forming liquids. In particular, the model exhibits: (i) a very long-lived metastable state, (ii) autocorrelation functions that show stretched exponential relaxation, (iii) a non-equilibrium timescale that appears to diverge at a well defined temperature, and (iv) low temperature aging behaviour characteristic of glasses.Comment: 6 pages, 5 figure

Ohta-Jasnow-Kawasaki Approximation for Nonconserved Coarsening under Shear

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.

Interface Fluctuations under Shear

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 reference

Why Do Protein Folding Rates Correlate with Metrics of Native Topology?

For almost 15 years, the experimental correlation between protein folding rates and the contact order parameter has been under scrutiny. Here, we use a simple simulation model combined with a native-centric interaction potential to investigate the physical roots of this empirical observation. We simulate a large set of circular permutants, thus eliminating dependencies of the folding rate on other protein properties (e.g. stability). We show that the rate-contact order correlation is a consequence of the fact that, in high contact order structures, the contact order of the transition state ensemble closely mirrors the contact order of the native state. This happens because, in these structures, the native topology is represented in the transition state through the formation of a network of tertiary interactions that are distinctively long-ranged

TrajPy: empowering feature engineering for trajectory analysis across domains

Trajectories, sequentially measured quantities that form a path, are an important presence in many different fields, from hadronic beams in physics to electrocardiograms in medicine. Trajectory anal-ysis requires the quantification and classification of curves either using statistical descriptors or physics-based features. To date, there is no extensive and user-friendly package for trajectory anal-ysis available, despite its importance and potential application across domains. We developed a free open-source python package named TrajPy as a complementary tool to empower trajectory analysis. The package showcases a friendly graphic user interface and provides a set of physical descriptors that help characterizing these intricate structures. In combina-tion with image analysis, it was already successfully applied to the study of mitochondrial motility in neuroblastoma cell lines and to the analysis of in silico models for cell migration. The TrajPy package was developed in Python 3 and released under the GNU GPL-3 license. Easy installation is available through PyPi and the development source code can be found in the repository https://github.com/ocbe-uio/TrajPy/. The package release is automatically archived under the DOI 10.5281/zenodo.3656044.Comment: 4 pages, 1 figur