1,119 research outputs found
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
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
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
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
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
The effect of local thermal fluctuations on the folding kinetics: a study from the perspective of the nonextensive statistical mechanics
Protein folding is a universal process, very fast and accurate, which works
consistently (as it should be) in a wide range of physiological conditions. The
present work is based on three premises, namely: () folding reaction is a
process with two consecutive and independent stages, namely the search
mechanism and the overall productive stabilization; () the folding kinetics
results from a mechanism as fast as can be; and () at nanoscale
dimensions, local thermal fluctuations may have important role on the folding
kinetics. Here the first stage of folding process (search mechanism) is focused
exclusively. The effects and consequences of local thermal fluctuations on the
configurational kinetics, treated here in the context of non extensive
statistical mechanics, is analyzed in detail through the dependence of the
characteristic time of folding () on the temperature and on the
nonextensive parameter .The model used consists of effective residues
forming a chain of 27 beads, which occupy different sites of a D infinite
lattice, representing a single protein chain in solution. The configurational
evolution, treated by Monte Carlo simulation, is driven mainly by the change in
free energy of transfer between consecutive configurations. ...Comment: 19 pages, 3 figures, 1 tabl
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 , whereas they are stable in .Comment: 3 pages, shorter version, additional reference
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