442 research outputs found
A phase-field-crystal approach to critical nuclei
We investigate a phase-field-crystal model for homogeneous nucleation.
Instead of solving the time evolution of a density field towards equilibrium we
use a String Method to identify saddle points in phase space. The saddle points
allow to obtain the nucleation barrier and the critical nucleus. The advantage
of using the phase-field-crystal model for this task is its ability to resolve
atomistic effects. The obtained results indicate different properties of the
critical nucleus compared with bulk crystals and show a detailed description of
the nucleation process.Comment: 12 pages, 5 figures, submitte
Relaxation of curvature induced elastic stress by the Asaro-Tiller-Grinfeld instability
A two-dimensional crystal on the surface of a sphere experiences elastic
stress due to the incompatibility of the crystal axes and the curvature. A
common mechanism to relax elastic stress is the Asaro-Tiller-Grinfeld (ATG)
instability. With a combined numerical and analytical approach we demonstrate,
that also curvature induced stress in surface crystals can be relaxed by the
long wave length ATG instability. The numerical results are obtained using a
surface phase-field crystal (PFC) model, from which we determine the
characteristic wave numbers of the ATG instability for various surface
coverages corresponding to different curvature induced compressions. The
results are compared with an analytic expression for the characteristic wave
number, obtained from a continuum approach which accounts for hexagonal
crystals and intrinsic PFC symmetries. We find our numerical results in
accordance with the analytical predictions.Comment: 6 pages, 5 figure
Controlling the energy of defects and interfaces in the amplitude expansion of the phase-field crystal model
One of the major difficulties in employing phase field crystal (PFC) modeling
and the associated amplitude (APFC) formulation is the ability to tune model
parameters to match experimental quantities. In this work we address the
problem of tuning the defect core and interface energies in the APFC
formulation. We show that the addition of a single term to the free energy
functional can be used to increase the solid-liquid interface and defect
energies in a well-controlled fashion, without any major change to other
features. The influence of the newly added term is explored in two-dimensional
triangular and honeycomb structures as well as bcc and fcc lattices in three
dimensions. In addition, a finite element method (FEM) is developed for the
model that incorporates a mesh refinement scheme. The combination of the FEM
and mesh refinement to simulate amplitude expansion with a new energy term
provides a method of controlling microscopic features such as defect and
interface energies while simultaneously delivering a coarse-grained examination
of the system.Comment: 14 pages, 9 figure
FLASH: ultra-fast protocol to identify RNA-protein interactions in cells
Determination of the in vivo binding sites of RNA-binding proteins (RBPs) is paramount to understanding their function and how they affect different aspects of gene regulation. With hundreds of RNA-binding proteins identified in human cells, a flexible, high-resolution, high-throughput, highly multiplexible and radioactivity-free method to determine their binding sites has not been described to date. Here we report FLASH (Fast Ligation of RNA after some sort of Affinity Purification for High-throughput Sequencing), which uses a special adapter design and an optimized protocol to determine protein-RNA interactions in living cells. The entire FLASH protocol, starting from cells on plates to a sequencing library, takes 1.5 days. We demonstrate the flexibility, speed and versatility of FLASH by using it to determine RNA targets of both tagged and endogenously expressed proteins under diverse conditions in vivo
continuum modelling of semiconductor heteroepitaxy an applied perspective
Semiconductor heteroepitaxy involves a wealth of qualitatively different, competing phenomena. Examples include three-dimensional island formation, injection of dislocations, mixing between film and substrate atoms. Their relative importance depends on the specific growth conditions, giving rise to a very complex scenario. The need for an optimal control over heteroepitaxial films and/or nanostructures is widespread: semiconductor epitaxy by molecular beam epitaxy or chemical vapour deposition is nowadays exploited also in industrial environments. Simulation models can be precious in limiting the parameter space to be sampled while aiming at films/nanostructures with the desired properties. In order to be appealing (and useful) to an applied audience, such models must yield predictions directly comparable with experimental data. This implies matching typical time scales and sizes, while offering a satisfactory description of the main physical driving forces. It is the aim of the present review to show tha..
Defects at grain boundaries: A coarse-grained, three-dimensional description by the amplitude expansion of the phase-field crystal model
We address a three-dimensional, coarse-grained description of dislocation
networks at grain boundaries between rotated crystals. The so-called amplitude
expansion of the phase-field crystal model is exploited with the aid of finite
element method calculations. This approach allows for the description of
microscopic features, such as dislocations, while simultaneously being able to
describe length scales that are orders of magnitude larger than the lattice
spacing. Moreover, it allows for the direct description of extended defects by
means of a scalar order parameter. The versatility of this framework is shown
by considering both fcc and bcc lattice symmetries and different rotation axes.
First, the specific case of planar, twist grain boundaries is illustrated. The
details of the method are reported and the consistency of the results with
literature is discussed. Then, the dislocation networks forming at the
interface between a spherical, rotated crystal embedded in an unrotated
crystalline structure, are shown. Although explicitly accounting for
dislocations which lead to an anisotropic shrinkage of the rotated grain, the
extension of the spherical grain boundary is found to decrease linearly over
time in agreement with the classical theory of grain growth and recent
atomistic investigations. It is shown that the results obtained for a system
with bcc symmetry agree very well with existing results, validating the
methodology. Furthermore, fully original results are shown for fcc lattice
symmetry, revealing the generality of the reported observations.Comment: 11 pages, 9 figure
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Bioinformatics and constraints
This article introduces the topic of bioinformatics to an audience of computer scientists. We discuss the definition of bioinformatics, give a classification of the problem areas which bioinformatics addresses, and illustrate these in detail with examples. We highlight those areas which we believe to be suitable for the application of constraint solving techniques, or where similar techniques are already used. Finally, we give some advice for computer scientists who are considering getting involved in bioinformatics, and provide a resource list and a reading list
Efficient chaining of seeds in ordered trees
We consider here the problem of chaining seeds in ordered trees. Seeds are
mappings between two trees Q and T and a chain is a subset of non overlapping
seeds that is consistent with respect to postfix order and ancestrality. This
problem is a natural extension of a similar problem for sequences, and has
applications in computational biology, such as mining a database of RNA
secondary structures. For the chaining problem with a set of m constant size
seeds, we describe an algorithm with complexity O(m2 log(m)) in time and O(m2)
in space
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