29,867 research outputs found
Prediction of RNA pseudoknots by Monte Carlo simulations
In this paper we consider the problem of RNA folding with pseudoknots. We use
a graphical representation in which the secondary structures are described by
planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze
the non-planar topologies of RNA structures and propose a classification of RNA
pseudoknots according to the minimal genus of the surface on which the RNA
structure can be embedded. This classification provides a simple and natural
way to tackle the problem of RNA folding prediction in presence of pseudoknots.
Based on that approach, we describe a Monte Carlo algorithm for the prediction
of pseudoknots in an RNA molecule.Comment: 22 pages, 14 figure
Computer-aided design and analysis of mechanisms
An introduction to the computer programs developed to assist in the design and analysis of mechanisms is presented. A survey of the various types of programs which are available is given, and the most widely used programs are compared. The way in which the programs are used is discussed, and demonstrated with an example
How to push a block along a wall
Some robot tasks require manipulation of objects that may be touching other fixed objects. The effects of friction and kinematic constraint must be anticipated, and may even be exploited to accomplish the task. An example task, a dynamic analysis, and appropriate effector motions are presented. The goal is to move a rectangular block along a wall, so that one side of the block maintains contact with the wall. Two solutions that push the block along the wall are discussed
Fast, Scalable, and Interactive Software for Landau-de Gennes Numerical Modeling of Nematic Topological Defects
Numerical modeling of nematic liquid crystals using the tensorial Landau-de
Gennes (LdG) theory provides detailed insights into the structure and
energetics of the enormous variety of possible topological defect
configurations that may arise when the liquid crystal is in contact with
colloidal inclusions or structured boundaries. However, these methods can be
computationally expensive, making it challenging to predict (meta)stable
configurations involving several colloidal particles, and they are often
restricted to system sizes well below the experimental scale. Here we present
an open-source software package that exploits the embarrassingly parallel
structure of the lattice discretization of the LdG approach. Our
implementation, combining CUDA/C++ and OpenMPI, allows users to accelerate
simulations using both CPU and GPU resources in either single- or multiple-core
configurations. We make use of an efficient minimization algorithm, the Fast
Inertial Relaxation Engine (FIRE) method, that is well-suited to large-scale
parallelization, requiring little additional memory or computational cost while
offering performance competitive with other commonly used methods. In
multi-core operation we are able to scale simulations up to supra-micron length
scales of experimental relevance, and in single-core operation the simulation
package includes a user-friendly GUI environment for rapid prototyping of
interfacial features and the multifarious defect states they can promote. To
demonstrate this software package, we examine in detail the competition between
curvilinear disclinations and point-like hedgehog defects as size scale,
material properties, and geometric features are varied. We also study the
effects of an interface patterned with an array of topological point-defects.Comment: 16 pages, 6 figures, 1 youtube link. The full catastroph
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