150 research outputs found
An integrated Bragg grating oxygen sensor using a hydrophobic sol-gel layer doped with an organic dye
Oxygen sensing is required for the understanding of many chemical processes across a diverse set of fields including medicine, environmental science and chemical synthesis. Oxygen sensing can be achieved through the use of electronic sensors. However, there are limitations associated with electronic sensors including susceptibility to electromagnetic interference and presenting a spark risk in flammable environments. Optical fiber and integrated optical chemical sensors overcome these limitations of electrical based sensing methods
The Origins of Phase Transitions in Small Systems
The identification and classification of phases in small systems, e.g.
nuclei, social and financial networks, clusters, and biological systems, where
the traditional definitions of phase transitions are not applicable, is
important to obtain a deeper understanding of the phenomena observed in such
systems. Within a simple statistical model we investigate the validity and
applicability of different classification schemes for phase transtions in small
systems. We show that the whole complex temperature plane contains necessary
information in order to give a distinct classification.Comment: 3 pages, 4 figures, revtex 4 beta 5, for further information see
http://www.smallsystems.d
Integrated planar Bragg grating oxygen sensor
We demonstrate an integrated planar Bragg grating sensor for the detection of oxygen by modification of the surface with a silica sol-gel containing immobilized methylene blue
Exploring energy landscapes: from molecular to mesoscopic systems
We review a comprehensive computational framework to survey the potential energy landscape for systems composed of rigid or partially rigid molecules. Illustrative case studies relevant to a wide range of molecular clusters and soft and condensed matter systems are discussed
Exploring energy landscapes: metrics, pathways, and normal mode analysis for rigid-body molecules
We present new methodology for exploring the energy landscapes of molecular systems, using angle-axis variables for the rigid-body rotational coordinates. The key ingredient is a distance measure or metric tensor, which is invariant to global translation and rotation. The metric is used to formulate a generalized nudged elastic band method for calculating pathways, and a full prescription for normal-mode analysis is described. The methodology is tested by mapping the potential energy and free energy landscape of the water octamer, described by the TIP4P potential
Network of Minima of the Thomson Problem and Smale's 7th Problem
The Thomson problem, arrangement of identical charges on the surface of a sphere, has found many applications in physics, chemistry and biology. Here, we show that the energy landscape of the Thomson problem for N particles with N=132, 135, 138, 141, 144, 147, and 150 is single funneled, characteristic of a structure-seeking organization where the global minimum is easily accessible. Algorithmically, constructing starting points close to the global minimum of such a potential with spherical constraints is one of Smaleâs 18 unsolved problems in mathematics for the 21st century because it is important in the solution of univariate and bivariate random polynomial equations. By analyzing the kinetic transition networks, we show that a randomly chosen minimum is, in fact, always âcloseâ to the global minimum in terms of the number of transition states that separate them, a characteristic of small world networks
Integrated Bragg grating sensors: achieving chemical sensing in liquid and gas flow systems
The sensing of chemical species is required within a diverse set of fields including industry, environmental monitoring and homeland security. The sensing of chemicals in liquid and gaseous environments has been traditionally achieved by electronic and electrochemical sensors. However, optical sensors demonstrate many benefits over these electronic systems, including remote interrogation of large sensor arrays via optical fibre and telecoms equipment, immunity from EM interference and absence of spark risk in flammable environments
Parallelization of the discrete gradient method of non-smooth optimization and its applications
We investigate parallelization and performance of the discrete gradient method of nonsmooth optimization. This derivative free method is shown to be an effective optimization tool, able to skip many shallow local minima of nonconvex nondifferentiable objective functions. Although this is a sequential iterative method, we were able to parallelize critical steps of the algorithm, and this lead to a significant improvement in performance on multiprocessor computer clusters. We applied this method to a difficult polyatomic clusters problem in computational chemistry, and found this method to outperform other algorithms. <br /
A Central Partition of Molecular Conformational Space. IV. Extracting information from the graph of cells
In previous works [physics/0204035, physics/0404052, physics/0509126] a
procedure was described for dividing the -dimensional
conformational space of a molecular system into a number of discrete cells,
this partition allowed the building of a combinatorial structure from data
sampled in molecular dynamics trajectories: the graph of cells, that encodes
the set of cells in conformational space that are visited by the system in its
thermal wandering. Here we outline a set of procedures for extracting useful
information from this structure: 1st) interesting regions in the volume
occupied by the system in conformational space can be bounded by a polyhedral
cone whose faces are determined empirically from a set of relations between the
coordinates of the molecule, 2nd) it is also shown that this cone can be
decomposed into a hierarchical set of smaller cones, 3rd) the set of cells in a
cone can be encoded by a simple combinatorial sequence.Comment: added an intrduction and reference
Dynamics of Lennard-Jones clusters: A characterization of the activation-relaxation technique
The potential energy surface (PES) of Lennard-Jones clusters is investigated
using the activation-relaxation technique (ART). This method defines events in
the configurational energy landscape as a two-step process: (a) a configuration
is first activated from a local minimum to a nearby saddle-point and (b) is
then relaxed to a new minimum. Although ART has been applied with success to a
wide range of materials such as a-Si, a-SiO2 and binary Lennard-Jones glasses,
questions remain regarding the biases of the technique. We address some of
these questions in a detailed study of ART-generated events in Lennard-Jones
(LJ) clusters, a system for which much is already known. In particular, we
study the distribution of saddle-points, the pathways between configurations,
and the reversibility of paths. We find that ART can identify all trajectories
with a first-order saddle point leaving a given minimum, is fully reversible,
and samples events following the Boltzmann weight at the saddle point.Comment: 8 pages, 7 figures in postscrip
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