Topologically invariant reaction coordinates for simulating multistate chemical reactions.

Evaluating free energy profiles of chemical reactions in complex environments such as solvents and enzymes requires extensive sampling, which is usually performed by potential of mean force (PMF) techniques. The reliability of the sampling depends not only on the applied PMF method but also the reaction coordinate space within the dynamics is biased. In contrast to simple geometrical collective variables that depend only on the positions of the atomic coordinates of the reactants, the E(gap) reaction coordinate (the energy difference obtained by evaluating a suitable force field using reactant and product state topologies) has the unique property that it is able to take environmental effects into account leading to better convergence, a more faithful description of the transition state ensemble and therefore more accurate free energy profiles. However, E(gap) requires predefined topologies and is therefore inapplicable for multistate reactions, in which the barrier between the chemically equivalent topologies is comparable to the reaction activation barrier, because undesired "side reactions" occur. In this article, we introduce a new energy-based collective variable by generalizing the E(gap) reaction coordinate such that it becomes invariant to equivalent topologies and show that it yields more well behaved free energy profiles than simpler geometrical reaction coordinates.

Parallel coordinates in computational engineering design

Modern Engineering Design involves the deployment of many computational tools. Re- search on challenging real-world design problems is focused on developing improvements for the engineering design process through the integration and application of advanced com- putational search/optimization and analysis tools. Successful application of these methods generates vast quantities of data on potential optimum designs. To gain maximum value from the optimization process, designers need to visualise and interpret this information leading to better understanding of the complex and multimodal relations between param- eters, objectives and decision-making of multiple and strongly conflicting criteria. Initial work by the authors has identified that the Parallel Coordinates interactive visualisation method has considerable potential in this regard. This methodology involves significant levels of user-interaction, making the engineering designer central to the process, rather than the passive recipient of a deluge of pre-formatted information. In the present work we have applied and demonstrated this methodology in two differ- ent aerodynamic turbomachinery design cases; a detailed 3D shape design for compressor blades, and a preliminary mean-line design for the whole compressor core. The first case comprises 26 design parameters for the parameterisation of the blade geometry, and we analysed the data produced from a three-objective optimization study, thus describing a design space with 29 dimensions. The latter case comprises 45 design parameters and two objective functions, hence developing a design space with 47 dimensions. In both cases the dimensionality can be managed quite easily in Parallel Coordinates space, and most importantly, we are able to identify interesting and crucial aspects of the relationships between the design parameters and optimum level of the objective functions under con- sideration. These findings guide the human designer to find answers to questions that could not even be addressed before. In this way, understanding the design leads to more intelligent decision-making and design space exploration. © 2012 AIAA.

Flexible representations of dynamics are used in object manipulation.

To manipulate an object skillfully, the brain must learn its dynamics, specifying the mapping between applied force and motion. A fundamental issue in sensorimotor control is whether such dynamics are represented in an extrinsic frame of reference tied to the object or an intrinsic frame of reference linked to the arm. Although previous studies have suggested that objects are represented in arm-centered coordinates [1-6], all of these studies have used objects with unusual and complex dynamics. Thus, it is not known how objects with natural dynamics are represented. Here we show that objects with simple (or familiar) dynamics and those with complex (or unfamiliar) dynamics are represented in object- and arm-centered coordinates, respectively. We also show that objects with simple dynamics are represented with an intermediate coordinate frame when vision of the object is removed. These results indicate that object dynamics can be flexibly represented in different coordinate frames by the brain. We suggest that with experience, the representation of the dynamics of a manipulated object may shift from a coordinate frame tied to the arm toward one that is linked to the object. The additional complexity required to represent dynamics in object-centered coordinates would be economical for familiar objects because such a representation allows object use regardless of the orientation of the object in hand.

Development and experimental validation of a mathematical model for friction between fabrics and a volar forearm phantom.

An analytical mathematical model for friction between a fabric strip and the volar forearm has been developed and validated experimentally. The model generalizes the common assumption of a cylindrical arm to any convex prism, and makes predictions for pressure and tension based on Amontons' law. This includes a relationship between the coefficient of static friction (mu) and forces on either end of a fabric strip in contact with part of the surface of the arm and perpendicular to its axis. Coefficients of friction were determined from experiments between arm phantoms of circular and elliptical cross-section (made from Plaster of Paris covered in Neoprene) and a nonwoven fabric. As predicted by the model, all values of mu calculated from experimental results agreed within +/- 8 per cent, and showed very little systematic variation with the deadweight, geometry, or arc of contact used. With an appropriate choice of coordinates the relationship predicted by this model for forces on either end of a fabric strip reduces to the prediction from the common model for circular arms. This helps to explain the surprisingly accurate values of mu obtained by applying the cylindrical model to experimental data on real arms.

Real time feature-based facial tracking using Lie algebras

We have developed a novel human facial tracking system that operates in real time at a video frame rate without needing any special hardware. The approach is based on the use of Lie algebra, and uses three-dimensional feature points on the targeted human face. It is assumed that the roughly estimated facial model (relative coordinates of the three-dimensional feature points) is known. First, the initial feature positions of the face are determined using a model fitting technique. Then, the tracking is operated by the following sequence: (1) capture the new video frame and render feature points to the image plane; (2) search for new positions of the feature points on the image plane; (3) get the Euclidean matrix from the moving vector and the three-dimensional information for the points; and (4) rotate and translate the feature points by using the Euclidean matrix, and render the new points on the image plane. The key algorithm of this tracker is to estimate the Euclidean matrix by using a least square technique based on Lie algebra. The resulting tracker performed very well on the task of tracking a human face.

The wave transmission coefficients and coupling loss factors of point connected structures

This analysis is concerned with the calculation of the elastic wave transmission coefficients and coupling loss factors between an arbitrary number of structural components that are coupled at a point. A general approach to the problem is presented and it is demonstrated that the resulting coupling loss factors satisfy reciprocity. A key aspect of the method is the consideration of cylindrical waves in two-dimensional components, and this builds upon recent results regarding the energetics of diffuse wavefields when expressed in cylindrical coordinates. Specific details of the method are given for beam and thin plate components, and a number of examples are presented. © 2002 Acoustical Society of America.

Acoustic radiation force of a Bessel beam on a porous sphere.

The possibility of using acoustic Bessel beams to produce an axial pulling force on porous particles is examined in an exact manner. The mathematical model utilizes the appropriate partial-wave expansion method in spherical coordinates, while Biot's model is used to describe the wave motion within the poroelastic medium. Of particular interest here is to examine the feasibility of using Bessel beams for (a) acoustic manipulation of fine porous particles and (b) suppression of particle resonances. To verify the viability of the technique, the radiation force and scattering form-function are calculated for aluminum and silica foams at various porosities. Inspection of the results has shown that acoustic manipulation of low porosity (<0.3) spheres is similar to that of solid elastic spheres, but this behavior significantly changes at higher porosities. Results have also shown a strong correlation between the backscattered form-function and the regions of negative radiation force. It has also been observed that the high-order resonances of the particle can be effectively suppressed by choosing the beam conical angle such that the acoustic contribution from that particular mode vanishes. This investigation may be helpful in the development of acoustic tweezers for manipulation of micro-porous drug delivery carrier and contrast agents.

Automated sparse 3D point cloud generation of infrastructure using its distinctive visual features

The commercial far-range (>10 m) spatial data collection methods for acquiring infrastructure’s geometric data are not completely automated because of the necessary manual pre- and/or post-processing work. The required amount of human intervention and, in some cases, the high equipment costs associated with these methods impede their adoption by the majority of infrastructure mapping activities. This paper presents an automated stereo vision-based method, as an alternative and inexpensive solution, to producing a sparse Euclidean 3D point cloud of an infrastructure scene utilizing two video streams captured by a set of two calibrated cameras. In this process SURF features are automatically detected and matched between each pair of stereo video frames. 3D coordinates of the matched feature points are then calculated via triangulation. The detected SURF features in two successive video frames are automatically matched and the RANSAC algorithm is used to discard mismatches. The quaternion motion estimation method is then used along with bundle adjustment optimization to register successive point clouds. The method was tested on a database of infrastructure stereo video streams. The validity and statistical significance of the results were evaluated by comparing the spatial distance of randomly selected feature points with their corresponding tape measurements.

Automated vision tracking of project related entities

Tracking of project related entities such as construction equipment, materials, and personnel is used to calculate productivity, detect travel path conflicts, enhance the safety on the site, and monitor the project. Radio frequency tracking technologies (Wi-Fi, RFID, UWB) and GPS are commonly used for this purpose. However, on large-scale sites, deploying, maintaining and removing such systems can be costly and time-consuming. In addition, privacy issues with personnel tracking often limits the usability of these technologies on construction sites. This paper presents a vision based tracking framework that holds promise to address these limitations. The framework uses videos from a set of two or more static cameras placed on construction sites. In each camera view, the framework identifies and tracks construction entities providing 2D image coordinates across frames. Combining the 2D coordinates based on the installed camera system (the distance between the cameras and the view angles of them), 3D coordinates are calculated at each frame. The results of each step are presented to illustrate the feasibility of the framework.

Innovative Stereo Vision-Based Approach to Generate Dense Depth Map of Transportation Infrastructure

Three-dimensional (3-D) spatial data of a transportation infrastructure contain useful information for civil engineering applications, including as-built documentation, on-site safety enhancements, and progress monitoring. Several techniques have been developed for acquiring 3-D point coordinates of infrastructure, such as laser scanning. Although the method yields accurate results, the high device costs and human effort required render the process infeasible for generic applications in the construction industry. A quick and reliable approach, which is based on the principles of stereo vision, is proposed for generating a depth map of an infrastructure. Initially, two images are captured by two similar stereo cameras at the scene of the infrastructure. A Harris feature detector is used to extract feature points from the first view, and an innovative adaptive window-matching technique is used to compute feature point correspondences in the second view. A robust algorithm computes the nonfeature point correspondences. Thus, the correspondences of all the points in the scene are obtained. After all correspondences have been obtained, the geometric principles of stereo vision are used to generate a dense depth map of the scene. The proposed algorithm has been tested on several data sets, and results illustrate its potential for stereo correspondence and depth map generation.

Effects of multi-scattering on the performance of a single-beam acoustic manipulation device.

The effects of multiple scattering on acoustic manipulation of spherical particles using helicoidal Bessel-beams are discussed. A closed-form analytical solution is developed to calculate the acoustic radiation force resulting from a Bessel-beam on an acoustically reflective sphere, in the presence of an adjacent spherical particle, immersed in an unbounded fluid medium. The solution is based on the standard Fourier decomposition method and the effect of multi-scattering is taken into account using the addition theorem for spherical coordinates. Of particular interest here is the investigation of the effects of multiple scattering on the emergence of negative axial forces. To investigate the effects, the radiation force applied on the target particle resulting from a helicoidal Bessel-beam of different azimuthal indexes (m = 1 to 4), at different conical angles, is computed. Results are presented for soft and rigid spheres of various sizes, separated by a finite distance. Results have shown that the emergence of negative force regions is very sensitive to the level of cross-scattering between the particles. It has also been shown that in multiple scattering media, the negative axial force may occur at much smaller conical angles than previously reported for single particles, and that acoustic manipulation of soft spheres in such media may also become possible.