KinImmerse: Macromolecular VR for NMR ensembles

<p>Abstract</p> <p>Background</p> <p>In molecular applications, virtual reality (VR) and immersive virtual environments have generally been used and valued for the visual and interactive experience – to enhance intuition and communicate excitement – rather than as part of the actual research process. In contrast, this work develops a software infrastructure for research use and illustrates such use on a specific case.</p> <p>Methods</p> <p>The Syzygy open-source toolkit for VR software was used to write the KinImmerse program, which translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment) or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE.</p> <p>Results</p> <p>In addition to molecular visualizations and navigation, KinImmerse provides a set of research tools for manipulation, identification, co-centering of multiple models, free-form 3D annotation, and output of results. The molecular research test case analyzes the local neighborhood around an individual atom within an ensemble of nuclear magnetic resonance (NMR) models, enabling immersive visual comparison of the local conformation with the local NMR experimental data, including target curves for residual dipolar couplings (RDCs).</p> <p>Conclusion</p> <p>The promise of KinImmerse for production-level molecular research in the DiVE is shown by the locally co-centered RDC visualization developed there, which gave new insights now being pursued in wider data analysis.</p

AFM Imaging of SWI/SNF action: mapping the nucleosome remodeling and sliding

We propose a combined experimental (Atomic Force Microscopy) and theoretical study of the structural and dynamical properties of nucleosomes. In contrast to biochemical approaches, this method allows to determine simultaneously the DNA complexed length distribution and nucleosome position in various contexts. First, we show that differences in the nucleo-proteic structure observed between conventional H2A and H2A.Bbd variant nucleosomes induce quantitative changes in the in the length distribution of DNA complexed with histones. Then, the sliding action of remodeling complex SWI/SNF is characterized through the evolution of the nucleosome position and wrapped DNA length mapping. Using a linear energetic model for the distribution of DNA complexed length, we extract the net wrapping energy of DNA onto the histone octamer, and compare it to previous studies.Comment: 25 pages,5 figures, to appear in Biophysical Journa

Advances in shape measurement in the digital world

The importance of particle shape in terms of its effects on the behaviour of powders and other particulate systems has long been recognised, but particle shape information has been rather difficult to obtain and use until fairly recently, unlike its better-known counterpart, particle size. However, advances in computing power and 3D image acquisition and analysis techniques have resulted in major progress being made in the measurement, description and application of particle shape information in recent years. Because we are now in a digital era, it is fitting that many of these advanced techniques are based on digital technology. This review article aims to trace the development of these new techniques, highlight their contributions to both academic and practical applications, and present a perspective for future developments

Microscopy and Analysis

Microscopes represent tools of the utmost importance for a wide range of disciplines. Without them, it would have been impossible to stand where we stand today in terms of understanding the structure and functions of organelles and cells, tissue composition and metabolism, or the causes behind various pathologies and their progression. Our knowledge on basic and advanced materials is also intimately intertwined to the realm of microscopy, and progress in key fields of micro- and nanotechnologies critically depends on high-resolution imaging systems. This volume includes a series of chapters that address highly significant scientific subjects from diverse areas of microscopy and analysis. Authoritative voices in their fields present in this volume their work or review recent trends, concepts, and applications, in a manner that is accessible to a broad readership audience from both within and outside their specialist area

Modeling and Simulation in Engineering

This book provides an open platform to establish and share knowledge developed by scholars, scientists, and engineers from all over the world, about various applications of the modeling and simulation in the design process of products, in various engineering fields. The book consists of 12 chapters arranged in two sections (3D Modeling and Virtual Prototyping), reflecting the multidimensionality of applications related to modeling and simulation. Some of the most recent modeling and simulation techniques, as well as some of the most accurate and sophisticated software in treating complex systems, are applied. All the original contributions in this book are jointed by the basic principle of a successful modeling and simulation process: as complex as necessary, and as simple as possible. The idea is to manipulate the simplifying assumptions in a way that reduces the complexity of the model (in order to make a real-time simulation), but without altering the precision of the results

Real-Time Path Planning for Automating Optical Tweezers based Particle Transport Operations

Optical tweezers (OT) have been developed to successfully trap, orient, and transport micro and nano scale components of many different sizes and shapes in a fluid medium. They can be viewed as robots made out of light. Components can be simply released from optical traps by switching off laser beams. By utilizing the principle of time sharing or holograms, multiple optical traps can perform several operations in parallel. These characteristics make optical tweezers a very promising technology for creating directed micro and nano scale assemblies. In the infra-red regime, they are useful in a large number of biological applications as well. This dissertation explores the problem of real-time path planning for autonomous OT based transport operations. Such operations pose interesting challenges as the environment is uncertain and dynamic due to the random Brownian motion of the particles and noise in the imaging based measurements. Silica microspheres having diameters between (1-20) µm are selected as model components. Offline simulations are performed to gather trapping probability data that serves as a measure of trap strength and reliability as a function of relative position of the particle under consideration with respect to the trap focus, and trap velocity. Simplified models are generated using Gaussian Radial Basis Functions to represent the data in a compact form. These metamodels can be queried at run-time to obtain estimated probability values accurately and efficiently. Simple trapping probability models are then utilized in a stochastic dynamic programming framework to compute optimum trap locations and velocities that minimizes the total, expected transport time by incorporating collision avoidance and recovery steps. A discrete version of an approximate partially observable Markov decision process algorithm, called the QMDP_NLTDV algorithm, is developed. Real-time performance is ensured by pruning the search space and enhancing convergence rates by introducing a non-linear value function. The algorithm is validated both using a simulator as well as a physical holographic tweezer set-up. Successful runs show that the automated planner is flexible, works well in reasonably crowded scenes, and is capable of transporting a specific particle to a given goal location by avoiding collisions either by circumventing or by trapping other freely diffusing particles. This technique for transporting individual particles is utilized within a decoupled and prioritized approach to move multiple particles simultaneously. An iterative version of a bipartite graph matching algorithm is also used to assign goal locations to target objects optimally. As in the case of single particle transport, simulation and some physical experiments are performed to validate the multi-particle planning approach

Technology 2000, volume 1

The purpose of the conference was to increase awareness of existing NASA developed technologies that are available for immediate use in the development of new products and processes, and to lay the groundwork for the effective utilization of emerging technologies. There were sessions on the following: Computer technology and software engineering; Human factors engineering and life sciences; Information and data management; Material sciences; Manufacturing and fabrication technology; Power, energy, and control systems; Robotics; Sensors and measurement technology; Artificial intelligence; Environmental technology; Optics and communications; and Superconductivity