Molecular simulations and visualization: introduction and overview

Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building

ExaViz: a Flexible Framework to Analyse, Steer and Interact with Molecular Dynamics Simulations

International audienceThe amount of data generated by molecular dynamics simulations of large molecular assemblies and the sheer size and complexity of the systems studied call for new ways to analyse, steer and interact with such calculations. Traditionally, the analysis is performed off-line once the huge amount of simulation results have been saved to disks, thereby stressing the supercomputer I/O systems, and making it increasingly difficult to handle post-processing and analysis from the scientist's office. The ExaViz framework is an alternative approach developed to couple the simulation with analysis tools to process the data as close as possible to their source of creation, saving a reduced, more manageable and pre-processed data set to disk. ExaViz supports a large variety of analysis and steering scenarios. Our framework can be used for live sessions (simulations short enough to be fully followed by the user) as well as batch sessions (long time batch executions). During interactive sessions, at run time, the user can display plots from analysis, visualise the molecular system and steer the simulation with a haptic device. We also emphasise how a Cave-like immersive environment could be used to leverage such simulations, offering a large display surface to view and intuitively navigate the molecular system

Microscope Embedded Neurosurgical Training and Intraoperative System

In the recent years, neurosurgery has been strongly influenced by new technologies. Computer Aided Surgery (CAS) offers several benefits for patients\u27 safety but fine techniques targeted to obtain minimally invasive and traumatic treatments are required, since intra-operative false movements can be devastating, resulting in patients deaths. The precision of the surgical gesture is related both to accuracy of the available technological instruments and surgeon\u27s experience. In this frame, medical training is particularly important. From a technological point of view, the use of Virtual Reality (VR) for surgeon training and Augmented Reality (AR) for intra-operative treatments offer the best results. In addition, traditional techniques for training in surgery include the use of animals, phantoms and cadavers. The main limitation of these approaches is that live tissue has different properties from dead tissue and that animal anatomy is significantly different from the human. From the medical point of view, Low-Grade Gliomas (LGGs) are intrinsic brain tumours that typically occur in younger adults. The objective of related treatment is to remove as much of the tumour as possible while minimizing damage to the healthy brain. Pathological tissue may closely resemble normal brain parenchyma when looked at through the neurosurgical microscope. The tactile appreciation of the different consistency of the tumour compared to normal brain requires considerable experience on the part of the neurosurgeon and it is a vital point. The first part of this PhD thesis presents a system for realistic simulation (visual and haptic) of the spatula palpation of the LGG. This is the first prototype of a training system using VR, haptics and a real microscope for neurosurgery. This architecture can be also adapted for intra-operative purposes. In this instance, a surgeon needs the basic setup for the Image Guided Therapy (IGT) interventions: microscope, monitors and navigated surgical instruments. The same virtual environment can be AR rendered onto the microscope optics. The objective is to enhance the surgeon\u27s ability for a better intra-operative orientation by giving him a three-dimensional view and other information necessary for a safe navigation inside the patient. The last considerations have served as motivation for the second part of this work which has been devoted to improving a prototype of an AR stereoscopic microscope for neurosurgical interventions, developed in our institute in a previous work. A completely new software has been developed in order to reuse the microscope hardware, enhancing both rendering performances and usability. Since both AR and VR share the same platform, the system can be referred to as Mixed Reality System for neurosurgery. All the components are open source or at least based on a GPL license

Vision-Augmented molecular dynamics simulation of nanoindentation

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University London.This thesis has contributed to the literature by providing a pathway to simplify the process of carrying out molecular dynamics simulation. As a part of the investigation, a user-friendly vision-augmented technique was developed to set up and carry out atomistic simulations using hand-gestures. The system is novel in its concept as it enables the user to directly manipulate the atomic structures on the screen, in 3D space using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations. The hand gestures are used to pick and place atoms on the screen allowing thereby the ease of preparing and carrying out molecular dynamics simulations in a more intuitive way. The end result is that users with limited expertise in developing molecular structures can now do so easily and intuitively by the use of body gestures to interact with the simulator to study the system in question. The proposed system was tested by performing parallel molecular dynamics simulations to study (i) crystal anisotropy of a diamond cubic substrate (crystalline silicon) using nanoindentation with a long-range (Screened bond order) Tersoff potential and (ii) crystal anisotropy of a body centre cubic metal (tantalum) using nanoindentation with an Embedded Atomic Method (EAM) type potential. The MD data was post-processed to reveal size effects observed in anisotropy of both these materials, namely, silicon and tantalum. The value of hardness and elastic modulus obtained from the MD data was found in accordance with what has been discovered previously by experiments, thereby validating the simulations. Based on this, it is anticipated that the proposed system will open up new horizons to the current methods on how an MD simulation is designed and executed.King Abdullah bin Abdul-Aziz Al- Saud Ministry of Higher Education and Northern Borders University, Kingdom of Saudi Arabi

3-D Interfaces for Spatial Construction

It is becoming increasingly easy to bring the body directly to digital form via stereoscopic immersive displays and tracked input devices. Is this space a viable one in which to construct 3d objects? Interfaces built upon two-dimensional displays and 2d input devices are the current standard for spatial construction, yet 3d interfaces, where the dimensionality of the interactive space matches that of the design space, have something unique to offer. This work increases the richness of 3d interfaces by bringing several new tools into the picture: the hand is used directly to trace surfaces; tangible tongs grab, stretch, and rotate shapes; a handle becomes a lightsaber and a tool for dropping simple objects; and a raygun, analagous to the mouse, is used to select distant things. With these tools, a richer 3d interface is constructed in which a variety of objects are created by novice users with relative ease. What we see is a space, not exactly like the traditional 2d computer, but rather one in which a distinct and different set of operations is easy and natural. Design studies, complemented by user studies, explore the larger space of three-dimensional input possibilities. The target applications are spatial arrangement, freeform shape construction, and molecular design. New possibilities for spatial construction develop alongside particular nuances of input devices and the interactions they support. Task-specific tangible controllers provide a cultural affordance which links input devices to deep histories of tool use, enhancing intuition and affective connection within an interface. On a more practical, but still emotional level, these input devices frame kinesthetic space, resulting in high-bandwidth interactions where large amounts of data can be comfortably and quickly communicated. A crucial issue with this interface approach is the tension between specific and generic input devices. Generic devices are the tradition in computing -- versatile, remappable, frequently bereft of culture or relevance to the task at hand. Specific interfaces are an emerging trend -- customized, culturally rich, to date these systems have been tightly linked to a single application, limiting their widespread use. The theoretical heart of this thesis, and its chief contribution to interface research at large is an approach to customization. Instead of matching an application domain's data, each new input device supports a functional class. The spatial construction task is split into four types of manipulation: grabbing, pointing, holding, and rubbing. Each of these action classes spans the space of spatial construction, allowing a single tool to be used in many settings without losing the unique strengths of its specific form. Outside of 3d interface, outside of spatial construction, this approach strikes a balance between generic and specific suitable for many interface scenarios. In practice, these specific function groups are given versatility via a quick remapping technique which allows one physical tool to perform many digital tasks. For example, the handle can be quickly remapped from a lightsaber that cuts shapes to tools that place simple platonic solids, erase portions of objects, and draw double-helices in space. The contributions of this work lie both in a theoretical model of spatial interaction, and input devices (combined with new interactions) which illustrate the efficacy of this philosophy. This research brings the new results of Tangible User Interface to the field of Virtual Reality. We find a space, in and around the hand, where full-fledged haptics are not necessary for users physically connect with digital form.</p

Haptics Rendering and Applications

There has been significant progress in haptic technologies but the incorporation of haptics into virtual environments is still in its infancy. A wide range of the new society's human activities including communication, education, art, entertainment, commerce and science would forever change if we learned how to capture, manipulate and reproduce haptic sensory stimuli that are nearly indistinguishable from reality. For the field to move forward, many commercial and technological barriers need to be overcome. By rendering how objects feel through haptic technology, we communicate information that might reflect a desire to speak a physically- based language that has never been explored before. Due to constant improvement in haptics technology and increasing levels of research into and development of haptics-related algorithms, protocols and devices, there is a belief that haptics technology has a promising future

Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations

International audienc

I-Light Symposium 2005 Proceedings

I-Light was made possible by a special appropriation by the State of Indiana. The research described at the I-Light Symposium has been supported by numerous grants from several sources. Any opinions, findings and conclusions, or recommendations expressed in the 2005 I-Light Symposium Proceedings are those of the researchers and authors and do not necessarily reflect the views of the granting agencies.Indiana University Office of the Vice President for Research and Information Technology, Purdue University Office of the Vice President for Information Technology and CI