Advancing computational biophysics with Virtual Reality

Modelos computacionais são ferramentas poderosas para explorar as propriedades de sistemas biológicos complexos. Na neurociência computacional, permitir fácil exploração e visualização computacional desses modelos é crucial para o progresso do campo. Nos últimos anos, os sistemas de visualização 3D e o hardware de realidade virtual tornaram-se mais acessíveis e isso abre uma janela de oportunidade para os serviços de visualização. O principal problema atual da visualização 3D diz respeito à usabilidade (ou seja, navegação e seleção). Durante esta dissertação, hipotetizaremos que a substituição do 3D por VR irá (1) superar os problemas de usabilidade mencionados e, eventualmente, (2) aumentar a eficácia dos utilizadores em relação às questões do campo de estudo (neurociência). Para avaliar os resultados do trabalho desenvolvido nesta dissertação, será realizada uma experiência de duas partes, em que um grupo de indivíduos deverá executar um conjunto de tarefas pré-determinadas e avaliar sua experiência usando 3D na primeira e VR na última parte. Além da autoavaliação da experiência, dados como tempo de conclusão e correção da tarefa também serão usados para quantificar a eficácia do método de visualização. Dada a experiência mencionada, um protótipo de uma aplicação (baseada na Web) com visualização de Realidade Virtual deve ser desenvolvido. A visualização 3D será fornecida por uma framework de código aberto baseada na Web, chamada Geppetto. Cada uma das decisões tomadas no desenvolvimento do protótipo será analisada adequadamente neste documento, bem como a literatura científica que servirá de base quando necessário. Além do estudo da Realidade Virtual propriamente dita, também serão analisados métodos padronizados para a visualização de informações (neuro) científicas. A solução proposta procurará constituir uma base de trabalho sólida e suficientemente genérica a ser aplicada, não apenas no contexto da neurociência, mas também em vários outros contextos onde a visualização de modelos através de Realidade Virtual poderá ser bem-sucedida.Computational models are powerful tools for exploring the properties of complex biological systems. In computational neuroscience, allowing easy computational exploration and visualization of this models is crucial for the progress of the field. In recent years, Virtual Reality hardware and visualization systems have become more affordable and this opens a window of opportunity for visualization services. The current major problem of 3D visualization concerns usability (i.e., navigation and selection). During this dissertation, we will hypothesize that the replacement of 3D for VR will (1) overcome the usability issues mentioned and eventually (2) boost user effectiveness regarding field of study (neuroscience) concerns. In order to evaluate the results of the work developed under this dissertation, a two-part experiment will be carried out where a group of individuals must perform a set of predetermined tasks and evaluate their experience using 3D in the first and VR in the last part. Besides the self-evaluation of the experiment, data such as completion time and task correctness will also be used to quantify the effectiveness of the visualization method. Given the aforementioned experiment, a prototype of a (web-based) application with Virtual Reality visualization shall be developed. The 3D visualization will be provided by a web-based open-sourced framework called Geppetto. Each of the decisions made in the development of the prototype will be properly analyzed in this document, as well as the scientific literature that will serve as a basis when necessary. Besides the study of Virtual Reality itself, standard methods with respect to the visualization of (neuro)scientific information will also be analyzed. The proposed solution will seek to constitute a solid and sufficiently generic work base to be applied, not only in the scope of neuroscience, but also in several other contexts where visualization through VR might be successful

Virtual Reality Simulator for Training in Myringotomy with Tube Placement

Myringotomy refers to a surgical incision in the eardrum, and it is often followed by ventilation tube placement to treat middle-ear infections. The procedure is difficult to learn; hence, the objectives of this work were to develop a virtual-reality training simulator, assess its face and content validity, and implement quantitative performance metrics and assess construct validity. A commercial digital gaming engine (Unity3D) was used to implement the simulator with support for 3D visualization of digital ear models and support for major surgical tasks. A haptic arm co-located with the stereo scene was used to manipulate virtual surgical tools and to provide force feedback. A questionnaire was developed with 14 face validity questions focusing on realism and 6 content validity questions focusing on training potential. Twelve participants from the Department of Otolaryngology were recruited for the study. Responses to 12 of the 14 face validity questions were positive. One concern was with contact modeling related to tube insertion into the eardrum, and the second was with movement of the blade and forceps. The former could be resolved by using a higher resolution digital model for the eardrum to improve contact localization. The latter could be resolved by using a higher fidelity haptic device. With regard to content validity, 64% of the responses were positive, 21% were neutral, and 15% were negative. In the final phase of this work, automated performance metrics were programmed and a construct validity study was conducted with 11 participants: 4 senior Otolaryngology consultants and 7 junior Otolaryngology residents. Each participant performed 10 procedures on the simulator and metrics were automatically collected. Senior Otolaryngologists took significantly less time to completion compared to junior residents. Junior residents had 2.8 times more errors as compared to experienced surgeons. The senior surgeons also had significantly longer incision lengths, more accurate incision angles, and lower magnification keeping both the umbo and annulus in view. All metrics were able to discriminate senior Otolaryngologists from junior residents with a significance of p \u3c 0.002. The simulator has sufficient realism, training potential and performance discrimination ability to warrant a more resource intensive skills transference study

Physics-based visual characterization of molecular interaction forces

Molecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering. Despite the development of automatic computational protocols, analysis of molecular interactions is still a major aspect where human comprehension and intuition are key to accelerate, analyze, and propose modifications to the molecule of interest. Most visualization algorithms help the users by providing an accurate depiction of the spatial arrangement: the atoms involved in inter-molecular contacts. There are few tools that provide visual information on the forces governing molecular docking. However, these tools, commonly restricted to close interaction between atoms, do not consider whole simulation paths, long-range distances and, importantly, do not provide visual cues for a quick and intuitive comprehension of the energy functions (modeling intermolecular interactions) involved. In this paper, we propose visualizations designed to enable the characterization of interaction forces by taking into account several relevant variables such as molecule-ligand distance and the energy function, which is essential to understand binding affinities. We put emphasis on mapping molecular docking paths obtained from Molecular Dynamics or Monte Carlo simulations, and provide time-dependent visualizations for different energy components and particle resolutions: atoms, groups or residues. The presented visualizations have the potential to support domain experts in a more efficient drug or enzyme design process.Peer ReviewedPostprint (author's final draft

Collaborative visualization and virtual reality in construction projects

In the Colombian construction industry it is recognized as a general practice that di!erent designers deliver 2D drawings to the project construction team -- Some 3D modeling applications are used but only with commercial intentions, thus wasting visualization tools that facilitate the understanding of the project, that allow the coordination of plans between di!erent specialists, and that can prevent errors with high impact on costs in the construction phase of the project -- As a continuation of the project "immersive virtual reality for construction" developed by EAFIT University, the present work intends to demonstrate how a collaborative virtual environment can be helpful in order to improve visualization of construction projects and achieve the interaction of di!erent specialties, evaluating the impact of collaborative work in the design process of the same -- The end result of this research is an application created using freely available tools and a use case scenario on how this application can be used to perform review meetings by di!erent specialist in real time -- Initial test on the system has been made with civil engineering students showing that this virtual reality tool ease the burden of performing reviews where traditionally plans and sharing the same geographical space were neede

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

SOFA: A Multi-Model Framework for Interactive Physical Simulation

International audienceSOFA (Simulation Open Framework Architecture) is an open-source C++ library primarily targeted at interactive computational medical simulation. SOFA facilitates collaborations between specialists from various domains, by decomposing complex simulators into components designed independently and organized in a scenegraph data structure. Each component encapsulates one of the aspects of a simulation, such as the degrees of freedom, the forces and constraints, the differential equations, the main loop algorithms, the linear solvers, the collision detection algorithms or the interaction devices. The simulated objects can be represented using several models, each of them optimized for a different task such as the computation of internal forces, collision detection, haptics or visual display. These models are synchronized during the simulation using a mapping mechanism. CPU and GPU implementations can be transparently combined to exploit the computational power of modern hardware architectures. Thanks to this flexible yet efficient architecture, \sofa{} can be used as a test-bed to compare models and algorithms, or as a basis for the development of complex, high-performance simulators

Retinal drug delivery: rethinking outcomes for the efficient replication of retinal behavior

The retina is a highly organized structure that is considered to be "an approachable part of the brain." It is attracting the interest of development scientists, as it provides a model neurovascular system. Over the last few years, we have been witnessing significant development in the knowledge of the mechanisms that induce the shape of the retinal vascular system, as well as knowledge of disease processes that lead to retina degeneration. Knowledge and understanding of how our vision works are crucial to creating a hardware-adaptive computational model that can replicate retinal behavior. The neuronal system is nonlinear and very intricate. It is thus instrumental to have a clear view of the neurophysiological and neuroanatomic processes and to take into account the underlying principles that govern the process of hardware transformation to produce an appropriate model that can be mapped to a physical device. The mechanistic and integrated computational models have enormous potential toward helping to understand disease mechanisms and to explain the associations identified in large model-free data sets. The approach used is modulated and based on different models of drug administration, including the geometry of the eye. This work aimed to review the recently used mathematical models to map a directed retinal network.The authors acknowledge the financial support received from the Portuguese Science and Technology Foundation (FCT/MCT) and the European Funds (PRODER/COMPETE) for the project UIDB/04469/2020 (strategic fund), co-financed by FEDER, under the Partnership Agreement PT2020. The authors also acknowledge FAPESP – São Paulo Research Foundation, for the financial support for the publication of the article.info:eu-repo/semantics/publishedVersio