Ambient occlusion and shadows for molecular graphics

Computer based visualisations of molecules have been produced as early as the 1950s to aid researchers in their understanding of biomolecular structures. An important consideration for Molecular Graphics software is the ability to visualise the 3D structure of the molecule in a clear manner. Recent advancements in computer graphics have led to improved rendering capabilities of the visualisation tools. The capabilities of current shading languages allow the inclusion of advanced graphic effects such as ambient occlusion and shadows that greatly improve the comprehension of the 3D shapes of the molecules. This thesis focuses on finding improved solutions to the real time rendering of Molecular Graphics on modern day computers. The methods of calculating ambient occlusion and both hard and soft shadows are examined and implemented to give the user a more complete experience when navigating large molecular structures

The design process for XR experiences

The act of telling stories has been a core part of the human experience since the days of cavemen standing around a fire to tell the story of the day's hunt (Balter). As new technologies are being developed, such as virtual reality headsets and cellphones with augmented reality capabilities, the designer's process has been challenged. We are increasingly living in a world where human experiences are separating from physical reality and moving toward an extended reality or XR. “Extended Reality” (XR) is the umbrella term used to describe VR (Virtual Reality), AR (Augmented Reality), and MR (Mixed Reality) as well as all future realities [any new experiences that might be created outside of the already existing realms] such technology, might bring. XR covers the full spectrum of real and virtual environments'' (Scribani). The challenge Designers are facing is how to effectively tell engaging stories using new and increasingly prevalent technologies within the XR envelope. Many experiences utilizing XR tend to focus on the technology and tools rather than the story. XR is the new “Wild West” in storytelling. There are no hard rules and no defined creative processes for crafting a successful experience within the technology. This thesis asks the question, can the theatrical design process help to create more successful XR experiences? Success being more social interaction and long-lasting engagement. Can a focus on human-centric stories make the experiences more engaging? In this thesis, I will be investigating three XR experiences and their varying design processes. The evaluation of this research will be qualitative rather than quantitative. The success or failure of these experiential XR designs will be determined through the lens of a collaborative theatrical designer.Theatre and Danc

High quality rendering of protein dynamics in space filling mode

Producing high quality depictions of molecular structures has been an area of academic interest for years, with visualisation tools such as UCSF Chimera, Yasara and PyMol providing a huge number of different rendering modes and lighting effects. However, no visualisation program supports per-pixel lighting effects with shadows whilst rendering a molecular trajectory in space filling mode. In this paper, a new approach to rendering high quality visualisations of molecular trajectories is presented. To enhance depth, ambient occlusion is included within the render. Shadows are also included to help the user perceive relative motions of parts of the protein as they move based on their trajectories. Our approach requires a regular grid to be constructed every time the molecular structure deforms allowing per-pixel lighting effects and ambient occlusion to be rendered every frame, at interactive refresh rates. Two different regular grids are investigated, a fixed grid and a memory efficient compact grid. The algorithms used allow trajectories of proteins comprising of up to 300,000 atoms in size to be rendered at ninety frames per second on a desktop computer using the GPU for general purpose computations. Regular grid construction was found to only take up a small proportion of the total time to render a frame. It was found that despite being slower to construct, the memory efficient compact grid outperformed the theoretically faster fixed grid when the protein being rendered is large, owing to its more efficient memory access patterns. The techniques described could be implemented in other molecular rendering software

CustomProcessingUnit: Reverse Engineering and Customization of Intel Microcode

Microcode provides an abstraction layer over the instruction set to decompose complex instructions into simpler micro-operations that can be more easily implemented in hardware. It is an essential optimization to simplify the design of x86 processors. However, introducing an additional layer of software beneath the instruction set poses security and reliability concerns. The microcode details are confidential to the manufacturers, preventing independent auditing or customization of the microcode. Moreover, microcode patches are signed and encrypted to prevent unauthorized patching and reverse engineering. However, recent research has recovered decrypted microcode and reverse-engineered read/write debug mechanisms on Intel Goldmont (Atom), making analysis and customization of microcode possible on a modern Intel microarchitecture. In this work, we present the first framework for static and dynamic analysis of Intel microcode. Building upon prior research, we reverse-engineer Goldmont microcode semantics and reconstruct the patching primitives for microcode customization. For static analysis, we implement a Ghidra processor module for decompilation and analysis of decrypted microcode. For dynamic analysis, we create a UEFI application that can trace and patch microcode to provide complete microcode control on Goldmont systems. Leveraging our framework, we reverse-engineer the confidential Intel microcode update algorithm and perform the first security analysis of its design and implementation. In three further case studies, we illustrate the potential security and performance benefits of microcode customization. We provide the first x86 Pointer Authentication Code (PAC) microcode implementation and its security evaluation, design and implement fast software breakpoints that are more than 1000x faster than standard breakpoints, and present constant-time microcode division, illustrating the potential security and performance benefits of microcode customization

Can smartphone technology be used to support an effective home exercise intervention to prevent falls amongst community dwelling older adults?: The TOGETHER feasibility RCT study protocol

INTRODUCTION: Falls have major implications for quality of life, independence and cost to the health service. Strength and balance training has been found to be effective in reducing the rate/risk of falls, as long as there is adequate fidelity to the evidence-based programme. Health services are often unable to deliver the evidence-based dose of exercise and older adults do not always sufficiently adhere to their programme to gain full outcomes. Smartphone technology based on behaviour-change theory has been used to support healthy lifestyles, but not falls prevention exercise. This feasibility trial will explore whether smartphone technology can support patients to better adhere to an evidence-based rehabilitation programme and test study procedures/outcome measures. METHODS AND ANALYSIS: A two-arm, pragmatic feasibility randomised controlled trial will be conducted with health services in Manchester, UK. Seventy-two patients aged 50+years eligible for a falls rehabilitation exercise programme from two community services will receive: (1) standard service with a smartphone for outcome measurement only or (2) standard service plus a smartphone including the motivational smartphone app. The primary outcome is feasibility of the intervention, study design and procedures. The secondary outcome is to compare standard outcome measures for falls, function and adherence to instrumented versions collected using smartphone. Outcome measures collected include balance, function, falls, strength, fear of falling, health-related quality of life, resource use and adherence. Outcomes are measured at baseline, 3 and 6-month post-randomisation. Interviews/focus groups with health professionals and participants further explore feasibility of the technology and trial procedures. Primarily analyses will be descriptive. ETHICS AND DISSEMINATION: The study protocol is approved by North West Greater Manchester East Research Ethics Committee (Rec ref:18/NW/0457, 9/07/2018). User groups and patient representatives were consulted to inform trial design, and are involved in study recruitment. Results will be reported at conferences and in peer-reviewed publications. A dissemination event will be held in Manchester to present the results of the trial. The protocol adheres to the recommended Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) checklist

Exploration of nanosilver calcium alginate-based multifunctional polymer wafers for wound healing

Wound care is an integral part of effective recovery. However, its associated financial burden on national health services globally is significant enough to warrant further research and development in this field. In this study, multifunctional polymer wafers were prepared, which provide antibacterial activity, high cell viability, high swelling capacity and a thermally stable medium which can be used to facilitate the delivery of therapeutic agents. The purpose of this polymer wafer is to facilitate wound healing, by creating nanosilver particles within the polymer matrix itself via a one-pot synthesis method. This study compares the use of two synthetic agents in tandem, detailing the effects on the morphology and size of nanosilver particles. Two synthetic methods with varying parameters were tested, with one method using silver nitrate, calcium chloride and sodium alginate, whilst the other included aloe vera gel as an extra component, which serves as another reductant for nanosilver synthesis. Both methods generated thermally stable alginate matrices with high degrees of swelling capacities (400–900%) coupled with interstitially formed nanosilver of varying shapes and sizes. These matrices exhibited controlled nanosilver release rates which were able to elicit antibacterial activity against MRSA, whilst maintaining an average cell viability value of above 90%. Based on the results of this study, the multifunctional polymer wafers that were created set the standard for future polymeric devices for wound healing. These polymer wafers can then be further modified to suit specific types of wounds, thereby allowing this multifunctional polymer wafer to be applied to different wounding scenarios