Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization

Tarini, Marco; Cignoni, Paolo; Montani, Claudio

doi:10.1109/tvcg.2006.115

Cited by 370 publications

(314 citation statements)

References 22 publications

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“…bSKAN and its interface with VASP allowed us to easily obtain accurate, noise-free contours far from the surface. Atomic graphics were created in QuteMol [38] and Vesta.…”

Section: Methodsmentioning

confidence: 99%

Direct visualization of quasi-ordered oxygen chain structures on Au(110)-(1 × 2)

et al. 2016

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The Au(110) surface offers unique advantages for atomically-resolved model studies of catalytic oxidation processes on gold. We investigate the adsorption of oxygen on Au(110) using a combination of scanning tunneling microscopy (STM) and density functional theory (DFT) methods. We identify the typical (empty-states) STM contrast resulting from adsorbed oxygen as atomic-sized dark features of electronic origin. DFT-based image simulations confirm that chemisorbed oxygen is generally detected indirectly, from the binding-induced electronic structure modification of gold. STM images show that adsorption occurs without affecting the general structure of the pristine Au(110) missing-row reconstruction. The tendency to form onedimensional structures is observed already at low coverage (<0.05ML), with oxygen adsorbing on alternate sides of the reconstruction ridges. Consistently, calculations yield preferred adsorption on the (111) facets of the reconstruction, on a 3-fold coordination site, with increased stability when adsorbed in chains. Gold atoms with two oxygen neighbors exhibit enhanced electronic hybridization with the O states. Finally, the species observed are reactive to CO oxidation at 200K and desorption of CO 2 leaves a clean and ordered gold surface.2

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“…bSKAN and its interface with VASP allowed us to easily obtain accurate, noise-free contours far from the surface. Atomic graphics were created in QuteMol [38] and Vesta.…”

Section: Methodsmentioning

confidence: 99%

Direct visualization of quasi-ordered oxygen chain structures on Au(110)-(1 × 2)

et al. 2016

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“…Ambient occlusion (AO) lighting [20] is applied as it accentuates global shape. As pointed out by [34], the regions made darker by ambient occlusion because of lower lighting accessibility are related to the regions with lower chemical accessibility. Interior points of clefts and pockets are made darker.…”

Section: Display Of Abstracted Surfacesmentioning

confidence: 95%

“…To provide for better comprehension of global shape, molecular visualizations have recently begun to use both global illumination and stylized shading. QuteMol [34] demonstrates the effectiveness of these techniques and shows how they can be implemented efficiently in hardware. However, QuteMol does not provide for shape abstraction; it provides only all-atom displays or space-filling diagrams.…”

Section: Conveying Shapementioning

confidence: 99%

“…Therefore, our system's primary display is stylized. Qutemol [34] showed the utility of stylized shading for molecular depiction. We apply several of their concepts to molecular surfaces.…”

Section: Display Of Abstracted Surfacesmentioning

confidence: 99%

“…In proteins, the motions range The standard approach (a), drawn with Pymol [11], shows the molecular surface pseudo-colored (from red to blue) with the charge distribution. Qutemol [34] (b), applies stylized lighting to a space filling representation. (c) applies stylized shading directly to the molecular surface.…”

Section: Introductionmentioning

confidence: 99%

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Molecular Surface Abstraction

Cipriano

Gleicher

2007

IEEE Trans. Visual. Comput. Graphics

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Abstract-In this paper we introduce a visualization technique that provides an abstracted view of the shape and spatio-physico-chemical properties of complex molecules. Unlike existing molecular viewing methods, our approach suppresses small details to facilitate rapid comprehension, yet marks the location of significant features so they remain visible. Our approach uses a combination of filters and mesh restructuring to generate a simplified representation that conveys the overall shape and spatio-physico-chemical properties (e.g. electrostatic charge). Surface markings are then used in the place of important removed details, as well as to supply additional information. These simplified representations are amenable to display using stylized rendering algorithms to further enhance comprehension. Our initial experience suggests that our approach is particularly useful in browsing collections of large molecules and in readily making comparisons between them.

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Engineering Strategies for Immunomodulatory Cytokine Therapies: Challenges and Clinical Progress

Pires

Hammond

Irvine

2021

Advanced Therapeutics

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Cytokines are immunoregulatory proteins involved in many pathological states with promising potential as therapeutic agents. A diverse array of cytokines has been studied in preclinical disease models since the 1950s, some of which became successful biopharmaceutical products with the advancement of recombinant protein technology in the 1980s. However, following these early approvals, clinical translation of these natural immune signaling molecules has been limited due to their pleiotropic action in many cell types, and the fact that they have evolved to act primarily locally in tissues. These characteristics, combined with poor pharmacokinetics, have hindered the delivery of cytokines via systemic administration routes due to dose-limiting toxicities. However, given their clinical potential and recent clinical successes in cancer immunotherapy, cytokines continue to be extensively pursued in preclinical and clinical studies, and a range of molecular and formulation engineering strategies are being applied to reduce treatment toxicity while maintaining or enhancing therapeutic efficacy. This review provides a brief background on the characteristics of cytokines and their history as clinical therapeutics, followed by a deeper discussion on the engineering strategies developed for cytokine therapies with a focus on the translational relevance of these approaches.

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Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization

Cited by 370 publications

References 22 publications

Direct visualization of quasi-ordered oxygen chain structures on Au(110)-(1 × 2)

Direct visualization of quasi-ordered oxygen chain structures on Au(110)-(1 × 2)

Molecular Surface Abstraction

Engineering Strategies for Immunomodulatory Cytokine Therapies: Challenges and Clinical Progress

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