Between Algorithm and Model: Different Molecular Surface Definitions for the Poisson-Boltzmann based Electrostatic Characterization of Biomolecules in Solution

The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric analysis seems to privilege the skin to the blobby surface, and points to an unexpected relationship between the non connectedness of the surface, caused by interstices in the solute volume, and the surface area dependence on atomic centers. In order to assess the ability to reproduce explicit solvent results, specific software tools have been developed to enable the use of the skin surface in Poisson-Boltzmann calculations with the DelPhi solver. Results indicate that the skin and Connolly surfaces have a comparable performance from this last point of view

The superhydrophobicity of polymer surfaces: Recent developments

Superhydrophobicity is the extreme water repellence of highly textured surfaces. The field of superhydrophobicity research has reached a stage where huge numbers of candidate treatments have been proposed and jumps have been made in theoretically describing them. There now seems to be a move to more practical concerns and to considering the demands of individual applications instead of more general cases. With these developments, polymeric surfaces with their huge variety of properties have come to the fore and are fast becoming the material of choice for designing, developing, and producing superhydrophobic surfaces. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1203–1217, 201

Моделювання фізичних явищ із застосуванням динаміки частинок

Метою даних методичних вказівок є знайомство студентів з методами створення систем частинок, вивчення їхніх основних властивостей, застосування впливу полів для отримання бажаного ефект

The role and mechanism of cytochrome P450 1B1 on the development of atherosclerosis; producing the animation for visual communication and education.

A large number of people are suffering from cardiovascular disease and losing their lives because of it. Atherosclerosis, a classic example of cardiovascular disease, is related to cytochrome p450 1B1 and other molecules in the development of the disease. Educational materials for patients and students on this topic are expected. Advantage, role and effectiveness of three-dimensional (3D) animation as a communication tool in biomedical science research and education have been proved. Therefore, 3D animation is a suitable medium to create visual material for atherosclerosis and related subject. Autodesk Maya 3D computer graphics software used for animation from modeling to animating and rendering in the production of the animation. Especially for various forms and details of the molecules in the animation, plugin, Molecular maya, was used in this project. About 3 minutes length of the animation contains basic background knowledge and information of atherosclerosis and molecular interactions in the development of mechanism of the disease

Localizing Protein in 3D Neural Stem Cell Culture: a Hybrid Visualization Methodology

The importance of 3-dimensional (3D) topography in influencing neural stem and progenitor cell (NPC) phenotype is widely acknowledged yet challenging to study. When dissociated from embryonic or post-natal brain, single NPCs will proliferate in suspension to form neurospheres. Daughter cells within these cultures spontaneously adopt distinct developmental lineages (neurons, oligodendrocytes, and astrocytes) over the course of expansion despite being exposed to the same extracellular milieu. This progression recapitulates many of the stages observed over the course of neurogenesis and gliogenesis in post-natal brain and is often used to study basic NPC biology within a controlled environment. Assessing the full impact of 3D topography and cellular positioning within these cultures on NPC fate is, however, difficult. To localize target proteins and identify NPC lineages by immunocytochemistry, free-floating neurospheres must be plated on a substrate or serially sectioned. This processing is required to ensure equivalent cell permeabilization and antibody access throughout the sphere. As a result, 2D epifluorescent images of cryosections or confocal reconstructions of 3D Z-stacks can only provide spatial information about cell position within discrete physical or digital 3D slices and do not visualize cellular position in the intact sphere. Here, to reiterate the topography of the neurosphere culture and permit spatial analysis of protein expression throughout the entire culture, we present a protocol for isolation, expansion, and serial sectioning of post-natal hippocampal neurospheres suitable for epifluorescent or confocal immunodetection of target proteins. Connexin29 (Cx29) is analyzed as an example. Next, using a hybrid of graphic editing and 3D modelling softwares rigorously applied to maintain biological detail, we describe how to re-assemble the 3D structural positioning of these images and digitally map labelled cells within the complete neurosphere. This methodology enables visualization and analysis of the cellular position of target proteins and cells throughout the entire 3D culture topography and will facilitate a more detailed analysis of the spatial relationships between cells over the course of neurogenesis and gliogenesis in vitro

Localizing Protein in 3D Neural Stem Cell Culture: a Hybrid Visualization Methodology

The importance of 3-dimensional (3D) topography in influencing neural stem and progenitor cell (NPC) phenotype is widely acknowledged yet challenging to study. When dissociated from embryonic or post-natal brain, single NPCs will proliferate in suspension to form neurospheres. Daughter cells within these cultures spontaneously adopt distinct developmental lineages (neurons, oligodendrocytes, and astrocytes) over the course of expansion despite being exposed to the same extracellular milieu. This progression recapitulates many of the stages observed over the course of neurogenesis and gliogenesis in post-natal brain and is often used to study basic NPC biology within a controlled environment. Assessing the full impact of 3D topography and cellular positioning within these cultures on NPC fate is, however, difficult. To localize target proteins and identify NPC lineages by immunocytochemistry, free-floating neurospheres must be plated on a substrate or serially sectioned. This processing is required to ensure equivalent cell permeabilization and antibody access throughout the sphere. As a result, 2D epifluorescent images of cryosections or confocal reconstructions of 3D Z-stacks can only provide spatial information about cell position within discrete physical or digital 3D slices and do not visualize cellular position in the intact sphere. Here, to reiterate the topography of the neurosphere culture and permit spatial analysis of protein expression throughout the entire culture, we present a protocol for isolation, expansion, and serial sectioning of post-natal hippocampal neurospheres suitable for epifluorescent or confocal immunodetection of target proteins. Connexin29 (Cx29) is analyzed as an example. Next, using a hybrid of graphic editing and 3D modelling softwares rigorously applied to maintain biological detail, we describe how to re-assemble the 3D structural positioning of these images and digitally map labelled cells within the complete neurosphere. This methodology enables visualization and analysis of the cellular position of target proteins and cells throughout the entire 3D culture topography and will facilitate a more detailed analysis of the spatial relationships between cells over the course of neurogenesis and gliogenesis in vitro

Interactive Sketching of Mannequin Poses

It can be easy and even fun to sketch humans in different poses. In contrast, creating those same poses on a 3D graphics 'mannequin' is comparatively tedious. Yet 3D body poses are necessary for various downstream applications. We seek to preserve the convenience of 2D sketching while giving users of different skill levels the flexibility to accurately and more quickly pose/refine a 3D mannequin. At the core of the interactive system, we propose a machine-learning model for inferring the 3D pose of a CG mannequin from sketches of humans drawn in a cylinder-person style. Training such a model is challenging because of artist variability, a lack of sketch training data with corresponding ground truth 3D poses, and the high dimensionality of human pose-space. Our unique approach to synthesizing vector graphics training data underpins our integrated ML-and-kinematics system. We validate the system by tightly coupling it with a user interface, and by performing a user study, in addition to quantitative comparisons

Winter tears: a study in computer animation

This project is a study into the art and science of Animation. Specifically, this project focuses on the development of story and character through the use of Computer Animation. From beginning to end, this animation comprises work done completely by the author. The main goal of the project was to understand the development process of an animated short through concentration on Story Development, Character Creation, and Character Animation. In totality, the completed work comprises 10 months of individual labor that began in July 2001 and ended in April 2002. These 10 months of work have resulted in the creation of a 5 minute animated short entitled Winter Tears. The spirit of the work was devoted towards expanding, testing, and solidifying the skill of the author. What has followed this long process is the best work that the author has produced to date. The process of the project was a constant struggle of both work and discovery. In addition to the primary goals, secondary goals were included. The first of these goals was the learning of an industry standard computer animation package called AliasWaveFrontMaya and the second the creation of an animation piece to be used in a portfolio for job applications. What the author hopes will be seen is a true love of animation and a profound respect for the amount of work and detail required for any animated piece in any discipline

Perancangan vfx air dan lumpur dalam film animasi 3d yang berjudul bandhawa

Dalam Film, efek visal merupakan salah satu unsur untuk membangun suasana dalam cerita. Selain menciptakan kesan natural, efek visual juga membuat visual yang lebih dinamis dan tidak kaku. Dalam laporan tugas akhir berjudul “Perancangan VFX Air dan Lumpur dalam Film Animasi 3D yang Berjudul ‘Bandhawa’” akan membahas mengenai percikan lumpur dan air serta lumpur yang menempel pada tokoh. Pembuatan riset ini untuk menjadi pedoman untuk penciptaan pergerakan efek visual. Penulis melakukan pengamatan ke sawah terasering dan beberapa video referensi serta melakukan eksperimen untuk menciptakan visual yang ingin dicapai. Penulis berharap agar laporan tugas akhir ini dapat bermanfaat untuk para 3D Digital VFX artist untuk mewujudkan VFX pada film animasi