The structure of Factin
Like the monomers themselves, the F-actin polymer Figure 15.02 is a polar structure with a barbed and a pointed end terms coined from an early observation of how filaments appeared in electron micrographs when bound to another protein, myosin. Under physiological conditions, filaments grow more rapidly at their barbed than at their pointed ends, a feature that led to the terms plus and minus end which are used interchangeably with barbed and pointed, respectively. The F-actin filament can be...
The selfAssembly expression
Save this file in your Maya Scripts directory under the following name selfAssembly.txt Unlike reset, this expression must run once every frame greater than frame 1. Again, this condition can be tested with an if statement. This is a runtime animation expression that updates the actin assembly simulation. Diffusion, collision avoidance, and reactions are parcelled off as procedures that are called when needed from Reminder variables that have been described previously will not be given a...
Setting attributes with the type flag
Unlike single-value, numerical attributes like translateX, visibility, and so on some attributes must be set using the type flag and an appropriate argument. Two common examples include compound transform and string attributes etAttr myGlobe.translate -type doub1e3 5 10 15 etAttr someObject.customAttribute -type fstring someValue String attributes are rare in Maya and usually take the form of a custom attribute in which you want to store textual information. Unlike numerical attributes like...
Animation using joints
Underlying the movements of animated characters the articulated CG actors you see in films and on television are what animators refer to as character rigs. A rig is a set of deformers and other tools that an animator uses to control everything from A skeleton rig applied to a polygonal cylinder. The surface CVs are under the influence of the joints. As the joints rotate, the surface deforms. Bones relate the joints to one another throughout the Scene Hierarchy and constrain the locations of...
Bump and displacement maps
Bump maps and displacement maps Figure 08.12 use grayscale procedural or bitmap textures to create surface relief at render time. This allows you to make alterations to surface topography that would be difficult if not impossible to model via conventional NURBS or polygon tools. Bump maps create the illusion of relief by altering the directions of surface normals, and therefore changing the way the light interacts with a surface. In contrast, a displacement map actually changes the topography...
Maya Cameras
Like a real camera, a Maya camera defines the visible region of a scene what will be captured in a rendering and any image distortion due to the type of simulated lens used. You are by now no doubt familiar with maneuvering the default perspective camera, persp, to view a scene. Persp and the other default cameras the orthographic front, top, and side have all the same attributes as a camera you would create, and therefore can be used to render. It is advisable, however, to use the default...
Advanced rendering techniques with the mental ray for Maya renderer
The developers of mental ray for Maya have incorporated numerous advances in 3D rendering that mimic real-world lighting and material situations. While these can improve the photorealism of a rendering, they can add substantially to your render times. Figure 11.04 shows examples of several of these rendering features. Examples of advance rendering techniques using the mental ray for Maya renderer. The molecule pictured here is hemoglobin. Examples of advance rendering techniques using the...
The Maya Hardware renderer
The Maya Hardware renderer uses your computer's video graphics card to render images faster than the software renderer. Due to the way it processes images, the hardware renderer does not support raytracing or Paint Effects. Nonetheless it works with a wide variety of Maya shaders and lighting effects, including transparency and shadows. Furthermore, a person skilled in compositing can do a lot to create sophisticated visual effects using only hardware-rendered animation. Because compositing...
Ramps
A ramp is a color or grayscale gradient. The gradient has one or more component s , each defined by a position value between zero and one, and a color or grayscale value Figure 08.11 . A ramp can be either a U or a V ramp, referring to its direction when applied to a surface we take a closer look at the UV coordinate system below . Ramps and their components can be connected to other nodes to drive attributes using color. Conversely, other nodes can be used to drive ramp colors. Maya has a...
References Ixb
1. Wolf K, Mazo I, Leung H, Engelke K, von Andrian UH, Deryugina EI, Strongin AY, Brocker E-B, Friedl P Compensation mechanism in tumor cell migration Mesenchymal-amoeboid transition after blocking of pericellular proteolysis. Journal of Cell Biology 160 267-277, 2003. 2. Pollard T Regulation of actin filament assembly by arp2 3 complex and formins' Annual Review of Biophysics and Biomolecular Structure 36 451-477, 2007. 3. Paluch E, Sykesa C, Prosta J, Bornens M Dynamic modes of the cortical...
State change probabilities
In their study, N amp L recorded the displacement of cell center points at regular 20 second time intervals and then determined the probabilities associated with moving from any of the 5 states to any other state. A moving cell would either continue on its present course, that is, remain in its current state, or change its course, that is, change to a new state. These probabilities are presented in Table 18.01, in a form we call the state change probability matrix. The data show a distinct...
Set up the next crawl cycle
In this section of code you will calculate the values necessary to move the cell, including the random motility direction, the effect of the chemoattractant, and the step a' a - y X c c chemoattractant strength 0.1 lt c lt 1 Four cases to consider for the angle y a-8 whencalculating alphaPrime, the direction resulting from both random motility and chemotaxis. sizes for each of the three motility stages protrusion, traction, and retraction. In order to execute this code, the following conditions...
Summary Qpr
Rendering is the creation of image files from a Maya scene. It is the final stage in the 3D production workflow and includes a series of creative steps covered in the last four chapters The final step of the rendering workflow involves customizing the Render Settings and then batch rendering your animation. The choice of renderer is usually made early on, before making Render View previews to test shaders, lights, and camera setup. A batch render can be started from within Maya, which allows...
Source the script elements
If you haven't done so already, save your makeSeeds and rule procedure files in your Maya Scripts directory. Make sure the file names match the respective procedures. For instance, the procedure called rule1 should be saved in a file called rule1.mel. You may have tested your procedures by entering them in the Script Editor as you created them. Likewise for expressions in the Expression Editor. If you haven't yet tested your scripts, there's a chance they may contain errors. If this is the...
Methods Encoding the algorithm Qnh
Unlike the previous project, in which the cellCrawl algorithm operated on a prebuilt geometry model, this project requires no initial file setup. Everything to grow the fiber scaffold model in silico is contained in the scripts you're about to build. We recommend composing them as you did the scripts in previous chapters in an external text editor, with each element procedure or expression saved in a separate text file within your Maya Scripts directory on your hard drive. When your code's...
Computer hardware and software
The Maya files and MEL scripts listed in this book and included on the CD-ROM were created and tested on a mid-range consumer-level PC with the following specifications OS Windows XP Professional 2002 Service Pack 2 PC Dell Dimension 8300 Graphics adapter ATI Radeon 9800 XT, 256 MB DDR The book's tutorials and projects have been developed over a number of versions of Maya, both in Windows and Mac OS. They have been tested to work in Maya 8.5 for Windows. Users of older versions of Maya may have...
Organize the scene hierarchy
cpk ends with a for. in loop that organizes the models into the hierarchy described back on page 358 . It collects like elements together under group nodes called chain_ A , chain_B , etc., and then collects these chains under a group node called molecule . In the Maya scene hierarchy, group nodes are parents and group members, their children. In the code that follows, you will use the string array variable, group to hold a lists of node names for groups of like elements within a given chain....
Methods Generating pseudopods
A principle creative element of your project is the way your cell changes shape, extruding and retracting pseudopodia, as it moves. This cycle of deformations and shape dynamics gives your model enhanced realism as a simulation of real cell activity. It also sets the stage for more advanced applications, such as the MEL code that links the mechanical properties of the cell and the locomotion forces to exact predictions of protrusion size and shape. But how to coax such smooth biomorphic...
Find the closest fiber
The following code finds the closest point on all of the fibers to the cell's position. This is the first instance where you'll employ the closestPointOnSurface nodes. A for loop is used to narrow down candidates for closest point. Each time through the loop the distance dist from the cell to the current fiber's closest point stored in cpos is compared to the value of shortestDist . If dist is less than shortestDist, then shortestDist is assigned the value of dist and the loop increments. Each...
Main loop Vgd
A for loop is used to increment through the cell population. MAIN BODY for j 3 j lt ce11Count j Test all but the current cell, if j i separation ce1lPos i - ce1lPos j dist mag separation Are the cells too close to one another if dist lt contactRange cell j is too close to cell i. totalSep separation When the matrix is hidden, cell trajectories show clearly where cells have transferred between fibers. You can apply the technique described in Chapter 13 to generate trajectory paths using Maya...
Subsurface scattering
The absorption and scattering of light beneath an object's surface is a property of many real-world materials, including organic tissues like skin. Maya can simulate this phenomenon with two mental ray for Maya subsurface scattering shading networks a fast, non-physically correct one Figure 11.04b and a slow, physically accurate one. Subsurface scattering is available in Maya 6.0 mental ray 3.3 and later. Subsurface scattering Maya 6.0 or later Help Maya Help Using Maya mental ray mental ray...
The animations look
A cancer animation that depicts the deadly cells as whimsical, anthropomorphic cartoon characters might work well for an audience of young children. However, it might also leave an audience of investment bankers ready to fund a new cancer drug less than impressed. Such qualities of overall visual appearance are often referred to as your film's look, a subject demanding careful attention right at the start of your project. The message or point of a film can be misunderstood, or lost entirely, if...
UV coordinates life on the surface
In addition to the XYZ local and world coordinates, Maya has a 2D coordinate system that it uses to map textures onto surfaces. U and V are analogous to X and Y on a flat surface, except that the U and V axes wrap around and deform with an object's surface. When you assign a texture to a surface through a material channel such as Color it automatically maps to the surface's UVs every location in a 2D texture image has a corresponding UV location. When you create a primitive model, Maya...
The Four panel view
You may have noticed that distance is difficult to gauge when translating the sphere in the perspective view. This is due to the visual distortion applied by this camera. The orthographic views show space without this perspective distortion and make it easier to see where objects really are, relative to one another in Maya's 3D space. We find the Four panel view shown in Figure 05.12 an effective layout for visualizing a scene, including multiple biological molecules or cells moving in complex...
Tutorial Deform the sphere using components
Before leaving your NURBS sphere behind, let's change its shape by transforming its components. Figure 05.14 shows the transformations you'll apply to each type of component. You will do manually what you might normally employ a Maya deformer, such as the Lattice Deformer, to do. However, through moving components by hand, you will get a sense of how a deformer works to change the shape of an object. Furthermore, surface deformations of the kind you're about to make are analogous to the kinds...
rule The random walk
To generate the meandering fiber paths, you'll employ a basic random walk algorithm. It uses Maya's random number generator the rand MEL function to select one of This project uses a rule-based design in order to move the seeds that determine the fiber paths. There are three rules, each parceled in a procedure called rule1 , rule2 , and rule3 , respectively. They are shown schematically in Figure 17.06. Each procedure is called from the moveSeeds expression at every frame during playback and...
Change the Move Tool Settings
Many of the tools in Maya, including the Move, Rotate, and Scale Tools, have settings that you can change. As an example, you'll change a Move Tool setting and observe its effect. To open the Move Tool settings palette 1. Double-click the Move Tool icon in the toolbox. or With the Move Tool active i.e. selected , choose Display UI Elements Tool Settings. 2. In the Move Tool Settings window, select Object. With this setting, the Move Tool will translate objects relative to their local object...
Mayas search path
When you installed Maya on your computer, a default Scripts directory was created for your user account. The path to this directory is Maya's search path. Every time you start Maya, the program queries the contents file names of its search path. When you use the source command, Maya scans its search path contents for the file. If the file exists on the search path, Maya sources it loads it into memory . If you add files to the Scripts directory when Maya is running, you will have to refresh the...
The computed organism
The 20th century's revolutionary decades of computer and software engineering were also years of astonishing progress in the sciences of biochemistry and cell biology. Some of the exciting details we' ll explore in the chapters ahead. Here we can briefly consider the implications of the basic fact, now universally accepted in the scientific community, that all living things all organisms are composed of chemicals, that is, molecules whose complex interactions set in motion the processes of...
MEL command mode Create edit and query
In the examples above, you used the polySphere command in its default create mode. Here you' ll explore the other two MEL command modes edit mode query. Edit mode makes changes to the attributes of an existing item. For example, change the radius of mySphere as follows 1. From the Script Editor menu bar, choose Edit ClearAll. 2. Type the following code in the input panel and press Enter polySphere -edit -radius 5 mySphere The -edit flag specifies the command mode and requires no arguments. The...
Orthographic Views
Orthographic turns a perspective camera into an orthographic gaze. Orthographic Width is related directly to the distance of the camera from its origin plane XY, XZ, or YZ . When you dolly an orthographic camera, you don't actually move it in the Z-direction, but rather increase or decrease its Width attribute. The remaining camera attributes are common to all shape nodes and won't be covered here. Maya Help Using Maya Rendering and Render Setup Rendering Rendering menus Panel menus View View...
Animation
Animation, we've seen, is the art of taking otherwise static images and objects and imparting a sense of motion, and life, to them. The property being animated called an attribute in Maya could be position, scale, shape, or color among others. For example, consider depicting a deflating balloon with a sequence of still images see Figure 03.12 . As air rushes out, we make the balloon careen in all directions and gradually shrink, so it winds up looking flatter, less bright and more opaque frame...
Nucleus and nCloth
With Maya 8 Autodesk introduced a new dynamics engine called Nucleus. As of Maya release 8.5 one module uses the engine nCloth. a system of dynamically linked particles available only in Maya Unlimited. Although designed to simulate the natural flow of clothing for computer-generated imagery CGI characters, nCloth can be used on all NURBS and polygon objects in Maya for the same kinds of projects you' d use soft bodies for, including the simulation of a wide variety of deformable materials. The...
Create the grid texture
When creating a shading network, you have the option of building it in the Hypershade, before assigning it to an object, or constructing it on the fly adding to it after it's been assigned. Here you' ll do the latter, connecting a procedural texture to the Color channel of lambert_plane, which is already connected to pPlanel. The texture is a grid pattern and one of the ready-made Maya procedural textures. 1. In the Hypershade, choose Create 2D Textures Grid or Click on the grid texture swatch...
cRule The random walk
This procedure returns a vector in UV space the result of the 5-state Markov process and calculates the persistence time until the next state change. The state change probabilities are defined by the sProb matrix in the expression called reset-Cells. This procedure takes three arguments the current cell index, i the float vsca1e, which is used to scale the magnitude of the random walk step size and the name of the surface, surfaceName, to which cell i is currently attached. This procedure...
Maya Paint Effects
Paint Effects is an FX and texturing painting module that allows you to draw strokes colored line and patterns in either 2D or 3D. You can use it to apply custom patterns and particle effects to geometry and curves in a 3D scene. Invented by Autodesk developer and computer graphics guru Duncan Brinsmead, Paint Effects is used widely in FX workflows for film and television to create organic elements such as trees, grass, and flowers, which can be animated to simulate growth. Biomedical Animator...
rule Bounding
Like ru1e1 and ru1e2 , this procedure takes the current seed, Si, as its argument and returns a vector to the moveSeeds expression. his procedure constrains seeds to the scaffold bounding box. The bounding box depth and width dimensions are stored in the cubeSize DECLARE THE VARIABLES. global vector seedPos global float cubeSize global string seedNames pbound The return vector for this procedure. outside The distance from the seed surface to a corresponding side of the bounding box. boundSca1e...
Fiber size packing density and shape
Table 17.02 gives you an idea of how fiber sizes are distributed throughout the dermis. Let's call this the fiber size distribution. A statistical histogram of the size distribution is shown in Figure 17.04 ' If the long axes of fibers are aligned on average with a major axis the Z-axis in this model their meandering paths will provide the overall multidirectional orientation that characterizes dermal collagen you can estimate the appropriate number of fibers for a given volume from the number...
Tissues and organs
Some cells are lone actors, like the patrolling lymphocytes of the immune system, which migrate throughout our bodies looking for foreign invaders. Most cells, however, aggregate by the thousands or millions into tissues, whose composition and hierarchy serve some functional goal. Still frame from an animation created in Maya demonstrating concepts of cytoskeleton dynamics as put forth by Harvard cell biologist Don Ingber. Scale bar m. Still frame from an animation created in Maya demonstrating...
Operator overloading
I n a programming language with operator overloading, certain operator symbols can have more than one meaning. A familiar example is the use of the symbol . It would not be unusual to write code today in which the plus sign could be invoked legitimately to add together pairs of data of diverse kinds pairs of integers, or pairs of decimal numbers, or two strings or vectors or matrices all with one little plus sign. To get a feel for the old days, just try this in a vintage language of the 1950s...
Increment the crawl cycle
The following section of code is executed at every frame for which the crawl cycle counter, Si, is greater then zero. Its function is to move first podl through each of its steps, then cellcenter, followed by pod2. The time remaining in each stage is given by i minus the time for the remaining stages. When the cell has finished moving when the retraction stage is finished and pod2 has returned to its default position relative to cellcenter the cell remains in state zero until i has counted down...
Random number generation in Maya
By now you've seen Maya's rand function used several times. Here we'll elaborate on random number generation and the relevant MEL functions. Essential to modeling events and processes that depend on probability are methods that simulate uncertainly within the otherwise deterministic working of the computer 's digital circuitry. Although various ways of doing this have found favor over the years such as storing tables of numbers drawn from unpredictable random natural events like flips of a coin...
Physical principles biophysics
Bourg DM PhysicsforGameDevelopers. O'Reilly, Sebastopol, CA, 2002. Dill KA, Bromberg S Molecular Driving Forces Statistical Thermodynamics in Chemistry and Biology. Garland , New York , 2003 . Howard J Mechanics ofMotorProteins and the Cytoskeleton. Sinauer, Sunderland, 2001. Jackson MB Molecular and Cellular Biophysics. Cambridge University Press, New York, 2006. Kennedy J, Eberhart RC, Shi Y Swarm Intelligence. Morgan Kaufmann, San Francisco, CA , 2001 . Lauffenburger DA, Linderman J J...
Dissociation reaction rate
In order to produce steady-state treadmilling behavior in the model, your dissociation rate must balance the plus end association rate the net subunit count should remain more or less constant throughout the simulation. Given the brisk pace of the nucleotide reactions estimated above we can expect that all subunits reaching the By building the rate constants into your model as variables you'll be able to alter them as you like to test their relative effects on treadmilling behavior. Like the...
Procedural versus keyframe animation
Generally speaking, Procedural animation refers to the use of computer procedures, or algorithms, to change attributes over time. The procedure can be as complicated as an algorithm for DNA replication or as simple as an instruction to make an attribute equal to a constant value the point is that it uses an instruction or set of instructions, not a recorded value, to determine the attribute value. The following example illustrates the difference between keyframe and procedural animation. Figure...
The cellCrawl expression
As you saw back in Chapter 12, an expression can be made in one of two ways. The first uses the MEL command expression and a single line of code. If the code is sufficiently long, you can break it up into multiple lines as long as you use the escape line break notation, n, at the end of each line. In longer expressions, escaping line breaks becomes tedious and can lead to errors when you add new lines to the code and forget to escape them. For this project we recommend the second way to make an...
The reset expression
As usual, we recommend building your MEL script in a text editor other than Maya's Script Editor and saving it often as you follow along with the project steps below. Save the file in your Maya Scripts directory under the following name Since this expression is to run only when Maya returns to frame 1, begin with a conditional if statement to this effect. To save space, we've foregone the usual file header information such as authors, creation date, and so on. This animation expression restores...
The Maya Vector renderer
A 2D picture on a computer screen is either a raster graphics image or a vector graphics image. A raster graphics image is a rectangular grid of pixels, each with its own color value. As you enlarge a raster image, the pixels become visible. Vector graphics images, on the other hand, are drawn using mathematical curves and polygons whose The Maya Vector renderer creates vector images that are defined by colored strokes and fills. This image, from a simulation of actin protein filament or...
Shape the cell with a Lattice Deformer
Lattice Deformers are powerful tools for shaping polygonal and NURBS surfaces and clusters of particles in Maya. Here you'll use a Lattice Deformer to flatten the cell bottom and spread out its edges. lattice -divisions 2 5 2 -objectCentered true -Idivisions 2 2 2 Figure 16.12 shows the lattice and cell together and the subsequent steps you' l l take, manipulating ' attice points to deform the cell. A lattice is like a hexahedron and its points like CVs as you translate, scale, or rotate them,...
Maya A brief history
Maya was released commercially in 1998 by the CG software firm Alias Wavefront A W for short , which was headquartered in Toronto, Canada. As the top-tier animation and visual effects VFX package it was by no means the work of a single software company in a single development effort. Maya incorporated the product lines of Toronto's Alias Research Alias for short , Wavefront Technologies Wavefront for short of Santa Barbara, and Thompson Digital Images TDI of Paris, into a single package....