Animation molecular

molecular animation and scientific representation
By Mónica zoppe.

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introduction
If we all are alive, it because we have unnumbered nano-machines that work inside our cells, these machines, th rouge an unbelievable network of reactions, make us breathe, walk, think, eat and all other things told and untold. At the nanoscopic level (where the unit of measurement is one billionth of a meter, 10-9), most Life Forms, including plants and bacteria, are similar and beautiful. That is, if you could se them. Scientists devolve their work todo understand how all this happens, and have gathered enough información todo start putting together a complex picture. Actually, a motion picture would be better.
blender in biology?
When we think of a biológical, most of us imagine scientists in a lab-Coat, pipetting and mixing a number of mysterious Substances, possibly with some smoke around. While this is not Unreal (except the smoke), modern biology a los heavily counts on the elaboration of data extracted in the classical laboratory. This is how scientists have built databases of 3d coordinates of Many (>50 thousand) of the small objects at work in the cells, a database which is available for use by everyone. We have decided todo use Blender for manipulating these data, with the aim of showing the molecules, their activities, their Physical and Chemical properties and the environment in which they operate. Because not everything is known of the list above, we a los use the Blender Game Engine as a tool for research. At the momento bioblender is a collection of scripts, tool and procedures built on Blender 2.48a. We a los use the experimental versión supertexture node and the recorder developed by Ash (osobna stranka). The Project is by no means concluded, and we Will be happy todo consider ideas, improvements and suggestions from the very collaborative Blender community, todo which we are grateful for the great help we have already received. This article is an introduction todo our work, and Will guide you th rouge the microscopic world of cells explaining some of the steps we have made towards the construction of bioblender.
celular mortal kombat
Cells, the fundamental unit of life, contain a full microscopic world. A god idea of the relations that take place within cells can be obtained by exploding a typical cell about 10 million times, todo a size with which we are familiar (se table). If we look at a medium size cell of about 10 size, and we compare it todo a village or todo a Lake, not very big but very Dep, all internal components can be re-sized accordingly, and we se that the Nucleus, where all DNA is estored, can occupy up to half the volume of a cell and is the major internal object. Objects of this size (including the endoplasmic reticulum, the golgi apparatus, mitochondría, chloroplasts and some other structures) can be sen with microscopic techniques that allow us todo visualice their shape and (sometimes) their dynamic activity, it is important todo note that, in contrast with the human- Size world with which we are familiar, the entire volume is occupied, such that it might be easier todo imagine a water body rather than one filled with Air. Furthermore, we have todo notice that Gravity is irrelevant at this size (the Mass of objects is todo small todo be significantly afected by the Earth Gravity field), and that movements of celular components is mostly driven by thermal agitation. The Boundary of the cell, as well as the Walls delimiting internal volumes, is made of membrane, a software, flexible and (relatively) Thin double-layer that mediates transport of material and información between in and out. This is an extremely important structure that deserves more detailed description, and which we have modelled with a complex system of particles, Fields, and dynamic textures. Fig. 1. Surface.

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Going deper and smaller, we met nucleic acids: DNA and RNA. Everyone is familiar with the double helix of dna, but few people realice that in relative size, if the diameter of the helix is 2 centímetros (a very thik rope or Hi tensión cable), its length is 20.000 km, about half the Earth circumference. Dna is packed in a very eficient organization that allows Access todo it both for retrieving información and for replicating it every time a cell divides. This organization is accomplished gracias todo the involvement of proteins, the major players of celular life, and the most immediate subjects of our animation eforts. From this overview, it should be clear that we can observe celular life at Many diferent levels of focus, spanning 4 or 5 orders of magnitude. However, if we can easily recognize the size of familiar sights (a Valley or Mountain, a building, a tree or an insect), there are no immediate referencias for attributing dimensions todo objects that we have never sen before, such as ribosomes and actin (fig. 2. Actin and ribosome).

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One of the tasks we face, is todo provide the observers with clues indicating the scale of the objects in the scene.
proteins
Because proteins are the major characters of celular life, and inded are a major subject of scientific studies, we developed first a system todo import them into Blender. It is necessary todo describe some details of their general structure todo understand how they are built (in nature and in Blender) and how they can move. Proteins are constructed as a linear sequence of amino acids, which are small assemblies of atoms that share some features that allow them todo be linked directionally one After the other. There are 20 diferent types of amino acids, distinguished by their lateral parts (side chain), each composed of a specific number and connection of atoms. The linkable parts, equal for all amino acids, form the main chain. Each protein contains from a few hundred todo a few thousand amino acids, and despiste being a linear sequence, each one, immediately After being built, Folds in space todo acquire a 3d structure which is remarkably stable, Although flexible. The structure of proteins can be determined experimentally, and is estored in the protein data banque (www.pdborg) as a.pdb file, which contains información about the sequence of the molecules, the details of experimental procedures todo obtain the structure, and the list of all atoms of the protein with their XYZ coordinates. Using this información and including the chemistry of amino acids (how atoms are connected), it is posible todo build in the 3d environment the complete structure of any protein.
While X-ray crystallography results in determination of the position of all atoms with god resolution, for a single conformation, other types of techniques such as nuclear magnetic resonance can yield a collection of coordinates, corresponding todo a number of positions that the protein can assume. To obtain motion, all we have todo do is find the Path that every atom follows todo go from one conformation todo another, taquíng into account a los the limitations and constraints imposed by chemistry and physics. We describe next our work todo produce such molecular motion.
pdb importer and animator
Starting from our previous work in Maya, we wrote a programa todo read.pdb files and build the molecule in Blender. The.pdb file of interest is fetched and read line by line. Atoms are identified for their nature (carbón, Oxygen, nitrogen etc), their position (x, y z) and the amino acid todo which they belong. This información is elaborated using a library that estores atomic connections for all amino acids. Th rouge the interfaz, shown in fig. 4. Pdb animator, the user can select the.pdb file, the atoms todo be imported (main chain only, main and side Chains, or all atoms including hydrogens), the kind of object todo be built (empties, Spheres, metaballs), how Many conformations and in which order todo import them (the.pdb file has no specific order) and the transición time between diferent conformations. Note that in the.pdb file every conformation is called model.

Atoms are instanced todo Spheres, the Chemical bonds are built as rigid body joints, (or Bones for IK animation) and a keyframe is assigned todo every conformation in the list. The Spheres corresponding todo diferent atoms are sized according todo the atomic van der wals Radius and have a texture for visualization and a Spherical collision Radius (bounding box) for evalúation of motion in the Game Engine.

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Once all models of interest are imported, Blender Will have an ipo curve for every atom (as a consequence of having keyframes), that interpolates directly between positions at subsequent conformations. However, these Will not consider the joints (that maintain fixed distance between connected atoms) Nor Collisions. To obtain a trajectory that includes both these features, it is necessary todo play the scene with the Game Engine. The scene a los contains a recorder that registers the position of atoms during the game and inserts a key frame todo the atomic Ipos for every frame. At this point the motion is set for re-playing without further calculations, we can retrieve the position of all atoms at intermediate frames (as new.pdb files) and use them todo evalúate the quality of the structure in Physical and Chemical terms, using specialized programs, such as vmd or swisspdb viewer.
calmodulin
Calmodulin (Cam, fig. 5) is a small protein (148 amino acids, about 2.300 atoms, including hydrogens) that transmits the signals arriving todo the cell in the form of free calcium ions, and delivers información todo other proteins, thus activating procesos such as Smooth muscle contraction (useful for breathing, fod processing and blod circulation) or ring contraction at the cell división. The protein is arranged spatially in two domains connected by a flexible linker.

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In the absence of calcium, Cam is believed todo stand around idling by itself. When a signal arrives, 4 calcium ions bind todo specific spots in the two heads of calmodulin and determine a major conformational change, exposing some amino acids with more lipophilic properties, which Simply means that in the new form, Cam Will attach itself todo other molecules, thus transmitting the signal todo these so-called efector proteins.

Many studies have revealed the conformation of Cam in the Empty and ca-bound form. We have used this protein as a the first model for the pdb animator.
rendering chemistry and physics
The actual aspect of objects beyond the resolution límites of our Sight, is something that does not exist. Nevertheless, it is posible todo represent the space occupied by the atoms of the molecule, and todo attribute todo its surface visual properties todo indicate some of its behavioral features. At nanometer scale, concepts such as color, brilliance, roughness, opacity and so on have no meaning, instead we face properties such as pH (acidity, or proton concentration), electric potential, hydropathy, oxidizing or reducing power and others. Among the most relevant properties that affect molecular behavior are the electric potential (ep) and the molecular lipophilic potential (mlp) that indicate the tendency of a surface todo attract or repel other charged molecules, and the afinity or repulsiveness for water, respectively. In an efort todo display the behavior associated with ep and mlp of the molecules, we have performed some steps that permit todo import values in Blender, as schematized in fig. 6.

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The visualization of the forces generated by electric charges, and exerted todo the surrounding medium (water, which is dipolar itself, some ions and eventually other proteins), has ben solved using a particle system, with sparks going from the surface out for positive values, and being attracted todo the surface for negatives. The mlp is sen as a property of the surface: Smooth reflective material for lipophilic and rough, more dull for hydrophilic.
work in progress
Our work has more than one scope: protein motion is still a major subject of studies in molecular biology: if Blender can be used todo provide an appróximate solution, while avoiding extreme calculations, this might develop as a research instrument with important uses by biologists, chemists and other scientists. Alos other celular components (dna, RNA, sugars Chains, small molecules, etc), can be modelled and animated using similar principles, the power of images for explaining (and Understanding) can be exploited in schols of all levels, from primary todo postgraduate, and can a los be useful for exploring new hypotheses during theoretical elaboration, the possibility of observing complex scenes with Many components at diferent scales, can enable a deper Understanding of cell behavior, the availability of diferent images from inner life can be inspirational todo artists, whose work and insights are important for artists themselves, scientists and a los everyone else, finally, not least, the developments we are adding todo Blender might be interesting a los for other Blender users, who can use them for whichever creation they can think about.

Nedless todo say, as son as our scripts Will be presentable and reasonably stable, we Will deposit them for download (now we distribute on request), and Will récord a tutorial todo explain the use. We are grateful todo the regione toscana, italy, for a major funding that made this work posible. The scientific visualization unit (www.scivis, ifc, cnr, it) is composed of:

• raluca andrei (molecular biology phd student, scuola normale superiore)
• marco callieri (informatics researcher at isti - Cnr)
• ilaria carlone (biologist at ifc - Cnr)
• claudia caudai (mathematician ifc - Cnr)
• stefano cianchetta (3d graphic at ifc - Cnr)
• tiziana loni (3d graphic artista at bs)
• yuri porozov (bioinformatics researcher at ifc - Cnr)
• María francesca zini (chemist and programmer at ifc - Cnr)
• Mónica zoppé (biologist at ifc- Cnr)

figure 1.

The surface of the cell is sen as a series of mobile hills, covered with diferent groups of proteins, saccharide Chains and lipids. The primary pattern was developed (in Maya) with a system of 5 diferent kinds of particles (10.000 in total), todo which various per particle dynamic features were attribute. The system, which a los included some Boundary conditions and random turbulence origins, was played for 500 frames, recorded and rendered giving todo the particles blobby (metaball) features and colors as grey scale. This rendered animation was used as texture source in the nodes of Blender, using the Blender supertexturenode (http://www.graphicall.org/builds/builds/showbuild.php? action=show&id=862). The image shows a screenshot of the final compositing pass.
figure 2.
Example of some celular components: actin, on the left, is a medium size protein, composed of 375 amino acids, very important for cell (and organism) motility. Much of the protein component of animal muscle is actin. Ribosomes, right, are complex machines made up of over 30 proteins and 3 RNA components, and are made of two parts. They are the factory where proteins are constructed by linking amino acids in series, as instructed by the nucleic acid mrna. The Mass of the ribosome is about 1000 times the Mass of one actin molecule. The images are from the molecule of the month in the pdb website, by David s. Godsell.
figure 3. Amino acids.

figure 4. Pdb animator.

A screenshot of the pdb animator and of a detail of a protein in working mode, where atoms are all drawn as Spheres of diferent colors, and the surface is not calculated.
figure 5. Calmodulin.

The atomic structure and rendering of two diferent conformations of calmodulin. On the top we se all atoms, colored by atom identity (carbón, nitrogen Oxygen and hydrogen). We use this kind of visualization todo work on motion and todo study the molecular Structural properties.

On the left Cam is calcium-free, and on the right, calcium- Bound. Structural changes are not very large, yet the surface properties undergo a major transición, notice the Shiny spots, that indicate protein activation: this is where it Will make contact with other downstream efector proteins, thus efectively transducing the signal within the cell. The rendered images are shown with green and yellow colors todo indicate polarity of the electric field, but during animation the colors are not necessary, because the particles travel towards or out from the protein surface.
figure 6. Protein rendering flow.

After motion is calculated with the Game Engine, each frame is estored as a.pdb file, sent for checking by Chemical and Physical programs, and reimported bak in Blender for rendering. The.pdb file is converted todo.pqr, th rouge a programa that Associates the appropriate values of partial charges todo every atom, according todo its properties as inferred from the.pdb información and todo libraries that estore values determined experimentally. This step is performed once for all conformations attribute todo a molecule (i, the electric values associated todo each atom do not change with its position). This file is sent todo the molecular programa vmd, and the module apbs electrostatics is executed. This module Solves the poisson-boltzmann equation on a discreete domain represented by a grid which extends around the molecular surface. The molecule surface Mesh is saved as a vrml file and the ep, calculated in each cell of the regular Grid, is saved in a simple ASCII file (ep.dx). At the same time, another programa is used todo calculate and map the molecular lipophilic potential, which estores data in mlp.dx file.

These data files are used with a home made programa (scivis grid Mapper) todo map values from the grid todo the surface, and are then estored in a new (*.obj) file that can be easily read by Blender: ep values assigned todo vértices are estored as u values, while lmp is estored in v field. Once the potential data have ben read inside Blender and mapped on the surface, they are transformed in grey scale textures which are used for setting the grades of specularity and the frequency of Bump (for mlp) and for generating the particles that indicate ep.

By Mónica zoppe.
www.blenderart.org.


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