This Maya animation provides a visual simulation of fibroblasts moving through extracellular matrix - the 3D matrix and behavior of the cell population through the matrix are based on mathematical models implemented in MEL.

>> View the animation at U. Toronto

This Siggraph award-winning animation depicts the molecular players and signaling processes underlying leukocyte migration, adhesion and extravasation. Structural components of the cytoskeleton and the extracellular matrix, in particular, are highlighted.

>> View the animation at Harvard BioVisions

An interpretative visualization of T-cell mobility from blood to lymph through the thymus-dependent zone of the lymph node using evidence-based research.

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This animation shows the process by which tumors recruit new blood vessels thereby facilitating the metastatic behavior of stray cells that enter the circulation.

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A solid tumor secretes angiogenic molecules that induce new blood vessels to form in the vicinity of the mass. These new vessels eventually grow into the tumor providing it with the necessary oxygen and nutrients for continued growth.

>> View the animation at SabPro

This stunning Maya animation covers the death receptor signaling pathway that originates with binding of the Fas/TNF family of ligands, triggering of the caspase cascade, cytochrome C release from the mitochondria, apoptosome activation, and ensuing signal amplification.

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A step-by-step depiction of a diversity-oriented organic synthesis reaction on beads (created for Professor Stuart Schreiber at Harvard/Broad). At the same time as the camera follows the reaction in 3D showing bond rearrangements, the viewer can simultaneously follow the reaction in standard stick notation at the bottom of the screen.

>> View the animation at Bloopatone

Spire mechanism - The protein Spire contains 4 WH2 domains which are each able to bind an actin monomer. A conformational change in linker 3 is thought to catalyze the formation of an actin nucleus.

>> View the animation at OneMicron

Spire & formin - The formin cappucino binds to Spire's KIND domain. While bound to Spire, cappucino is unable to act as an actin nucleator, but does not inhibit Spire's nucleation activity.

>> View the animation at OneMicron

This movie presents a simulation of the behavior of selected cytoskeletal components as external forces are applied to the model (representing the forces of cell migration).

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ParM polymerization dynamics - ParM polymerizes bidirectionally at the same rate at either end. ATP hydrolysis (shown as color change to red) occurs spontaneously. When a filament end loses its ATP 'cap,' the filament undergoes rapid depolymerization from that end in a process termed dynamic instability.

>> View the animation at OneMicron

Kinesin walking along a microtubule protofilament demonstrating how energy exchanges combine with binding events to create forward motion.

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This Maya animation depicts the dynamic self-assembly and dissassembly processes of microtubules. The animation incoporates atomic resolution structural information for tubulin (as it undergoes a GTP vs GDP-induced conformational change), as well as cryoEM data for 'protofilament peels' and 'helical ribbons' from the Nogales lab.

>> View the animation at HHMI

This animation describes the translation of chemical bond energy of ATP into the sliding motion of thick/thin filaments in our muscle fibers.

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DNA segregation by ParM - ParM binds to DNA-binding proteins, called ParR (orange proteins) around which segments of genomic DNA are coiled. Sister plasmid segregation is achieved through bidirectional insertional polymerization of the ParM filaments.

>> View the animation at OneMicron

Mechanotransduction through the cytoskeleton: a hypothetical model of mechano-biochemical conversion through protein-protein interaction. This animation depicts the tensegrity model of the cell's cytoskeleton.

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Covers the early stages of embyronic development (including fertilization, cleavage, blastocyst formation, implantation, cell migration in the inner cell mass and formation of the embryo's germ layers and neural tube formation).

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This animation briefly summarizes the early stages of development and highlights/maps the organ systems in the adult that result from the 3 embryonic germ layers.

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This movie was created to commemorate the 50th anniversary of a revolutionary theory called ‘Clonal Selection’ by Nobel Laureate, Sir Frank Macfarlane Burnet.  The animation shows how clonal selection works during a bacterial infection of the throat.

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This animation shows the different levels of chromatin packing - starting with wrapping of DNA around histone octamers and nucleosome assembly, all the way to chromosome condensation during mitosis.

>> View the animation at WEHI

A series of short animations highlighting the structureand flexibility of the DNA double-helix.

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This animation depicts the proces of DNA recombination. The DNA plasmid is first digested with the restriction endonuclease enzyme ecoRI. Then, a piece of DNA encoding a gene is inserted into the plasmid by DNA ligase.

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Dimerization of FKBP12 & FRAP is shown upon binding of the small molecule rapamycin.

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This animation illustrates a theoretical means by which fatty acids may have been synthesized along the sides of mineral walls of hydrothermal vents or (in this case) a geyser

>> View the animation at OneMicron

Fatty acids formed in the geyser accumulate in droplets. Evaporation of the droplets causes the fatty acids to aggregate into small wind-blown particulates. This animation illustrates a theorietical means by which fatty acids may have been distributed on the early Earth

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De novo vesicle formation from fatty acid micelles - Protons are represented by the small glowing spheres. Upon protonation, the micelle structure becomes more fluid and may allow for larger numbers of micelles to join together. Vesicle formation occurs by chance after the fatty acid sheet has reached a threshold surface area.

>> View the animation at OneMicron

Although the vesicle structure itself as a whole is extremely stable, individual fatty acids within vesicles are extremely dynamic and are constantly joining and leaving the vesicle membrane.  Protonated fatty acids (shown by the glowing hydrogen in the head group and the lighter colored tail) readily flip between the inner and outer leaflets of the membrane.

>> View the animation at OneMicron

Polar molecules such as AMP may enter fatty acid vesicles through interactions between the fatty acid head groups and the small molecule.

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This animation describes the transfer of chemiosmotic energy into rotational energy, and ultimately into the chemical bond energy of ATP.

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The rotary mechanism of mitochondrial ATP synthase.

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View from above and then below the F1 domain along the rotating γ-subunit.

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How the rotating γ-subunit imposes the conformational states on a β-subunit required for substrate binding, ATP formation and ATP release.

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Three conformations of a catalytic β-subunit produced by 120º rotations of the central γ-subunit.

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Changes in the positions of sidechains in the catalytic site of F1-ATPase bringing about binding and subsequent hydrolysis of ATP.

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This Maya animation covers the death receptor signaling pathway that originates with binding of the Fas ligand, triggering of the caspase cascade, cytochrome C release from the mitochondria, apoptosome activation, and ensuing signal amplification.

>> View the animation at Harvard BioVisions

A fly-through the morphing ATPase structure in surface representation

.

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A detailed atomic look at the molecular interactions that stabilize ADP/ATP in the F1-F0 ATPase active site.

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This animation depicts hemoglobin molecules binding to oxygen. The mutant form of hemoglobin is also shown and results in the assembly of the long stiff protein fibers characteristic of the disease sickle cell anemia.

>> View the animation at WEHI

An animation that takes the viewer from the tissue level (i.e. a capillary inside a gut villus) all the way to the molecular level (by taking a look at the conformational changes that occur as a result of oxygen release by hemoglobin).

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A 3D animation depicting the early molecular events underlying long term potentiation in the spinal cord of pain pathways. (Click on the icon in the "Master's Research Project Examples 2002-2005 area of the page).

>> View the animation at U. Toronto

This series of animations depicts the processes of flagellar motion and assembly in molecular detail (also called the "Protonic Nanomachine Project").

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This 3DS Max fly-through animation uses experimentally-derived concentrations of the 50 most abundant components of the E. coli cytoplasm (not counting DNA).

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This animation shows the mapping of 70S ribosome positioning and orientation data from a tomogram of Sprioplasma melliferum using pattern recognition.

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This Maya animation depicts the process of ubiquitin-dependent degradation in the proteasome. The effect of mutant ataxin no this process is also shown.

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Still one of the more complex and beautiful molecular animations ever made, this movie shows the components and dynamic processes involved in the replication of both the leading and lagging strands of DNA.

>> View the animation at WEHI

This animation shows the dancing heptameric complex responsible for unwinding the DNA double helix in bacteriophage and how it is subsequently used as a site for primer synthesis.

>> View the animation at SciAnaFilms

This animation shows how a tri-nucletoide repeat can cause the DNA polymerase to 'slip' and incorporate additional nucleotides during the replication process.

>> View the animation at HHMI

This Maya animation shows cleavage of double-stranded RNA into short RNA fragements by the Dicer ribonuclease.

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A short animated sequence showing how RNA can fold back onto itself (through the formation of intramolecula base-pairing).

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Dynamics of Lck in the T cell synapse - Upon T cell activation, clusters of signaling proteins form microdomains in the cell membrane. Some proteins, like the tyrosine kinase Lck (white) can freely diffuse between these clusters. Interactions between Lck and proteins in the signalling cluster can cause Lck to become immobilized.

>> View the animation at OneMicron

A molecular view of the surface of a stem cell highlighting the binding of G-CSF by its receptor, dimerization, signal transduction and the resulting effect on cell division and growth.

>> View the animation at WEHI

An animation showing stem cell colonies expanding in the bone marrow. Some daughter cells differentiate intowhite blood cells and migrate into the blood, while others remain stem cells.

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A series of animations with audio and text commentary that clearly explain the basics od stem cell biology (including their unique characteristics, pluripotency in the early embryo, presence in adult tissues and embryonic stem cels in culture).

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Transcription factors assemble at a DNA promoter region found at the start of a gene. Promoter regions are characterised by the DNA's base sequence, which contains the repetition TATATA É and for this reason is known as the "TATA box".

>> View the animation at WEHI

The RNA polymerase unzips a small portion of the DNA helix exposing the bases on each strand. One of the strands acts as a template for the synthesis of an RNA molecule. The base-sequence code is transcribed by matching these DNA bases with RNA subunits, forming a long RNA polymer chain.

>> View the animation at WEHI

This animation show the effects of MECP2 DNA methylation (CpG islands) on recruitment of Sina3/HDAC, nuclesome modification and gene silencing.

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This animation highlights the structure of p53 protein and its binding to a cognate promoter. Recruitment of RNA polymerase and transcription are also shown.

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A detailed animation highlighting the key residues and side chains within a polymerase active site and the polymerization mechanism.

>> View the animation at SciAnaFilms

Shows the effects of drug-binding to the PPAR-delta transcription factor receptor on DNA - a repressor is released thereby turning on the muscle delta network on genes. Oxidative metabolism is activated and leads to reduction of fat pads in adipose tissue.

>> View the animation at HHMI

Shows fat cells in the adipose tissue adjacent to muscle - storage / breakdown of the cell's fat droplet affects the balance of secreted adiponectin and resistin hormones. The effect of drugs against PPAR gamma is also shown to affect this balance and resulting insulin sensitivity.

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This visualization rotates the assembled ribosome and then shows (using a cut-away) the path of entry of the tRNA during the elongation cycle.

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An animation highlighting the structural domains of elongation factor Tu and the surface involved in tRNA binding. The conformational change in the switch helix that occurs as a result of GTP hydrolysis results in the release of the tRNA.

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A visualization of a cell's cytosplasm derived from electron tomography data from Brad Marsh's laboratory. The different components - nucleus, microtubules, mitochondria, ribosomes, smooth ER, rough ER, Golgi - are highlighted in separate 'passes' and then overaid as one. A great reminder of how crowded cellular interiors are!

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This animation compares the structure of ribosome complexes in either IRES-mRNA (Internal RIbosome Entry Sequence) or capped-mRNA conformations.

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A detailed animation that covers all the central steps in prokaryotic translation (including initiation, elongation and termination steps with many of the invidual protein factors involved in each).

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Shows the 70S ribosome conformation change that occurs upon binding of elongation factor G.

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This Maya animation depicts the process by which the translating ribosome is halted by the signal recognition particle (SRP). The ribosome is subsequently brought to the membrane and docked with a channel to translocate the nascent polypeptide chain.

>> View the animation at Bloopatone

Part 3 in Drew Berry's "Central Dogma" animations - the mRNA (yellow) is decoded inside the ribosome (purple and light blue) and translated into a chain of amino acids (red) as aminoacyl-tRNAs (green) deliver each amino-acid cargo (red/pink tip) to the ribosome.

>> View the animation at WEHI

One of the largest molecular dynamic simulations in biology - studies the interactions of tRNA as it enters the ribosome.

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A movie showing how aminoacyl-tRNA acts as a flexible molecular spring during codon recognition and accomodation.

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An accurate visualization of the Bacteriophage T4 based on Cryo-EM datasets of the virus. The scope of the animation is to show the infection process of T4 into an E. coli cell. All scientific data sets and motion based off of research from Michael Rossmann Laboratory (Purdue University).

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A Maya-rendered visualization of a VMD molecular dynamics simulation. Created for David Chandler's lab at UC Berkeley, this movie depicts the physics of viral capsid formation while summarizing some of the technical steps involved in its creation.

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A narrated animation depicting the events that lead to Dengue virus entry into a host cell. In particular, rearrangements and conformational changes in the Dengue glycoprotein E are shown. These lead to membrane fusion and subsequent release of the viral payload into the host cell cytoplasm. Created for WGBH.

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A visualization of the capsid protein lattice structure that forms during the assembly of immature HIV-1 particles. (Click on the icon in the "Master's Research Project Examples 2002-2005 area of the page).

>> View the animation at U. Toronto

This Maya animation depicts the process by which HIV's gp41 protein mediates the fusion of viral and cellular membranes during virus entry. In addition, strategies for inhibiting this process with peptide or small molecule inhibitors are shown.

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This animation represents part-1 of a 2-part series depicting the events of the malaria parasite lifecycle.
The parasite is shown entering the human host following a mosquito bite and we follow its progression initially to the liver and subsequently targeting erythrocytes on a large scale.

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This 1985 animation (programmed in GRAMPS) describes the structure of the poliovirus (seen here at near-atomic resolution). Icoshedral symmetry of the capsid, positioning and interaction of each of the V 1 - 4 proteins is described in detail.

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A sequence depicting Pseudomonas infection of lung epithelial cells.

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