From joan@gorgonio.oac.ucla.edu Fri Aug 31 16:45:52 2001 Return-Path: Received: from gorgonio.oac.ucla.edu (gorgonio.oac.ucla.edu [128.97.60.12]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id f7VLjqr14278 for ; Fri, 31 Aug 2001 16:45:52 -0500 (CDT) Received: (from joan@localhost) by gorgonio.oac.ucla.edu (AIX4.3/8.9.3/8.9.3) id OAA16108; Fri, 31 Aug 2001 14:45:51 -0700 Message-Id: <200108312145.OAA16108@gorgonio.oac.ucla.edu> X-Mailer: exmh version 2.0.1 12/23/97 To: John Stone Subject: message 2 In-reply-to: Your message of Thu, 23 Aug 2001 17:24:29 -0500 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Fri, 31 Aug 2001 14:45:51 -0700 From: Joan Slottow Status: RO Content-Length: 7231 Lines: 143 In the pictures of the tiled display you will see: 4 machines, 4 monitors (the control unit monitor running vmd with the vmd gui, and a little window in which we move the mouse to have the display move, and the 3 monitors showing the picture), the keyboard, the keyboard switch, and the network switch The 3 rendering displays have extron electronics boxes attatched to them feeding their signals to the portal. We are interested in experimenting to see if we can use the tiled display in place of the onyx2. We are also interested in being able to build larger tiled displays that UCLA departments can install cheaply for themselves. In order to do that we have to be able to run the kind of software that those in the departments are interested in running. We use VMD ourselves when giving demos in the Portal in order to interest others to either use the Portal or to use various vis software. What you are seeing are from various "scenarios" that we run in the Portal as demos. Here is some of the text that goes along with it: Nanotechnology involves designing and building machines that operate at the molecular level. The pump are showing was designed by Dr. Eric Drexler at the Institute for Molecular Manufacturing. We are using the VMD program, a free program from the University of Illinois at Urbana Champaign, to display it. This is an exploded view of the pump as a jpeg file, displayed by the xv program. On the left is a wall and the pump housing; on the right is the pump rotor. Now we are using the VMD program to read the pump from a data file in PDB, Protein Data Bank, format - essentially a list of atoms, their positions, and their connectivity. With VMD, we can manipulate the image to look at the pump from different angles. In particular, please note the spiral pattern on the rotor. This pattern works together with lateral groovs on the inside of the pump housing to capture a single neon atom and move it through the pump. With VMD, we can display the parts of the pump individually. Here we have just the pump housing, seen head-on, with the wall in the background, the housing coming toward you. We can change the display model. We see the housing displayed as lines connecting atoms. We can also display it as a ball-and-stick model. everal other display models are available, including Van Der Waal's surfaces. This looks the most like the original image. We can rotate the pump to examine different parts of it. We can zoom in to get a closer look, or back out. We can move it horizontally and vertically. Here is the rotor again, first as lines, then as a ball-and-stick model, and finally as Van Der Waal's surfaces. We can rotate the rotor to the same orientation as we left the housing. Finally we can combine the housing and the rotor and turn the pump on. About the only thing we haven't done here is actually introduce something to be pumped. By the way, Aeint says that the current issue of Scientific American is on nanotechnology and that Eric Drexler wrote on of the articles. This visualization is of a large protein with reactant, transition and product states. It allows you to visualize what the transition state should actually look like. This simplified model contains the most important amino acid residues important for the catalysis of the reaction. It is significantly smaller, so rendering and real-time motion is much more fluid. This data comes from the work of Dean Tantillo, a graduate student in Professor Ken Houk's group, who is nearing the completion of his Ph.D. The vmd scenarios were created by Michael Bartberger and Aeint de Boer. In a chemical reaction, atoms in the input molecules (called reactants) combine in the presence of catalysts and energy to produce different molecules (called the products). In the body, enzymes act as catalysts. Energy is needed to force the reactants and catalysts into what is called the transition state after which the recombination of atoms occurs. The transition state is the highest point on a bell-shaped curve between the reactants and the products. Specifically, this research looks at the binding properties of certain enzymes to stabilize the transition state structure. One application of this research might enable you to inject something like the molecules created during the transition state into the immune system and cause it to generate proteins that bind to foreign bodies. This would be analogous to ?mini-evolution.? They are also studying the bindings of small organic molecules in the transition state to determine their ability to catalyze other organic reactions. This could result in the efficient creation of drug-like compounds formed from synthetic organic chemistry that would mimic the transition state binding of an antibody. Everything in chemistry relates to where atoms are in space. Two-dimensional displays do not allow you to see those relationships. Equally, atomic positive and negative charges are interacting throughout the protein. Different atoms binding on the outside of the protein can affect the middle and visa versa. The 3-dimensional capability of the portal allows one to see spatial relationships between atoms, and the large screen allows one to see the details of what is going on in the area of interest (center of the molecule) without losing the context of the entire protein. By actually immersing oneself in the protein you are allowed to be inside ?looking out? which creates a whole different experience and interpretations of relationships and interactions. Eventually our ability to implement ?haptic? feedback will allow the chemist to feel the forces involved. Building a complex protein of this size with physical models would take years, occupy a large space, and be available to only a few people at the location. The third example is from Prof David Eisenberg http://www.doe-mbi.ucla.edu/Peop le/Eisenberg/Structures UCLA (in conjunction with UC Santa Barbara) was awarded the California Nanosystems Institute (CNSI) recently. In preparation and planning for the computer and related facilities to go into the new, not-yet constructed building, for the CNSI, they have been showing Eisenberg's stuff running in VMD in the Portal. By the way, when you look at it, (it shown as ribbons) you will see how bad the image is. It looks that way because the NVidia GeForce 2 cards we have in the tiled display machines don't do antialiasing. When we show images produced on the onyx2, they dont look that way. Joan