Researchers at the Wyss Institute for Biologically Inspired Engineering at Harvard University have created more than 100 3-D nanostructures using DNA building blocks that function like Lego bricks — a major advance from the two-dimensional structures the same team built a few months ago.In effect, the advance means researchers went from being able to build a flat wall of Legos to building a house. The new method, featured as a cover research article in the Nov. 30 issue of Science, is the next step toward using DNA nanotechnologies for more sophisticated applications than ever possible before, such as “smart” medical devices that target drugs selectively to disease sites, programmable imaging probes, templates for precisely arranging inorganic materials in the manufacturing of next generation computer circuits, and more.The nanofabrication technique, called “DNA-brick self-assembly,” uses short, synthetic strands of DNA that work like interlocking Lego bricks. It capitalizes on the ability to program DNA to form into predesigned shapes thanks to the underlying “recipe” of DNA base pairs: A (adenosine) only binds to T (thymine), and C (cytosine) only binds to G (guanine).Earlier this year, the Wyss team reported in Nature how they could create a collection of two-dimensional shapes by stacking one DNA brick (42 bases in length) upon another.But there’s a “twist” in the new method required to build in 3-D.The trick is to start with an even smaller DNA brick (32 bases in length), which changes the orientation of every matched-up pair of bricks to a 90-degree angle — giving every two Legos a 3-D shape. In this way, the team can use these bricks to build “out” in addition to “up,” and eventually form 3-D structures, such as a 25-nanometer solid cube containing hundreds of bricks. The cube becomes a “master” DNA “molecular canvas”; in this case, the canvas was composed of 1,000 “voxels,” which correspond to eight base-pairs and measure about 2.5 nanometers in size — meaning this is architecture at its tiniest.The master canvas is where the modularity comes in: By simply selecting subsets of specific DNA bricks from the large cubic structure, the team built 102 3-D structures with sophisticated surface features, as well as intricate interior cavities and tunnels.“This is a simple, versatile, and robust method,” says Peng Yin, Wyss core faculty member and senior author on the study.Another method used to build 3-D structures, called DNA origami, is tougher to use to build complex shapes, Yin said, because it relies on a long “scaffold” strand of DNA that folds to interact with hundreds of shorter “staple” strands — and each new shape requires a new scaffold routing strategy and hence new staples. In contrast, the DNA brick method does not use any scaffold strand and therefore has a modular architecture; each brick can be added or removed independently.“We are moving at lightning speed in our ability to devise ever more powerful ways to use biocompatible DNA molecules as structural building blocks for nanotechnology, which could have great value for medicine as well as nonmedical applications,” says Wyss Institute Director Donald Ingber.The research team led by Yin, who is also an assistant professor of systems biology at Harvard Medical School (HMS), included Wyss postdoctoral fellow Yonggang Ke and Wyss graduate student Luvena Ong. Another contributor was Wyss core faculty member William Shih, who also holds appointments at HMS and at the Harvard-affiliated Dana-Farber Cancer Institute. To learn more about the team’s work, visit its website.The research was supported by the Office of Naval Research, the Army Research Office, the National Science Foundation, the National Institutes of Health, and the Wyss Institute for Biologically Inspired Engineering at Harvard University.
In the first blog in this series we talked about programmable fabrics and their use causes. In this blog we’ll look at what a programmable fabric actually looks like.The following diagram shows the high-level architecture of a programmable fabric:The programmable fabric can be broken down into two main layers, the control plane and the data plane.Control Plane LayerThe control plane layer is responsible for configuring and managing the data plane and is normally more centrally located, i.e., one per PoP or region.The control plane is normally divided into three separate domains – Fabric, Telemetry & Configuration and Management – to allow them to scale independently. However, they could be implemented in one software controller, for example in a small-scale implementation.1. Fabric ControllerThe Fabric Controller controls the loading and programming of the data plane pipeline using the P4 Runtime interface to communicate with the data plane’s programmable forwarding engine as shown in the diagram below.There will be a number of controller applications or “network functions” that talk to the fabric controller to control various aspects of the programmable fabric.The Fabric Management applications manage the underlying network fabric setup and configuration. It can also be thought of as a number of virtualized switch and router network functions that provide the underlying network fabric using the programmable fabric.The Fabric Management applications rely on user plane functionality being implemented in the P4 pipeline in the PFE.The NF control plane uses a CUPS (Control User Plane Separation) methodology to implement the control plane portion of a Network Function while the user plane functions are pushed down into the “data plane node” as described in this document.2. Telemetry ControllerThe Telemetry Controller allows applications (i.e. Fault Management) to collect telemetry on the network elements in the programmable fabric using the Programmable Fabric’s gNMI streaming interface. It is expected that other applications will use things like machine learning to provide more intelligent decisions and provide control loop feedback into the Fabric Controller applications to provide pre-emptive service reconfiguration and repair as we move towards autonomous networks.3. Configuration and Management ControllerThe Configuration and Management Controller will provide applications with common north bound interfaces and models for the configuration and management of the programmable fabric.The OpenConfig group provides a set of network data models that allow network functions to be managed using a common set of tools and protocols. The gNMI and gNOI interfaces use the OpenConfig models to allow efficient access to configure and manage the network functions in the Programmable Fabric.Data Plane LayerThe data plane does the bulk of the network traffic forwarding only sending exception or control packets up to the control plane for processing (i.e. DHCP for a new IPoE session in a BNG-c). While the data plane might normally be thought of as a standalone network switch in the network it could also be a SmartNIC in a compute server that allows the programmable fabric to be extended up into the server (i.e. using P4 to define a pipeline in an FPGA SmartNIC).The data plane is normally made up of several components:Data Plane Node (DPN):is used to describe the hardware that houses the data plane forwarding function (i.e. all the components below). This could be a stand alone network switch with a PFE like Intel/Barefoot’s Tofino chip or a compute server with a P4 based SmartNIC like Intel’s PAC N3000.Data Plane Agent (DP-Agent):provides the standardised north bound data plane interfaces (i.e. P4 Runtime, gNMI and gNOI) that allow the control plane network functions to communicate with the data plane. An example implementation of the DP-Agent is the ONF’s Stratum project.Network Function user plane (NF-u):the user plane portions of network functions can be defined in the programmable pipeline (i.e. using P4 for example) and then loaded into the PFE to process packets. These functions are programmed by their control plane counters parts (i.e. BNG-c, UPF-c, Fabric Manager-c) in order to handle the bulk of the traffic in the PFE without needing to go up to the control plane for processing.Programmable Forwarding Engine (PFE):the actual hardware that does the packet forwarding. Some examples of a PFE could be the P4 based switch chipset like Intel/Barefoot’s Tofino chipset, or another could be an FPGA based SmartNIC using P4 to define the packet forwarding pipeline.Dell Technologies is committed to driving disaggregation and innovation through open architectures and the competitiveness this brings to our customer’s networks. The high-level architecture described in this blog is in line with the Open Networking Forum’s Stratum and NG-SDN projects and provides open building blocks that allow telecommunication providers to build open, scalable and cost effective edge solutions.
Published on November 10, 2010 at 12:00 pm Contact Mark: [email protected] | @mark_cooperjr Facebook Twitter Google+ Comments As assistant coaches under one of the most revered coaches of all time, Charlie Strong and Skip Holtz helped turn around a program together. The former South Carolina coordinators helped turn a winless Gamecocks team into an Outback Bowl champion in one year. Now they are each turning around their own programs as head coaches. Strong spent four seasons as the Gamecocks’ defensive coordinator under his coaching mentor, Lou Holtz. That’s where Strong and Skip Holtz share a common thread — through Skip’s father. The legendary Lou Holtz brought Strong under his wing for many years. And of course, he had Skip. ‘We have a bond there that we’re really good friends,’ Strong said Monday in the Big East coaches’ teleconference. ‘Skip’s an outstanding football coach.’ Eight years since they last coached together, Strong and Skip Holtz will face off Saturday as Louisville (5-4, 2-2 Big East) takes on South Florida (5-3, 2-2). Both coaches have taken different routes to reach their current positions, but now each finds himself building up a Big East program in his first year.AdvertisementThis is placeholder text And each coach comes from the influences of Lou Holtz. Strong was a defensive line coach on Lou’s staff on Notre Dame from 1995-96. He remained even after Lou left, until 1999, when Strong made the jump to South Carolina to become Lou’s defensive coordinator at his new job. While Strong was being mentored at Notre Dame, Skip Holtz was the head coach at Connecticut, at the time a Division I-AA school. He had success there, even winning 10 games in 1998. But when his father took over the Gamecocks’ head coaching job, Skip signed on to become the offensive coordinator. The heads of the staff were set: Lou Holtz as head coach, Skip Holtz as offensive coordinator, Charlie Strong as defensive coordinator. That’s how it would be for four years, as the coaching staff built up a program that was one of the worst in Division I-A when they took over. ‘It was a program similar to this (Louisville) when we took over,’ Strong said. ‘We did not win any games our first year, but came back and won two straight Outback Bowls.’ Turning around a program that had won one game the year before they arrived strengthened Skip Holtz and Strong’s relationship. They suffered through a 0-11 season their first year together. And they got to see the building of the South Carolina program firsthand. ‘I’ve known Charlie for a long time,’ Holtz said. ‘Him and (Strong’s wife) Vickie are just great people, and our kids have played together. … I think the world of Charlie.’ Both Strong and Holtz also got to reap the benefits of turning around a program together. After the 2002 season, Strong bolted from South Carolina to take the same role as defensive coordinator at Florida. Strong was the only assistant retained by current UF head coach Urban Meyer when he took over for the 2005 season. Strong was eventually promoted to associate head coach under Meyer, in addition to his defensive coordinator role. Strong won two national championships at Florida, and he turned that success into his current job with the Cardinals. Now he has a Louisville team picked to finish last in the Big East at the beginning of the season on the cusp of becoming bowl eligible. He has the Louisville defense looking like the Florida defenses that continually fought for the SEC title. And like the Gamecocks defenses that won back-to-back Outback Bowls. ‘They come after you, they’re very, very aggressive,’ Holtz said about a Charlie Strong defense. ‘They’re not ‘sit back and let you dictate.’ They’re going to try and dictate the game on defense.’ Holtz left South Carolina after the 2003 season to become the head coach at East Carolina. There, he took the Pirates to four bowls in five seasons. In 2008, his team upset nationally ranked powers Virginia Tech and West Virginia. He joined the Big East this season with South Florida, and after a slow start to conference play, he has the Bulls looking to clinch a bowl as well this weekend. ‘If you look at it, when he coached at Connecticut, he had great success,’ Strong said. ‘Then he came to South Carolina, and he leaves South Carolina and at East Carolina he does a great job. ‘He understands the game and knows exactly how to get his players to go and play.’ Saturday, the two friends and former co-workers who know a great deal about each other will square off, with the winner becoming bowl eligible. It would be a monumental win for either school. Louisville hasn’t made a bowl since 2006, but USF has never won at the Cardinals’ home stadium. It will be Holtz’s offense vs. Strong’s defense. This time, on opposite sides. And neither coach is taking the other side lightly. ‘I think he’s a great football coach, I think he’s a great person, and he’s doing a great job at Louisville,’ Holtz said. ‘I think when you say this is a typical Charlie Strong defense, yeah, it is.’ Big man on campus RB Jeremy Wright Freshman Louisville Last week: 19 carries, 98 yards, 2 TDs Louisville entered last Saturday’s game at Syracuse as a bit of an underdog. The Cardinals were banged up, missing both its starting quarterback and running back. But Wright took advantage of the opportunity. With only two games on the Big East schedule last week, Wright stood out with a big performance in a 28-20 win at Syracuse. The freshman, filling in for Louisville’s star running back Bilal Powell, ran for 98 yards and a pair of scores as the Cardinals won its first road Big East game in 12 tries. Wright broke open the scoring in the first quarter with a 28-yard touchdown run to put UL up 7-0. Later on, his 12-yard touchdown run put Louisville back on top for good, 21-17. The backup running back set career highs in just about every rushing statistic Saturday. He entered the game with only 14 carries on the season. And he proved that if UL was to be missing Powell for any extended period of time, he could be a serviceable fill-in. ‘He is not very big,’ UL head coach Charlie Strong said, ‘but can get behind his pads and has enough speed, quickness and strength to make the runs and make people miss him.’ [email protected]