Since 1991, our team of computer scientists, chemists and physicists have worked together to develop an advanced, virtual-environment interface to scanned-probe microscopes. The interface has provided insights and useful capabilities well beyond those of the traditional interface. This paper lists the particular visualization and control techniques that have enabled actual scientific discovery, including specific examples of insight gained using each technique. This information can help scientists determine which features are likely to be useful in their particular application, and which would be just sugar coating. It can also guide computer scientists to suggest the appropriate type of interface to help solve a particular problem. We have found benefit in advanced rendering with natural viewpoint control (but not always), from semi-automatic control techniques, from force feedback during manipulation, and from storing/replaying data for an entire experiment. These benefits come when the system is well-integrated into the existing tool and allows export of the data to standard visualization packages.

The NanoManipulator system has been expanded from a virtual-reality interface for a specific scanning tunneling microscope to include control of atomic force microscopes. The current state of the system is reviewed, and new tools extending the user's feel and control in manipulation and fabrication in the mesoscopic regime are detailed. Manipulations that could not be performed using the techniques available from commercial SPM systems are demonstrated, and the direction of ongoing research is outlined.

The design of a synchronous system having a global clock must account for propagation-delay-induced phase shifts experienced by the clock signal (clock skew) in its distribution network. As clock speeds and system diameters increase, this requirement becomes increasingly constraining on system designs. The paper describes a method that exploits properties of standing waves to reduce substantially clock skews due to unequal path lengths, for distribution network diameters up to several meters. The basic principles are developed for a loaded transmission line, and then applied to an arbitrary branching tree of such lines to implement a clock distribution network. The extension of this method to two- and three-dimensional distribution media is also presented, suggesting the feasibility of implementing printed circuit board clock planes exhibiting negligible phase shift over their extents.>

As networks approach gigabit performance, supercomputer host interfaces are becoming the communication bottleneck.The Network Interface Unit (NIU) is a highperformance host interface for Pixel Planes 5, a custom graphics supercomputer.The design offers both performance and programmability through a balance of ahtamarshaling hardware and an embedded processor.In this paper, we describe the NW hardware and jirmware architecture.We present some prelitw"nary peq$ormance measurements and assess the applicability of this design for the targeted environment.We also comment on its suitability for other environments and outline plans for the future work.PemnissiOn to copy witkut fee df or pan of Ibis mat.xial is gmntaf, pmvikd that tbe copie6 are not made or diswilmted for direct commercial adva"lage, the ACM copyright nctice and ibe tide of the publication and 124 its date appear, and notice is given that copying is by permission of tbe Assxiation for Commting Machinery.To copy otbenvise, or to repubkb, requires a fee andkr specific permission.

We present an atomic-scale teleoperation system that uses a head-mounted display and force-feedback manipulator arm for a user interface and a Scanning Tunneling Microscope (STM) as a sensor and effector.The system approximates presence at the atomic scale, placing the scientist on the surface, in control, w h i l e the experiment is happening.A scientist using the Nanomanipulator can view incoming STM data, feel the surface, and modify the surface (using voltage pulses) in real time.The Nanomanipulator has been used to study the effects of bias pulse duration on the creation of gold mounds.We intend to use the system to make controlled modifications to silicon surfaces.

A special-purpose computer system has been designed to accelerate scanning large databases of DNA and protein sequences (biosequences) for patterns of interest. The system consists of a custom-designed circuit board installed in a host workstation and associated software. The board features a variable number of identical full-custom ASICs. Each biological sequence comparative analysis node. (BioSCAN) ASIC, in turn, features a large one-dimensional systolic array of identical processing elements (PEs). The BioSCAN system scans approximately two million database elements per second. For typical problems this results in a 1000-fold speedup over current workstations.>

In this paper, a new optical system for real-time, three-dimensional position tracking is described. This system adopts an "inside-out" tracking paradigm. The working environment is a room where the ceiling is lined with a regular pattern of infrared LEDs flashing under the system's control. Three cameras are mounted on a helmet which the user wears. Each camera uses a lateral effect photodiode as the recording surface. The 2D positions of the LED images inside the field of view of the cameras are detected and reported in real time. The measured 2D image positions and the known 3D positions of the LEDs are used to compute the position and orientation of the camera assembly in space.We have designed an iterative algorithm to estimate the 3D position of the camera assembly in space. The algorithm is a generalized version of the Church's method, and allows for multiple cameras with nonconvergent nodal points. Several equations are formulated to predict the system's error analytically. The requirements of accuracy, speed, adequate working volume, light weight and small size of the tracker are also addressed.A prototype was designed and built to demonstrate the integration and coordination of all essential components of the new tracker. This prototype uses off-the-shelf components and can be easily duplicated. Our results indicate that the new system significantly out-performs other existing systems. The new tracker provides more than 200 updates per second, registers 0.1-degree rotational movements and 2-millimeter translational movements, and processes a working volume about 1,000 ft3 (10 ft on each side).