A Perturbation Scheme for Spherical Arrangements with Application to Molecular Modeling

We describe a software package for computing and manipulating the subdivision of a sphere by a collection of (not necessarily great) circles and for computing the boundary surface of the union of spheres. We present problems that arise in the implementation of the software and the solutions that we have found for them. At the core of the paper is a novel perturbation scheme to overcome degeneracies and precision problems in computing spherical arrangements while using floating point arithmetic. The scheme is relatively simple, it balances between the efficiency of computation and the magnitude of the perturbation, and it performs well in practice. In one O(n) time pass through the data, it perturbs the inputs necessary to insure no potential degeneracies and then passes the perturbed inputs on to the geometric algorithm. We report and discuss experimental results. Our package is a major component in a larger package aimed to support geometric queries on molecular models; it is currently employed by chemists working in "rational drug design." The spherical subdivisions are used to construct a geometric model of a molecule where each sphere represents an atom. We also give an overview of the molecular modeling package and detail additional features and implementation issues.

Revised Report on the Algorithmic Language Scheme

Data and procedures and the values they amass, Higher-order functions to combine and mix and match, Objects with their local state, the message they pass, A property, a package, the control of point for a catch- In the Lambda Order they are all first-class. One thing to name them all, one things to define them, one thing to place them in environments and bind them, in the Lambda Order they are all first-class. Keywords: Scheme, Lisp, functional programming, computer languages.

MIT Scheme Reference Manual

MIT Scheme is an implementation of the Scheme programming language that runs on many popular workstations. The MIT Scheme Reference Manual describes the special forms, procedures, and datatypes provided by the implementation for use by application programmers.

RABBIT: A Compiler for SCHEME

We have developed a compiler for the lexically-scoped dialect of LISP known as SCHEME. The compiler knows relatively little about specific data manipulation primitives such as arithmetic operators, but concentrates on general issues of environment and control. Rather than having specialized knowledge about a large variety of control and environment constructs, the compiler handles only a small basis set which reflects the semantics of lambda-calculus. All of the traditional imperative constructs, such as sequencing, assignment, looping, GOTO, as well as many standard LISP constructs such as AND, OR, and COND, are expressed in macros in terms of the applicative basis set. A small number of optimization techniques, coupled with the treatment of function calls as GOTO statements, serve to produce code as good as that produced by more traditional compilers. The macro approach enables speedy implementation of new constructs as desired without sacrificing efficiency in the generated code. A fair amount of analysis is devoted to determining whether environments may be stack-allocated or must be heap-allocated. Heap-allocated environments are necessary in general because SCHEME (unlike Algol 60 and Algol 68, for example) allows procedures with free lexically scoped variables to be returned as the values of other procedures; the Algol stack-allocation environment strategy does not suffice. The methods used here indicate that a heap-allocating generalization of the "display" technique leads to an efficient implementation of such "upward funargs". Moreover, compile-time optimization and analysis can eliminate many "funargs" entirely, and so far fewer environment structures need be allocated at run time than might be expected. A subset of SCHEME (rather than triples, for example) serves as the representation intermediate between the optimized SCHEME code and the final output code; code is expressed in this subset in the so-called continuation-passing style. As a subset of SCHEME, it enjoys the same theoretical properties; one could even apply the same optimizer used on the input code to the intermediate code. However, the subset is so chosen that all temporary quantities are made manifest as variables, and no control stack is needed to evaluate it. As a result, this apparently applicative representation admits an imperative interpretation which permits easy transcription to final imperative machine code. These qualities suggest that an applicative language like SCHEME is a better candidate for an UNCOL than the more imperative candidates proposed to date.

Performance Evaluation of the Scheme 86 and HP Precision Architecture

The Scheme86 and the HP Precision Architectures represent different trends in computer processor design. The former uses wide micro-instructions, parallel hardware, and a low latency memory interface. The latter encourages pipelined implementation and visible interlocks. To compare the merits of these approaches, algorithms frequently encountered in numerical and symbolic computation were hand-coded for each architecture. Timings were done in simulators and the results were evaluated to determine the speed of each design. Based on these measurements, conclusions were drawn as to which aspects of each architecture are suitable for a high- performance computer.

Asymptotically Zero Energy Computing Using Split-Level Charge Recovery Logic

The dynamic power requirement of CMOS circuits is rapidly becoming a major concern in the design of personal information systems and large computers. In this work we present a number of new CMOS logic families, Charge Recovery Logic (CRL) as well as the much improved Split-Level Charge Recovery Logic (SCRL), within which the transfer of charge between the nodes occurs quasistatically. Operating quasistatically, these logic families have an energy dissipation that drops linearly with operating frequency, i.e., their power consumption drops quadratically with operating frequency as opposed to the linear drop of conventional CMOS. The circuit techniques in these new families rely on constructing an explicitly reversible pipelined logic gate, where the information necessary to recover the energy used to compute a value is provided by computing its logical inverse. Information necessary to uncompute the inverse is available from the subsequent inverse logic stage. We demonstrate the low energy operation of SCRL by presenting the results from the testing of the first fully quasistatic 8 x 8 multiplier chip (SCRL-1) employing SCRL circuit techniques.

Dissociated Dipoles: Image representation via non-local comparisons

A fundamental question in visual neuroscience is how to represent image structure. The most common representational schemes rely on differential operators that compare adjacent image regions. While well-suited to encoding local relationships, such operators have significant drawbacks. Specifically, each filter's span is confounded with the size of its sub-fields, making it difficult to compare small regions across large distances. We find that such long-distance comparisons are more tolerant to common image transformations than purely local ones, suggesting they may provide a useful vocabulary for image encoding. . We introduce the "Dissociated Dipole," or "Sticks" operator, for encoding non-local image relationships. This operator de-couples filter span from sub-field size, enabling parametric movement between edge and region-based representation modes. We report on the perceptual plausibility of the operator, and the computational advantages of non-local encoding. Our results suggest that non-local encoding may be an effective scheme for representing image structure.

A DHT-Based Grid Resource Indexing and Discovery Scheme

This paper presents a DHT-based grid resource indexing and discovery (DGRID) approach. With DGRID, resource-information data is stored on its own administrative domain and each domain, represented by an index server, is virtualized to several nodes (virtual servers) subjected to the number of resource types it has. Then, all nodes are arranged as a structured overlay network or distributed hash table (DHT). Comparing to existing grid resource indexing and discovery schemes, the benefits of DGRID include improving the security of domains, increasing the availability of data, and eliminating stale data.