Inexpensive Workstations Research Articles

Thermodynamic Integration in 3n Dimensions without Biases or Alchemy for Protein Interactions.

Thermodynamic integration (TI), a powerful formalism for computing Gibbs free energy, has been implemented for many biophysical processes with alchemical schemes that require delicate human efforts to choose/design biasing potentials for sampling the desired biophysical events and to remove their artifactitious consequences afterwards. Theoretically, an alchemical scheme is exact but practically, an unsophisticated implementation of this exact formula can cause error amplifications. Small relative errors in the input parameters can be amplified many times in their propagation into the computed free energy [due to subtraction of similar numbers such as (105 ± 5)‒(100 ± 5) = 5 ± 7]. In this paper, we present an unsophisticated implementation of TI in 3n dimensions (3nD) (n=1,2,3…) for the potential of mean force along a 3nD path connecting one state in the bound state ensemble to one state in the unbound state ensemble. Fluctuations in these 3nD are integrated in the bound and unbound state ensembles but not along the 3nD path. Using TI3nD, we computed the standard binding free energies of three protein complexes: trometamol in Salmonella effector SpvD (n=1), biotin-avidin (n=2), and Colicin E9 endonuclease with cognate immunity protein Im9 (n=3). We employed three different protocols in three independent computations of E9-Im9 to show TI3nD's robustness. We also computed the hydration energies of ten biologically relevant compounds (n=1 for water, acetamide, urea, glycerol, trometamol, ammonium and n=2 for erythritol, 1,3-propanediol, xylitol, biotin). Each of the 15 computations is accomplishable within one (for hydration) to ten (for E9-Im9) days on an inexpensive GPU workstation. The computed results all agree with the available experimental data.

Clinical Validation of a Ray-Casting Analytical Dose Engine for Spot Scanning Proton Delivery Systems.

Purpose:To describe and validate the dose calculation algorithm of an independent second-dose check software for spot scanning proton delivery systems with full width at half maximum between 5 and 14 mm and with a negligible spray component.Methods:The analytical dose engine of our independent second-dose check software employs an altered pencil beam algorithm with 3 lateral Gaussian components. It was commissioned using Geant4 and validated by comparison to point dose measurements at several depths within spread-out Bragg peaks of varying ranges, modulations, and field sizes. Water equivalent distance was used to compensate for inhomogeneous geometry. Twelve patients representing different disease sites were selected for validation. Dose calculation results in water were compared to a fast Monte Carlo code and ionization chamber array measurements using dose planes and dose profiles as well as 2-dimensional–3-dimensional and 3-dimensional–3-dimensional γ-index analysis. Results in patient geometry were compared to Monte Carlo simulation using dose–volume histogram indices, 3-dimensional–3-dimensional γ-index analysis, and inpatient dose profiles.Results:Dose engine model parameters were tuned to achieve 1.5% agreement with measured point doses. The in-water γ-index passing rates for the 12 patients using 3%/2 mm criteria were 99.5% ± 0.5% compared to Monte Carlo. The average inpatient γ-index analysis passing rate compared to Monte Carlo was 95.8% ± 2.9%. The average difference in mean dose to the clinical target volume between the dose engine and Monte Carlo was −0.4% ± 1.0%. For a typical plan, dose calculation time was 2 minutes on an inexpensive workstation.Conclusions:Following our commissioning process, the analytical dose engine was validated for all treatment sites except for the lung or for calculating dose–volume histogram indices involving point doses or critical structures immediately distal to target volumes. Monte Carlo simulations are recommended for these scenarios.

VIEW-DEPENDENT RENDERING FOR LARGE POLYGONAL MODELS OVER NETWORKS

In this paper we are presenting a novel approach that enables the rendering of large-shared datasets at interactive rates using inexpensive workstations. Our algorithm is based on view-dependent rendering and client-server technology — servers host large datasets and manage the selection of the various levels of detail, while clients receive blocks of update operations which are used to generate the appropriate level of detail in an incremental manner. We assume that servers are capable machines in terms of storage capacity and computational power and clients are inexpensive workstations which have limited 3D rendering capabilities. For optimization purposes we have developed two similar approaches — one for local area networks and the other for wide area networks. For the second approach we have performed several changes to adapt to the limitation of the wide area networks. To avoid network latency we have developed two powerful mechanisms that cache the adapt operation blocks on the clients' side and predict the future view-parameters of clients based on their recent behavior. Our approach dramatically reduces the amount of memory used by each client and the entire computing system since the dataset is stored only once in the local memory of the server. In addition, it decreases the load on the network as a result of the incremental update contributed by view-dependent rendering.

Linear Elastic Waves

Elastic waves propagating in simple media manifest a surprisingly rich collection of phenomena. Although some can't withstand the complexities of Earth's structure, the majority only grow more interesting and more important as remote sensing probes for seismologists studying the planet's interior. To fully mine the information carried to the surface by seismic waves, seismologists must produce accurate models of the waves. Great strides have been made in this regard. Problems that were entirely intractable a decade ago are now routinely solved on inexpensive workstations. The mathematical representations of waves coded into algorithms have grown vastly more sophisticated and are troubled by many fewer approximations, enforced symmetries, and limitations. They are far from straightforward, and seismologists using them need a firm grasp on wave propagation in simple media. Linear Elastic Waves, by applied mathematician John G. Harris, responds to this need.

Distributed shared memory with log based consistency for operations with commutative law or associative law

AbstractWith progress in high‐performance networks, cluster systems with high‐performance and inexpensive work stations or personal computers are attracting much attention. For the cluster systems to become popular, it is necessary that it be easy to develop programs on them. Distributed Shared Memory is the key to achieving this objective. But Distributed Shared Memory cannot achieve high performance for all application programs. In particular, programs which frequently modify the same fields by multiple nodes cannot attain high performance with Distributed Shared Memory. In this paper, we propose Distributed Shared Memory with Log Based Consistency for such application programs, such as aggregation applications in the business application area. In this scheme, consistency is maintained by transferring logs among multiple nodes for operations with the commutative law or associative law. Distributed Shared Memory with Log Based Consistency can achieve much better performance than the traditional Distributed Shared Memory. Its performance is almost the same as that of SMP parallel computers. © 2001 Scripta Technica, Syst Comp Jpn, 32(8): 10–19, 2001

Alternative approach for solving indefinite symmetrical system of equation

In this work, an alternative approach is proposed for solving system of sparse, symmetrical, indefinite equations. The key idea here is first to transform the original indefinite system into a new (modified) system of symmetrical, “definite” equations which can be conveniently used to obtain the “intermediate solution”. This “intermediate” solution is then transformed back into the “original” space to obtain the “original” unknown vector. To validate the formulas developed in our paper, several NASA indefinite system of equations have been solved (ranging from 51 to 15,367 indefinite equations) on inexpensive workstations.

A case study of a distributed high-performance computing system for neurocomputing

We model here a distributed implementation of cross-stopping, a combination of cross-validation and early-stopping techniques, for the selection of the optimal architecture of feed-forward networks. Due to the very large computational demand of the method, we use the RAIN system (Redundant Array of Inexpensive workstations for Neurocomputing) as a target platform for the experiments and show that this kind of system can be effectively used for computational intensive neurocomputing tasks.

Adaptive meshing techniques for viscous flow calculations on mixed element unstructured meshes

An adaptive refinement strategy based on hierarchical element subdivision is formulated and implemented for meshes containing arbitrary mixtures of tetrahedra, hexahedra, prisms and pyramids. Special attention is given to keeping memory overheads as low as possible. This procedure is coupled with an algebraic multigrid flow solver which operates on mixed-element meshes. Inviscid flows as well as viscous flows are computed on adaptively refined tetrahedral, hexahedral, and hybrid meshes. The efficiency of the method is demonstrated by generating an adapted hexahedral mesh containing 3 million vertices on a relatively inexpensive workstation.

Coding for the storage and communication of visualisations of 3D medical data

The transmission of the large store of information contained in 3D medical data sets through limited capacity channels, is a critical procedure in many telemedicine applications. In this paper, techniques are presented for the compression of visualisations of 3D image data for efficient storage and transmission. Methods are first presented for the transmission of the 3D surface of the objects using contour following methods. Alternatively, the visualisation at the receiver may be based on a series of depth maps corresponding to some motion of the object, specified by the medical observer. Depth maps may be transmitted by using depth map motion compensated prediction. Alternatively, a wire-mesh model of the depth map may be formed and transmitted by encoding the motion of its nodes. All these methods are used for the transmission of the 3D image with visualisation carried out at the receiver. Methods are also developed for efficient transmission of the images visualised at the encoder site. These methods allow remote interactive manipulation (rotation, translation, zoom) of the 3D objects, and may be implemented even if the receiver is a relatively simple and inexpensive workstation or a simple monitor. In all above cases, the coding of binocular views of the 3D scene is examined and recommendations are made for the implementation of coders of stereo views of 3D medical data.

Visualization of 3D fields and medical data and using VRML

This paper describes the visualization of 3D medical images and 3D fields on inexpensive workstations or personal computers. VRML 2.0 and Java language are used through the Web interface for manipulating 3D models. 3D data are typically stored and processed on powerful servers accessible by using TCP/IP. Surface rendering of CT and MRI images is done by applying the marching cube algorithm, and then simplifying the obtained triangular meshes and transforming them into VRML format. Various virtual tools may be used for field visualization and object examination and manipulation. The developed concepts and software may also be implemented for visualization of spatial fields in aerodynamics, fluid dynamics simulation, thermodynamics, etc.

Automated flight path planning for virtual endoscopy.

In this paper, a novel technique for rapid and automatic computation of flight paths for guiding virtual endoscopic exploration of three-dimensional medical images is described. While manually planning flight paths is a tedious and time consuming task, our algorithm is automated and fast. Our method for positioning the virtual camera is based on the medial axis transform but is much more computationally efficient. By iteratively correcting a path toward the medial axis, the necessity of evaluating simple point criteria during morphological thinning is eliminated. The virtual camera is also oriented in a stable viewing direction, avoiding sudden twists and turns. We tested our algorithm on volumetric data sets of eight colons, one aorta and one bronchial tree. The algorithm computed the flight paths in several minutes per volume on an inexpensive workstation with minimal computation time added for multiple paths through branching structures (10%-13% per extra path). The results of our algorithm are smooth, centralized paths that aid in the task of navigation in virtual endoscopic exploration of three-dimensional medical images.

Feasibility of ReproSystem in Indonesia

This paper describes Indonesias telecommunications system and discusses the feasibility of adopting the computer-based system MomCare for extending reproductive health care expertise to remote sites. The paper was presented at a pre-congress seminar entitled Learning Without Walls that was held on October 13-14 1995 in Bali Indonesia in conjunction with the XVth Asian and Oceanic Congress of Obstetrics and Gynecology. A small group of decision makers was given the opportunity to update its knowledge of the information revolution and to explore the possible impact on health care education and training. The MomCare system allows experts at referral centers to work with clinicians at remote sites using real-time transfer of video voice images and computer files. Telemedicine transfers allow for video conferencing still or slow motion image transfer electronic mail text dialogue white boarding and file transfer functions. Indonesias communication system includes a local telephone network; a long-distance network linked by fiber optic cables and coaxial cables microwaves submarine cables and satellites; and an international network of over 3770 circuits. Other facilities include the Packet-Switched Data Network based on digital transmission cellular mobile radio services and radio trunking. State-of-the-art systems can transmit data at rates up to 2400 bps and achieve high-quality nonfading links over short distances and non-line-of-sight paths. Indonesia is continuing to expand links increase transmission speeds and use data compression techniques at lower bandwidths in order to facilitate communication exchanges. The Johns Hopkins University has already demonstrated the utility of a system of inexpensive workstations to provide medical care. MomCare is feasible in Indonesia. The only question is the extent and speed with which to transfer the technology.

Distributed Finite-Element Analysis on Network of Workstations—Algorithms

We present distributed algorithms for the finite-element (FE) analysis of large structures on a loosely coupled multicomputer such as a cluster of inexpensive workstations. The focus is on the development of a coarse-grained preconditioned conjugate gradient (PCG) solver based on the element-by-element approach to solve the resulting system of linear equations. To account for the slow communication speed of the ethernet network connecting workstations, techniques such as redundant computations to eliminate communication, efficient data distribution, and algorithmic restructuring to reduce communication frequency have been developed to coarsen task granularity. We present a data distribution and data movement strategy based on set theory. Due to the general nature of the data distribution scheme, the algorithms are versatile and can be applied to the analysis of unstructured FE domains consisting of a combination of various types of elements.

Transmission line modelling (TLM) for the simulation of circuits and fields

The widespread introduction of powerful and inexpensive computer workstations in industry and education has provided a new impetus to the development and application of numerical simulation as an analysis and design tool. Increasingly, larger parts of the design process are simulation based, thus leading to lower costs and right-first-time designs. Moreover, the development of the digital computer has led to a re-examination of how numerical models of physical systems are constructed and operated. Significant advances have been made in model construction and application and this process, spurred by rapid technological development, is set to continue. In this article a modern and efficient simulation technique known as the transmission-line modelling (TLM) method is described and its application to electromagnetics and other areas is illustrated.

Finite element calculation of fields around the end region of a turbine generator test rig

The use of surface impedance elements and the use of volume elements when modeling at test rig using the MEGA package are compared. The test rig is representative of a turbine generator. The work is supported by practical measurements. Experimental results indicate that it is possible to model 3-D fields in large-scale objects containing nonlinear conducting iron using finite elements. Two methods for modeling the iron are compared: conventional volume elements and surface impedance elements. Both methods give similar results, but the latter method is much more economical. Some complex devices are impractical to model on inexpensive workstations without using surface impedance elements. >

Space: A unique environment for process modeling R&D

The convergence of extremely fast and relatively inexpensive computer workstations with powerful simulation software is catalyzing the adoption of process modeling in many metallurgical applications. Utilization of the low-gravity environment of space will speed the technical validation of the methodologies and enable extremely accurate determinations of the many necessary thermophysical properties.

Computer-aided image analysis and graphics in biological microscopy at higher voltages

The range of problems accessible to study using high voltage microscopy encompasses structures that span a wide range of dimensions from Angstroms to tens of microns. Structurally oriented cell biologists and neurobiologists examine cells, tissues, organelles and macromolecules in order to gain insight into cellular and molecular physiology by relating structure to function. Comprehension of these structures can be greatly enhanced by the application of computer aided three dimensional reconstruction and analysis techniques.The past decade has seen an explosive growth in the capabilities for the digital acquisition of images. At the same time, the availability of relatively inexpensive graphics workstations and sophisticated image processing and analysis software packages has made graphics and imaging techniques accessible to most research laboratories. However, the complexity of problems studied in the biological sciences has always presented a challenge to the techniques used in the analysis, and methods based on computer graphics are certainly no exception to this rule.

Hybrid modeling in meteorological applications Part I: Concepts and approaches

Hybrid modeling entails the combination of a numerical weather prediction model and a “symbolic” model. The latter uses symbolic objects, their characterizing attributes and sets of behavioral constrains which prescribe changes in the states of these objects as functions of time, space, and other imposed quantitative or heuristic conditions. Integration of these two modeling components for an on-line, real-time, operational system is feasible only if both the numerical and the symbolic model can be executed in a “distributed” mode, i.e. at a user's location rather than in a central weather service office. This condition entails the design of a numerical model that can run on relatively inexpensive desktop workstations or high-end PCs. Given such a capability, the output from the numerical model can be used to satisfy a number of behavioral constraints of objects (such as “thunderstorm”, “blizzard”, etc.), defined in the symbolic model. These constraints can be embedded “invisibly” as functions of time and pixel location on the computer screen, to be called upon as soon as the respective object is activated, e.g. by placing an “icon” on the screen.

Comparison of numerical calculations with phantom experiments and clinical measurements

Three-dimensional models, while fundamentally desirable in hyperthermia treatment simulation, are only beginning to emerge and may take a number of years to perfect for routine clinical use. Two dimensional calculations, on the other hand, can be efficiently performed on today's inexpensive computer workstations; however, the accuracy of two-dimensional models in the pretreatment planning context is questionable. This paper investigates the ability of a general two-dimensional finite element model to predict power deposition patterns in phantoms and temperature distributions during actual clinical treatments. The experiments and simulations have been performed for an annular phased array (APA) operating at 70 MHz. Comparisons between model predictions and measurements show that quantitative agreement occurs in phantoms containing moderate complexities in heterogeneity, but that only qualitative agreement appears possible in clinical treatments. However, the results suggest that the lack of blood flow information may contribute as much, if not more, to the uncertainties in the clinical predictions than the two-dimensional nature of the model itself.

EB8002: An Educational Board Based on the Z8002 Family

This paper presents a single board microcomputer which, in conjunction with a terminal console, constitutes a powerful but inexpensive work station for the instruction of undergraduate and graduate students in computer engineering. The hardware includes 64 K bytes of RAM, 64 K bytes of EPROM (storing a monitor, an editor, an assembler, and a debugger software), six serial ports, two parallel ports with timer capabilities, and a wire-wrap area. The microcomputer can be connected to a host system that acts simply as a nonvolatile storage and printing center.