Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

THE DESIGN AND ANALYSIS OF EXPERIMENTS. By Oscar Kempthorne. New York, John Wiley and Sons, Inc., 1952. 631 pp. $8.50. This book by a teacher of statistics (as well as a consultant for \"experimenters\") is a comprehensive study of the philosophical background for the statistical design of experiment. It is necessary to have some facility with algebraic notation and manipulation to be able to use the volume intelligently. The problems are presented from the theoretical point of view, without such practical examples as would be helpful for those not acquainted with mathematics. The mathematical justification for the techniques is given. As a somewhat advanced treatment of the design and analysis of experiments, this volume will be interesting and helpful for many who approach statistics theoretically as well as practically. With emphasis on the \"why,\" and with description given broadly, the author relates the subject matter to the general theory of statistics and to the general problem of experimental inference. MARGARET J. ROBERTSON

The Design and Analysis of Experiments

Summary Background Since December, 2019, Wuhan, China, has experienced an outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Epidemiological and clinical characteristics of patients with COVID-19 have been reported but risk factors for mortality and a detailed clinical course of illness, including viral shedding, have not been well described. Methods In this retrospective, multicentre cohort study, we included all adult inpatients (≥18 years old) with laboratory-confirmed COVID-19 from Jinyintan Hospital and Wuhan Pulmonary Hospital (Wuhan, China) who had been discharged or had died by Jan 31, 2020. Demographic, clinical, treatment, and laboratory data, including serial samples for viral RNA detection, were extracted from electronic medical records and compared between survivors and non-survivors. We used univariable and multivariable logistic regression methods to explore the risk factors associated with in-hospital death. Findings 191 patients (135 from Jinyintan Hospital and 56 from Wuhan Pulmonary Hospital) were included in this study, of whom 137 were discharged and 54 died in hospital. 91 (48%) patients had a comorbidity, with hypertension being the most common (58 [30%] patients), followed by diabetes (36 [19%] patients) and coronary heart disease (15 [8%] patients). Multivariable regression showed increasing odds of in-hospital death associated with older age (odds ratio 1·10, 95% CI 1·03–1·17, per year increase; p=0·0043), higher Sequential Organ Failure Assessment (SOFA) score (5·65, 2·61–12·23; p Interpretation The potential risk factors of older age, high SOFA score, and d-dimer greater than 1 μg/mL could help clinicians to identify patients with poor prognosis at an early stage. Prolonged viral shedding provides the rationale for a strategy of isolation of infected patients and optimal antiviral interventions in the future. Funding Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences; National Science Grant for Distinguished Young Scholars; National Key Research and Development Program of China; The Beijing Science and Technology Project; and Major Projects of National Science and Technology on New Drug Creation and Development.

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study

In the choice of an estimator for the spectrum of a stationary time series from a finite sample of the process, the problems of bias control and consistency, or "smoothing," are dominant. In this paper we present a new method based on a "local" eigenexpansion to estimate the spectrum in terms of the solution of an integral equation. Computationally this method is equivalent to using the weishted average of a series of direct-spectrum estimates based on orthogonal data windows (discrete prolate spheroidal sequences) to treat both the bias and smoothing problems. Some of the attractive features of this estimate are: there are no arbitrary windows; it is a small sample theory; it is consistent; it provides an analysis-of-variance test for line components; and it has high resolution. We also show relations of this estimate to maximum-likelihood estimates, show that the estimation capacity of the estimate is high, and show applications to coherence and polyspectrum estimates.

Spectrum estimation and harmonic analysis

Preface 1 Introduction 1.1 Compression Techniques 1.1.1 Lossless Compression 1.1.2 Lossy Compression 1.1.3 Measures of Performance 1.2 Modeling and Coding 1.3 Organization of This Book 1.4 Summary 1.5 Projects and Problems 2 Mathematical Preliminaries 2.1 Overview 2.2 A Brief Introduction to Information Theory 2.3 Models 2.3.1 Physical Models 2.3.2 Probability Models 2.3.3. Markov Models 2.3.4 Summary 2.5 Projects and Problems 3 Huffman Coding 3.1 Overview 3.2 "Good" Codes 3.3. The Huffman Coding Algorithm 3.3.1 Minimum Variance Huffman Codes 3.3.2 Length of Huffman Codes 3.3.3 Extended Huffman Codes 3.4 Nonbinary Huffman Codes 3.5 Adaptive Huffman Coding 3.5.1 Update Procedure 3.5.2 Encoding Procedure 3.5.3 Decoding Procedure 3.6 Applications of Huffman Coding 3.6.1 Lossless Image Compression 3.6.2 Text Compression 3.6.3 Audio Compression 3.7 Summary 3.8 Projects and Problems 4 Arithmetic Coding 4.1 Overview 4.2 Introduction 4.3 Coding a Sequence 4.3.1 Generating a Tag 4.3.2 Deciphering the Tag 4.4 Generating a Binary Code 4.4.1 Uniqueness and Efficiency of the Arithmetic Code 4.4.2 Algorithm Implementation 4.4.3 Integer Implementation 4.5 Comparison of Huffman and Arithmetic Coding 4.6 Applications 4.6.1 Bi-Level Image Compression-The JBIG Standard 4.6.2 Image Compression 4.7 Summary 4.8 Projects and Problems 5 Dictionary Techniques 5.1 Overview 5.2 Introduction 5.3 Static Dictionary 5.3.1 Diagram Coding 5.4 Adaptive Dictionary 5.4.1 The LZ77 Approach 5.4.2 The LZ78 Approach 5.5 Applications 5.5.1 File Compression-UNIX COMPRESS 5.5.2 Image Compression-the Graphics Interchange Format (GIF) 5.5.3 Compression over Modems-V.42 bis 5.6 Summary 5.7 Projects and Problems 6 Lossless Image Compression 6.1 Overview 6.2 Introduction 6.3 Facsimile Encoding 6.3.1 Run-Length Coding 6.3.2 CCITT Group 3 and 4-Recommendations T.4 and T.6 6.3.3 Comparison of MH, MR, MMR, and JBIG 6.4 Progressive Image Transmission 6.5 Other Image Compression Approaches 6.5.1 Linear Prediction Models 6.5.2 Context Models 6.5.3 Multiresolution Models 6.5.4 Modeling Prediction Errors 6.6 Summary 6.7 Projects and Problems 7 Mathematical Preliminaries 7.1 Overview 7.2 Introduction 7.3 Distortion Criteria 7.3.1 The Human Visual System 7.3.2 Auditory Perception 7.4 Information Theory Revisted 7.4.1 Conditional Entropy 7.4.2 Average Mutual Information 7.4.3 Differential Entropy 7.5 Rate Distortion Theory 7.6 Models 7.6.1 Probability Models 7.6.2 Linear System Models 7.6.3 Physical Models 7.7 Summary 7.8 Projects and Problems 8 Scalar Quantization 8.1 Overview 8.2 Introduction 8.3 The Quantization Problem 8.4 Uniform Quantizer 8.5 Adaptive Quantization 8.5.1 Forward Adaptive Quantization 8.5.2 Backward Adaptive Quantization 8.6 Nonuniform Quantization 8.6.1 pdf-Optimized Quantization 8.6.2 Companded Quantization 8.7 Entropy-Coded Quantization 8.7.1 Entropy Coding of Lloyd-Max Quantizer Outputs 8.7.2 Entropy-Constrained Quantization 8.7.3 High-Rate Optimum Quantization 8.8 Summary 8.9 Projects and Problems 9 Vector Quantization 9.1 Overview 9.2 Introduction 9.3 Advantages of Vector Quantization over Scalar Quantization 9.4 The Linde-Buzo-Gray Algorithm 9.4.1 Initializing the LBG Algorithm 9.4.2 The Empty Cell Problem 9.4.3 Use of LBG for Image Compression 9.5 Tree-Structured Vector Quantizers 9.5.1 Design of Tree-Structured Vector Quantizers 9.6 Structured Vector Quantizers 9.6.1 Pyramid Vector Quantization 9.6.2 Polar and Spherical Vector Quantizers 9.6.3 Lattice Vector Quantizers 9.7 Variations on the Theme 9.7.1 Gain-Shape Vector Quantization 9.7.2 Mean-Removed Vector Quantization 9.7.3 Classified Vector Quantization 9.7.4 Multistage Vector Quantization 9.7.5 Adaptive Vector Quantization 9.8 Summary 9.9 Projects and Problems 10 Differential Encoding 10.1 Overview 10.2 Introduction 10.3 The Basic Algorithm 10.4 Prediction in DPCM 10.5 Adaptive DPCM (ADPCM) 10.5.1 Adaptive Quantization in DPCM 10.5.2 Adaptive Prediction in DPCM 10.6 Delta Modulation 10.6.1 Constant Factor Adaptive Delta Modulation (CFDM) 10.6.2 Continuously Variable Slope Delta Modulation 10.7 Speech Coding 10.7.1 G.726 10.8 Summary 10.9 Projects and Problems 11 Subband Coding 11.1 Overview 11.2 Introduction 11.3 The Frequency Domain and Filtering 11.3.1 Filters 11.4 The Basic Subband Coding Algorithm 11.4.1 Bit Allocation 11.5 Application to Speech Coding-G.722 11.6 Application to Audio Coding-MPEG Audio 11.7 Application to Image Compression 11.7.1 Decomposing an Image 11.7.2 Coding the Subbands 11.8 Wavelets 11.8.1 Families of Wavelets 11.8.2 Wavelets and Image Compression 11.9 Summary 11.10 Projects and Problems 12 Transform Coding 12.1 Overview 12.2 Introduction 12.3 The Transform 12.4 Transforms of Interest 12.4.1 Karhunen-Loeve Transform 12.4.2 Discrete Cosine Transform 12.4.3 Discrete Sine Transform 12.4.4 Discrete Walsh-Hadamard Transform 12.5 Quantization and Coding of Transform Coefficients 12.6 Application to Image Compression-JPEG 12.6.1 The Transform 12.6.2 Quantization 12.6.3 Coding 12.7 Application to Audio Compression 12.8 Summary 12.9 Projects and Problems 13 Analysis/Synthesis Schemes 13.1 Overview 13.2 Introduction 13.3 Speech Compression 13.3.1 The Channel Vocoder 13.3.2 The Linear Predictive Coder (Gov.Std.LPC-10) 13.3.3 Code Excited Linear Prediction (CELP) 13.3.4 Sinusoidal Coders 13.4 Image Compression 13.4.1 Fractal Compression 13.5 Summary 13.6 Projects and Problems 14 Video Compression 14.1 Overview 14.2 Introduction 14.3 Motion Compensation 14.4 Video Signal Representation 14.5 Algorithms for Videoconferencing and Videophones 14.5.1 ITU_T Recommendation H.261 14.5.2 Model-Based Coding 14.6 Asymmetric Applications 14.6.1 The MPEG Video Standard 14.7 Packet Video 14.7.1 ATM Networks 14.7.2 Compression Issues in ATM Networks 14.7.3 Compression Algorithms for Packet Video 14.8 Summary 14.9 Projects and Problems A Probability and Random Processes A.1 Probability A.2 Random Variables A.3 Distribution Functions A.4 Expectation A.5 Types of Distribution A.6 Stochastic Process A.7 Projects and Problems B A Brief Review of Matrix Concepts B.1 A Matrix B.2 Matrix Operations C Codes for Facsimile Encoding D The Root Lattices Bibliography Index

Introduction to data compression

By use of an interpolated fast-Fourier-transform (FFT) algorithms are developed for multiparameter measurements upon periodic signals. Eight pertinent measurements, such as fundamental frequency, phase, and amplitude, are made with enhanced accuracy compared to existing algorithms, including tapered-window-FFT algorithms. For the more general case of nonharmonic multitone signals also the method is shown to yield exact amplitudes and phases if the tone frequencies are known beforehand. These measurements are useful in a variety of applications ranging from analog testing of printed-circuit boards to measurement of Doppler signals in radar detection.

High-Accuracy Analog Measurements via Interpolated FFT

Advanced Machining Processes

A technique is proposed for the detection of tumors in digital mammography. Detection is performed in two steps: segmentation and classification. In segmentation, regions of interest are first extracted from the images by adaptive thresholding. A further reliable segmentation is achieved by a modified Markov random field (MRF) model-based method. In classification, the MRF segmented regions are classified into suspicious and normal by a fuzzy binary decision tree based on a series of radiographic, density-related features. A set of normal (50) and abnormal (45) screen/film mammograms were tested. The latter contained 48 biopsy proven, malignant masses of various types and subtlety. The detection accuracy of the algorithm was evaluated by means of a free response receiver operating characteristic curve which shows the relationship between the detection of true positive masses and the number of false positive alarms per image. The results indicated that a 90% sensitivity can be achieved in the detection of different types of masses at the expense of two falsely detected signals per image. The algorithm was notably successful in the detection of minimal cancers manifested by masses /spl les/10 mm in size. For the 16 such cases in the authors' dataset, a 94% sensitivity was observed with 1.5 false alarms per image. An extensive study of the effects of the algorithm's parameters on its sensitivity and specificity was also performed in order to optimize the method for a clinical, observer performance study. >

Markov random field for tumor detection in digital mammography

A new precision finishing process for complex internal geometries using smart magnetorheological polishing fluid is developed. Magnetorheological abrasive flow finishing (MRAFF) process provides better control over rheological properties of abrasive laden magnetorheological finishing medium. Magnetorheological (MR) polishing fluid comprises of carbonyl iron powder and silicon carbide abrasives dispersed in the viscoplastic base of grease and mineral oil; it exhibits change in rheological behaviour in presence of external magnetic field. This smart behaviour of MR-polishing fluid is utilized to precisely control the finishing forces, hence final surface finish. A hydraulically powered experimental setup is designed to study the process characteristics and performance. The setup consists of two MR-polishing fluid cylinders, two hydraulic actuators, electromagnet, fixture and supporting frame. Experiments were conducted on stainless steel workpieces at different magnetic field strength to observe its effect on final surface finish. No measurable change in surface roughness is observed after finishing at zero magnetic field. However, for the same number of cycles the roughness reduces gradually with the increase of magnetic field. This validates the role of rheological behaviour of magnetorheological polishing fluid in performing finishing action.

Design and development of the magnetorheological abrasive flow finishing (MRAFF) process

The high temperature gradients generated at the gap during electrical discharge machining (EDM) result in large localized thermal stresses in a small heat-affected zone. These thermal stresses can lead to micro-cracks, decrease in strength and fatigue life and possibly catastrophic failure. A finite element model has been developed to estimate the temperature field and thermal stresses due to Gaussian distributed heat flux of a spark during EDM. First, the developed code calculates the temperature in the workpiece and then the thermal stress field is estimated using this temperature field. The effects of various process variables (current and duty cycle) on temperature distribution and thermal stress distribution have been reported. The results of the analysis show high temperature gradient zones and the regions of large stresses where, sometimes, they exceed the material yield strength.

Vijay Kumar Jain

Papers

High-Accuracy Analog Measurements via Interpolated FFT

Advanced Machining Processes

Markov random field for tumor detection in digital mammography

Design and development of the magnetorheological abrasive flow finishing (MRAFF) process

Thermal stresses due to electrical discharge machining