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

Preface. Preface to the First Edition. Contributors. Contributors to the First Edition. Chapter 1. Fundamentals of Impedance Spectroscopy (J.Ross Macdonald and William B. Johnson). 1.1. Background, Basic Definitions, and History. 1.1.1 The Importance of Interfaces. 1.1.2 The Basic Impedance Spectroscopy Experiment. 1.1.3 Response to a Small-Signal Stimulus in the Frequency Domain. 1.1.4 Impedance-Related Functions. 1.1.5 Early History. 1.2. Advantages and Limitations. 1.2.1 Differences Between Solid State and Aqueous Electrochemistry. 1.3. Elementary Analysis of Impedance Spectra. 1.3.1 Physical Models for Equivalent Circuit Elements. 1.3.2 Simple RC Circuits. 1.3.3 Analysis of Single Impedance Arcs. 1.4. Selected Applications of IS. Chapter 2. Theory (Ian D. Raistrick, Donald R. Franceschetti, and J. Ross Macdonald). 2.1. The Electrical Analogs of Physical and Chemical Processes. 2.1.1 Introduction. 2.1.2 The Electrical Properties of Bulk Homogeneous Phases. 2.1.2.1 Introduction. 2.1.2.2 Dielectric Relaxation in Materials with a Single Time Constant. 2.1.2.3 Distributions of Relaxation Times. 2.1.2.4 Conductivity and Diffusion in Electrolytes. 2.1.2.5 Conductivity and Diffusion-a Statistical Description. 2.1.2.6 Migration in the Absence of Concentration Gradients. 2.1.2.7 Transport in Disordered Media. 2.1.3 Mass and Charge Transport in the Presence of Concentration Gradients. 2.1.3.1 Diffusion. 2.1.3.2 Mixed Electronic-Ionic Conductors. 2.1.3.3 Concentration Polarization. 2.1.4 Interfaces and Boundary Conditions. 2.1.4.1 Reversible and Irreversible Interfaces. 2.1.4.2 Polarizable Electrodes. 2.1.4.3 Adsorption at the Electrode-Electrolyte Interface. 2.1.4.4 Charge Transfer at the Electrode-Electrolyte Interface. 2.1.5 Grain Boundary Effects. 2.1.6 Current Distribution, Porous and Rough Electrodes- the Effect of Geometry. 2.1.6.1 Current Distribution Problems. 2.1.6.2 Rough and Porous Electrodes. 2.2. Physical and Electrochemical Models. 2.2.1 The Modeling of Electrochemical Systems. 2.2.2 Equivalent Circuits. 2.2.2.1 Unification of Immitance Responses. 2.2.2.2 Distributed Circuit Elements. 2.2.2.3 Ambiguous Circuits. 2.2.3 Modeling Results. 2.2.3.1 Introduction. 2.2.3.2 Supported Situations. 2.2.3.3 Unsupported Situations: Theoretical Models. 2.2.3.4 Unsupported Situations: Equivalent Network Models. 2.2.3.5 Unsupported Situations: Empirical and Semiempirical Models. Chapter 3. Measuring Techniques and Data Analysis. 3.1. Impedance Measurement Techniques (Michael C. H. McKubre and Digby D. Macdonald). 3.1.1 Introduction. 3.1.2 Frequency Domain Methods. 3.1.2.1 Audio Frequency Bridges. 3.1.2.2 Transformer Ratio Arm Bridges. 3.1.2.3 Berberian-Cole Bridge. 3.1.2.4 Considerations of Potentiostatic Control. 3.1.2.5 Oscilloscopic Methods for Direct Measurement. 3.1.2.6 Phase-Sensitive Detection for Direct Measurement. 3.1.2.7 Automated Frequency Response Analysis. 3.1.2.8 Automated Impedance Analyzers. 3.1.2.9 The Use of Kramers-Kronig Transforms. 3.1.2.10 Spectrum Analyzers. 3.1.3 Time Domain Methods. 3.1.3.1 Introduction. 3.1.3.2 Analog-to-Digital (A/D) Conversion. 3.1.3.3 Computer Interfacing. 3.1.3.4 Digital Signal Processing. 3.1.4 Conclusions. 3.2. Commercially Available Impedance Measurement Systems (Brian Sayers). 3.2.1 Electrochemical Impedance Measurement Systems. 3.2.1.1 System Configuration. 3.2.1.2 Why Use a Potentiostat? 3.2.1.3 Measurements Using 2, 3 or 4-Terminal Techniques. 3.2.1.4 Measurement Resolution and Accuracy. 3.2.1.5 Single Sine and FFT Measurement Techniques. 3.2.1.6 Multielectrode Techniques. 3.2.1.7 Effects of Connections and Input Impedance. 3.2.1.8 Verification of Measurement Performance. 3.2.1.9 Floating Measurement Techniques. 3.2.1.10 Multichannel Techniques. 3.2.2 Materials Impedance Measurement Systems. 3.2.2.1 System Configuration. 3.2.2.2 Measurement of Low Impedance Materials. 3.2.2.3 Measurement of High Impedance Materials. 3.2.2.4 Reference Techniques. 3.2.2.5 Normalization Techniques. 3.2.2.6 High Voltage Measurement Techniques. 3.2.2.7 Temperature Control. 3.2.2.8 Sample Holder Considerations. 3.3. Data Analysis (J. Ross Macdonald). 3.3.1 Data Presentation and Adjustment. 3.3.1.1 Previous Approaches. 3.3.1.2 Three-Dimensional Perspective Plotting. 3.3.1.3 Treatment of Anomalies. 3.3.2 Data Analysis Methods. 3.3.2.1 Simple Methods. 3.3.2.2 Complex Nonlinear Least Squares. 3.3.2.3 Weighting. 3.3.2.4 Which Impedance-Related Function to Fit? 3.3.2.5 The Question of "What to Fit" Revisited. 3.3.2.6 Deconvolution Approaches. 3.3.2.7 Examples of CNLS Fitting. 3.3.2.8 Summary and Simple Characterization Example. Chapter 4. Applications of Impedance Spectroscopy. 4.1. Characterization of Materials (N. Bonanos, B. C. H. Steele, and E. P. Butler). 4.1.1 Microstructural Models for Impedance Spectra of Materials. 4.1.1.1 Introduction. 4.1.1.2 Layer Models. 4.1.1.3 Effective Medium Models. 4.1.1.4 Modeling of Composite Electrodes. 4.1.2 Experimental Techniques. 4.1.2.1 Introduction. 4.1.2.2 Measurement Systems. 4.1.2.3 Sample Preparation-Electrodes. 4.1.2.4 Problems Associated With the Measurement of Electrode Properties. 4.1.3 Interpretation of the Impedance Spectra of Ionic Conductors and Interfaces. 4.1.3.1 Introduction. 4.1.3.2 Characterization of Grain Boundaries by IS. 4.1.3.3 Characterization of Two-Phase Dispersions by IS. 4.1.3.4 Impedance Spectra of Unusual Two-phase Systems. 4.1.3.5 Impedance Spectra of Composite Electrodes. 4.1.3.6 Closing Remarks. 4.2. Characterization of the Electrical Response of High Resistivity Ionic and Dielectric Solid Materials by Immittance Spectroscopy (J. Ross Macdonald). 4.2.1 Introduction. 4.2.2 Types of Dispersive Response Models: Strengths and Weaknesses. 4.2.2.1 Overview. 4.2.2.2 Variable-slope Models. 4.2.2.3 Composite Models. 4.2.3 Illustration of Typical Data Fitting Results for an Ionic Conductor. 4.3. Solid State Devices (William B. Johnson and Wayne L. Worrell). 4.3.1 Electrolyte-Insulator-Semiconductor (EIS) Sensors. 4.3.2 Solid Electrolyte Chemical Sensors. 4.3.3 Photoelectrochemical Solar Cells. 4.3.4 Impedance Response of Electrochromic Materials and Devices (Gunnar A. Niklasson, Anna Karin Johsson, and Maria Stromme). 4.3.4.1 Introduction. 4.3.4.2 Materials. 4.3.4.3 Experimental Techniques. 4.3.4.4 Experimental Results on Single Materials. 4.3.4.5 Experimental Results on Electrochromic Devices. 4.3.4.6 Conclusions and Outlook. 4.3.5 Time-Resolved Photocurrent Generation (Albert Goossens). 4.3.5.1 Introduction-Semiconductors. 4.3.5.2 Steady-State Photocurrents. 4.3.5.3 Time-of-Flight. 4.3.5.4 Intensity-Modulated Photocurrent Spectroscopy. 4.3.5.5 Final Remarks. 4.4. Corrosion of Materials (Digby D. Macdonald and Michael C. H. McKubre). 4.4.1 Introduction. 4.4.2 Fundamentals. 4.4.3 Measurement of Corrosion Rate. 4.4.4 Harmonic Analysis. 4.4.5 Kramer-Kronig Transforms. 4.4.6 Corrosion Mechanisms. 4.4.6.1 Active Dissolution. 4.4.6.2 Active-Passive Transition. 4.4.6.3 The Passive State. 4.4.7 Point Defect Model of the Passive State (Digby D. Macdonald). 4.4.7.1 Introduction. 4.4.7.2 Point Defect Model. 4.4.7.3 Electrochemical Impedance Spectroscopy. 4.4.7.4 Bilayer Passive Films. 4.4.8 Equivalent Circuit Analysis (Digby D. Macdonald and Michael C. H. McKubre). 4.4.8.1 Coatings. 4.4.9 Other Impedance Techniques. 4.4.9.1 Electrochemical Hydrodynamic Impedance (EHI). 4.4.9.2 Fracture Transfer Function (FTF). 4.4.9.3 Electrochemical Mechanical Impedance. 4.5. Electrochemical Power Sources. 4.5.1 Special Aspects of Impedance Modeling of Power Sources (Evgenij Barsoukov). 4.5.1.1 Intrinsic Relation Between Impedance Properties and Power Sources Performance. 4.5.1.2 Linear Time-Domain Modeling Based on Impedance Models, Laplace Transform. 4.5.1.3 Expressing Model Parameters in Electrical Terms, Limiting Resistances and Capacitances of Distributed Elements. 4.5.1.4 Discretization of Distributed Elements, Augmenting Equivalent Circuits. 4.5.1.5 Nonlinear Time-Domain Modeling of Power Sources Based on Impedance Models. 4.5.1.6 Special Kinds of Impedance Measurement Possible with Power Sources-Passive Load Excitation and Load Interrupt. 4.5.2 Batteries (Evgenij Barsoukov). 4.5.2.1 Generic Approach to Battery Impedance Modeling. 4.5.2.2 Lead Acid Batteries. 4.5.2.3 Nickel Cadmium Batteries. 4.5.2.4 Nickel Metal-hydride Batteries. 4.5.2.5 Li-ion Batteries. 4.5.3 Impedance Behavior of Electrochemical Supercapacitors and Porous Electrodes (Brian E. Conway). 4.5.3.1 Introduction. 4.5.3.2 The Time Factor in Capacitance Charge or Discharge. 4.5.3.3 Nyquist (or Argand) Complex-Plane Plots for Representation of Impedance Behavior. 4.5.3.4 Bode Plots of Impedance Parameters for Capacitors. 4.5.3.5 Hierarchy of Equivalent Circuits and Representation of Electrochemical Capacitor Behavior. 4.5.3.6 Impedance and Voltammetry Behavior of Brush Electrode Models of Porous Electrodes. 4.5.3.7 Impedance Behavior of Supercapacitors Based on Pseudocapacitance. 4.5.3.8 Deviations of Double-layer Capacitance from Ideal Behavior: Representation by a Constant-phase Element (CPE). 4.5.4 Fuel Cells (Norbert Wagner). 4.5.4.1 Introduction. 4.5.4.2 Alkaline Fuel Cells (AFC). 4.5.4.3 Polymer Electrolyte Fuel Cells (PEFC). 4.5.4.4 Solid Oxide Fuel Cells (SOFC). Appendix. Abbreviations and Definitions of Models. References. Index.

Impedance spectroscopy : theory, experiment, and applications

The calculation of rate coefficients is a discipline of nonlinear science of importance to much of physics, chemistry, engineering, and biology. Fifty years after Kramers' seminal paper on thermally activated barrier crossing, the authors report, extend, and interpret much of our current understanding relating to theories of noise-activated escape, for which many of the notable contributions are originating from the communities both of physics and of physical chemistry. Theoretical as well as numerical approaches are discussed for single- and many-dimensional metastable systems (including fields) in gases and condensed phases. The role of many-dimensional transition-state theory is contrasted with Kramers' reaction-rate theory for moderate-to-strong friction; the authors emphasize the physical situation and the close connection between unimolecular rate theory and Kramers' work for weakly damped systems. The rate theory accounting for memory friction is presented, together with a unifying theoretical approach which covers the whole regime of weak-to-moderate-to-strong friction on the same basis (turnover theory). The peculiarities of noise-activated escape in a variety of physically different metastable potential configurations is elucidated in terms of the mean-first-passage-time technique. Moreover, the role and the complexity of escape in driven systems exhibiting possibly multiple, metastable stationary nonequilibrium states is identified. At lower temperatures, quantum tunneling effects start to dominate the rate mechanism. The early quantum approaches as well as the latest quantum versions of Kramers' theory are discussed, thereby providing a description of dissipative escape events at all temperatures. In addition, an attempt is made to discuss prominent experimental work as it relates to Kramers' reaction-rate theory and to indicate the most important areas for future research in theory and experiment.

Reaction-rate theory: fifty years after Kramers

Glasses can be formed by many routes. In some cases, distinct polyamorphic forms are found. The normal mode of glass formation is cooling of a viscous liquid. Liquid behavior during cooling is classified between "strong" and "fragile," and the three canonical characteristics of relaxing liquids are correlated through the fragility. Strong liquids become fragile liquids on compression. In some cases, such conversions occur during cooling by a weak first-order transition. This behavior can be related to the polymorphism in a glass state through a recent simple modification of the van der Waals model for tetrahedrally bonded liquids. The sudden loss of some liquid degrees of freedom through such first-order transitions is suggestive of the polyamorphic transition between native and denatured hydrated proteins, which can be interpreted as single-chain glass-forming polymers plasticized by water and cross-linked by hydrogen bonds. The onset of a sharp change in d dT( is the Debye-Waller factor and T is temperature) in proteins, which is controversially indentified with the glass transition in liquids, is shown to be general for glass formers and observable in computer simulations of strong and fragile ionic liquids, where it proves to be close to the experimental glass transition temperature. The latter may originate in strong anharmonicity in modes ("bosons"), which permits the system to access multiple minima of its configuration space. These modes, the Kauzmann temperature T(K), and the fragility of the liquid, may thus be connected.

https://science.sciencemag.org/content/sci/267/5206/1924.full.pdf

Formation of glasses from liquids and biopolymers.

This paper describes the compatibility of poly(dimethylsiloxane) (PDMS) with organic solvents; this compatibility is important in considering the potential of PDMS-based microfluidic devices in a number of applications, including that of microreactors for organic reactions. We considered three aspects of compatibility:  the swelling of PDMS in a solvent, the partitioning of solutes between a solvent and PDMS, and the dissolution of PDMS oligomers in a solvent. Of these three parameters that determine the compatibility of PDMS with a solvent, the swelling of PDMS had the greatest influence. Experimental measurements of swelling were correlated with the solubility parameter, δ (cal1/2 cm-3/2), which is based on the cohesive energy densities, c (cal/cm3), of the materials. Solvents that swelled PDMS the least included water, nitromethane, dimethyl sulfoxide, ethylene glycol, perfluorotributylamine, perfluorodecalin, acetonitrile, and propylene carbonate; solvents that swelled PDMS the most were diisopropylam...

Solvent compatibility of poly(dimethylsiloxane)-based microfluidic devices.

Dynamic properties, derived from dielectric relaxation spectra of glass-formers at variable temperature and pressure, are used to characterize and classify any resolved or unresolved secondary relaxation based on their different behaviors. The dynamic properties of the secondary relaxation used include: (1) the pressure and temperature dependences; (2) the separation between its relaxation time τβ and the primary relaxation time τα at any chosen τα; (3) whether τβ is approximately equal to the independent (primitive) relaxation time τ0 of the coupling model; (4) whether both τβ and τ0 have the same pressure and temperature dependences; (5) whether it is responsible for the “excess wing” of the primary relaxation observed in some glass-formers; (6) how the excess wing changes on aging, blending with another miscible glass-former, or increasing the molecular weight of the glass-former; (7) the change of temperature dependence of its dielectric strength Δeβ and τβ across the glass transition temperature Tg; ...

Classification of secondary relaxation in glass-formers based on dynamic properties.

Correlation of polymer segmental chain dynamics with temperature-dependent time-scale shifts

We review the important general dynamic and thermodynamic properties of structural glass-forming substances and classify them into 12 different categories. Our understanding of glass-forming substances is incomplete until all these properties have been explained. The dynamic properties considered include those relating to the high frequency fast relaxation, the Johari–Goldstein β-relaxation, and the slow structural α-relaxation. Practically all the important relaxation and diffusion processes in the time region extending from 10−13 to 106 s have been discussed. We show from experimental data that the properties in different categories bear some relations to each other. Some issues that impede progress of our understanding of the behavior of glass-forming substances are accentuated by formulating them as questions. Answers to these questions by future experimental and theoretical investigations will improve our understanding. Specific suggestions for future research efforts that can provide some answers to these questions are also made. Within the same property in each category, by examining a large number of glass-formers, a pattern of variation is found which correlates with the departure of the structural relaxation of the glass-former from exponential decay or the quantity, (1−β), where β is the fractional exponent in the Kohlrausch expression, exp[−(t/τ)β]. These patterns, as well as their correlations with (1−β), suggest that the salient dynamic properties (or phenomenology) of glass-forming substances are all governed by the non-exponential nature of the structural relaxation, i.e., the quantity (1−β). Therefore, a theory or model capable of relating the structural relaxation time τ to (1−β) has the potential of explaining many of the salient dynamic properties of glass-forming substances.

Dynamic and thermodynamic properties of glass-forming substances

The third edition of this well known textbook discusses the diverse physical states and associated properties of polymeric materials. The contents of the book have been conveniently divided into two general parts, 'Physical States of Polymers' and 'Characterization Techniques'. Written by seven of the leading figures in the polymer science community, this third edition has been thoroughly updated and expanded. As in the second edition, all of the chapters contain general introductory material and comprehensive literature citations designed to give newcomers to the field an appreciation of the subject and how it fits into the general context of polymer science. Containing numerous problem sets and worked examples this third edition provides enough core material for a one semester survey course at the advanced undergraduate or graduate level.

Physical Properties of Polymers

Some time ago, one of us'.' introduced a model of relaxation in complex systems in which the relaxation rate conventionally considered as time independent in simpler systems may become time dependent. Relaxations are manifested by the decay (or saturating growth) of some macroscopic variable such as polarization, stress, electric field, volume, or enthalpy, in appropriate complex systems such as glasses, amorphous polymers, polymer melts, viscous liquids, ionic conductors, and amorphous semicond u c t o r ~ . ~ The mechanism for the macroscopic relaxation can often be traced on the microscopic level, however, to a fundamental relaxation mode with simple relaxation rate W, = 7;' of the primitive species (PS) that is isolated except for its interaction with the heat bath. The PS can be a molecular moiety or a structural unit in structural relaxations; a dipolar group or a mobile charged entity (ionic or electronic) in dielectric relaxations; a polymer chain in polymer melt terminal viscoelastic relaxation; etc. In many complex systems, the fundamental relaxation mode often occurs within the domain of short-range order so that all PSs have essentially the same W,. For example, most glasses, metallic glasses, and viscous liquids have some short-range order. Even in a linear polymer melt, monodispersive samples can be prepared such that all chains have almost the same length (or molecular weight, M ) . Here the PS can be identified as the individual polymer chains. An example of a fundamental mode is the terminal ( p = 1) Rouse mode4 which describes the longest wavelength relaxation of the chain. The simple relaxation rate W, is the same for all chains. It is the nature of complex systems, however, that an individual PS cannot be considered to be completely isolated from other PSs or other neighboring species. Rather, a PS is coupled via molecular, ionic, electronic, or other interactions with its complex environment, an environment that may include other PSs. Relaxation of a PS then involves sequential cooperative adjustments by both its complex environment and the PS itself. For the example of entangled monodisperse linear polymer melts, the terminal Rouse mode of any chain cannot relax without coupling via entanglements with other chains. Such cooperative adjustments act to slow the simple relaxation rate W, at times longer than a time t , = w;' that is characteristic of the cooperative adjustments. The time t , is determined by the complex environment, which has a

K. L. Ngai

Papers

Classification of secondary relaxation in glass-formers based on dynamic properties.

Correlation of polymer segmental chain dynamics with temperature-dependent time-scale shifts

Dynamic and thermodynamic properties of glass-forming substances

Physical Properties of Polymers

Three Coupled Relations for Relaxations in Complex Systemsa