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

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Numerical Heat Transfer And Fluid Flow

Preface Introduction 1. Fluid field equations and modal analysis in rigid containers 2. Linear forced sloshing 3. Viscous damping and sloshing suppression devices 4. Weakly nonlinear lateral sloshing 5. Equivalent mechanical models 6. Parametric sloshing (Faraday's waves) 7. Dynamics of liquid sloshing impact 8. Linear interaction of liquid sloshing with elastic containers 9. Nonlinear interaction under external and parametric excitations 10. Interactions with support structures and tuned sloshing absorbers 11. Dynamics of rotating fluids 12. Microgravity sloshing dynamics Bibliography Index.

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Liquid Sloshing Dynamics

Over the past few years, establishment and adaptation of cell-based assays for drug development and testing has become an important topic in high-throughput screening (HTS). Most new assays are designed to rapidly detect specific cellular effects reflecting action at various targets. However, although more complex than cell-free biochemical test systems, HTS assays using monolayer or suspension cultures still reflect a highly artificial cellular environment and may thus have limited predictive value for the clinical efficacy of a compound. Today's strategies for drug discovery and development, be they hypothesis free or mechanism based, require facile, HTS-amenable test systems that mimic the human tissue environment with increasing accuracy in order to optimize preclinical and preanimal selection of the most active molecules from a large pool of potential effectors, for example, against solid tumors. Indeed, it is recognized that 3-dimensional cell culture systems better reflect the in vivo behavior of most cell types. However, these 3-D test systems have not yet been incorporated into mainstream drug development operations. This article addresses the relevance and potential of 3-D in vitro systems for drug development, with a focus on screening for novel antitumor drugs. Examples of 3-D cell models used in cancer research are given, and the advantages and limitations of these systems of intermediate complexity are discussed in comparison with both 2-D culture and in vivo models. The most commonly used 3-D cell culture systems, multicellular spheroids, are emphasized due to their advantages and potential for rapid development as HTS systems. Thus, multicellular tumor spheroids are an ideal basis for the next step in creating HTS assays, which are predictive of in vivo antitumor efficacy.

The use of 3-D cultures for high-throughput screening: the multicellular spheroid model.

Bioreactors for tissue mass culture: Design, characterization, and recent advances

Preface . Acknowledgements . 1 Equations, General Concepts and Methods of Analysis. 1.1 Pattern Formation and Nonlinear Dynamics. 1.2 The Navier-Stokes Equations. 1.3 Energy Equality and Dissipative Structures. 1.4 Flow Stability, Bifurcations and Transition to Chaos. 1.5 Linear Stability Analysis: Principles and Methods. 1.6 Energy Stability Theory. 1.7 Numerical Integration of the Navier-Stokes Equations. 1.8 Some Universal Properties of Chaotic States. 1.9 The Maxwell Equations. 2 Classical Models, Characteristic Numbers and Scaling Arguments. 2.1 Buoyancy Convection and the Boussinesq Model. 2.2 Convection in Space. 2.3 Marangoni Flow. 2.4 Exact Solutions of the Navier-Stokes Equations for Thermal Problems. 2.5 Conductive, Transition and Boundary-layer Regimes. 3 Examples of Thermal Fluid Convection and Pattern Formation in Nature and Technology. 3.1 Technological Processes: Small-scale Laboratory and Industrial Setups. 3.2 Examples of Thermal Fluid Convection and Pattern Formation at the Mesoscale. 3.3 Planetary Structure and Dynamics: Convective Phenomena. 3.4 Atmospheric and Oceanic Phenomena. 4 Thermogravitational Convection: The Rayleigh-Benard Problem. 4.1 Nonconfined Fluid Layers and Ideal Straight Rolls. 4.2 The Busse Balloon. 4.3 Some Considerations About the Role of Dislocation Dynamics. 4.4 Tertiary and Quaternary Modes of Convection. 4.5 Spoke Pattern Convection. 4.6 Spiral Defect Chaos, Hexagons and Squares. 4.7 Convection with Lateral Walls. 4.8 Two-dimensional Models. 4.9 Three-dimensional Parallelepipedic Enclosures: Classification of Solutions and Possible Symmetries. 4.10 The Circular Cylindrical Problem. 4.11 Spirals: Genesis, Properties and Dynamics. 4.12 From Spirals to SDC: The Extensive Chaos Problem. 4.13 Three-dimensional Convection in a Spherical Shell. 5 The Dynamics of Thermal Plumes and Related Regimes of Motion. 5.1 Introduction. 5.2 Free Plume Regimes. 5.3 The Flywheel Mechanism: The 'Wind' of Turbulence. 5.4 Multiplume Configurations Originated from Discrete Sources of Buoyancy. 6 Systems Heated from the Side: The Hadley Flow. 6.1 The Infinite Horizontal Layer. 6.2 Two-dimensional Horizontal Enclosures. 6.3 The Infinite Vertical Layer: Cats-eye Patterns and Temperature Waves. 6.4 Three-dimensional Parallelepipedic Enclosures. 6.5 Cylindrical Geometries under Various Heating Conditions. 7 Thermogravitational Convection in Inclined Systems. 7.1 Inclined Layer Convection. 7.2 Inclined Side-heated Slots. 8 Thermovibrational Convection. 8.1 Equations and Relevant Parameters. 8.2 Fields Decomposition. 8.3 The TFD Distortions. 8.4 High Frequencies and the Thermovibrational Theory. 8.5 States of Quasi-equilibrium and Related Stability. 8.6 Primary and Secondary Patterns of Symmetry. 8.7 Medium and Low Frequencies: Possible Regimes and Flow Patterns. 9 Marangoni-Benard Convection. 9.1 Introduction. 9.2 High Prandtl Number Liquids: Patterns with Hexagons, Squares and Triangles. 9.3 Liquid Metals: Inverted Hexagons and High-order Solutions. 9.4 Effects of Lateral Confinement. 9.5 Temperature Gradient Inclination. 10 Thermocapillary Convection. 10.1 Basic Features of Steady Marangoni Convection. 10.2 Stationary Multicellular Flow and Hydrothermal Waves. 10.3 Annular Configurations. 10.4 The Liquid Bridge. 11 Mixed Buoyancy-Marangoni Convection. 11.1 The Canonical Problem: The Infinite Horizontal Layer. 11.2 Finite-sized Systems Filled with Liquid Metals. 11.3 Typical Terrestrial Laboratory Experiments with Transparent Liquids. 11.4 The Rectangular Liquid Layer. 11.5 Effects Originating from the Walls. 11.6 The Open Vertical Cavity. 11.7 The Annular Pool. 11.8 The Liquid Bridge on the Ground. 12 Hybrid Regimes with Vibrations. 12.1 RB Convection with Vertical Shaking. 12.2 Complex Order, Quasi-periodic Crystals and Superlattices. 12.3 RB Convection with Horizontal or Oblique Shaking. 12.4 Laterally Heated Systems and Parametric Resonances. 12.5 Control of Thermogravitational Convection. 12.6 Mixed Marangoni-Thermovibrational Convection. 12.7 Modulation of Marangoni-Benard Convection. 13 Flow Control by Magnetic Fields. 13.1 Static and Uniform Magnetic Fields. 13.2 Historical Developments and Current Status. 13.3 Rotating Magnetic Fields. 13.4 Gradients of Magnetic Fields and Virtual Microgravity. References . Index .

Thermal Convection: Patterns, Evolution and Stability

This analysis deals with advances in tissue-engineering models and computational methods as well as with novel results on the relative importance of "controlling forces" in the growth of organic constructs. Specifically, attention is focused on the rotary culture system, because this technique has proven to be the most practical solution for providing a suitable culture environment supporting three-dimensional tissue assemblies. From a numerical point of view, the growing biological specimen gives rise to a moving boundary problem. A "volume-of-fraction" method is specifically and carefully developed according to the complex properties and mechanisms of organic tissue growth and, in particular, taking into account the sensitivity of the construct/liquid interface to the effect of the fluid-dynamic shear stress (it induces changes in tissue metabolism and function that elicit a physiological response from the biological cells). The present study uses available data to introduce a set of growth models. The surface conditions are coupled to the transfer of mass and momentum at the specimen/culture-medium interface and lead to the introduction of a group of differential equations for the nutrient concentration around the sample and for the evolution of tissue mass displacement. The models are then used to show how the proposed surface kinetic laws can predict (through sophisticated numerical simulations) many of the known characteristics of biological tissues grown using rotating-wall perfused vessel bioreactors. This procedure provides a validation of the models and associated numerical method and also gives insight into the mechanisms of the phenomena. The interplay between the increasing size of the tissue and the structure of the convective field is investigated. It is shown that this interaction is essential in determining the time evolution of the tissue shape. The size of the growing specimen plays a critical role with regard to the intensity of convection and the related shear stresses. Convective effects, in turn, are found to impact growth rates, tissue size, and morphology, as well as the mechanisms driving growth. The method exhibits novel capabilities to predict and elucidate experimental observations and to identify cause-and-effect relationships.

Organic tissues in rotating bioreactors: fluid-mechanical aspects, dynamic growth models, and morphological evolution.

Flotation of liquid droplets on pool surfaces, in the presence of temperature differences, is studied experimentally and numerically. Coalescence or sinking of the droplet is prevented by the thermal Marangoni motion, owing to the surface tension imbalance at the pool surface. The mechanism is the same as that investigated in previous works on coalescence and wetting prevention in the presence of temperature differences. If the droplet is colder than the liquid surface, the flow is directed radially towards the drop; this radial flow field drags the ambient air under the drop, thus creating an air film and avoiding a direct contact between the droplet and the pool molecules.The surface velocities are measured visually with a CCD camera to image the motion of tracers floating on the pool surface; the surface temperature distributions along the pool and the droplet surfaces are measured by an infrared thermocamera. The experimental results are correlated by numerical results obtained under the assumption of spherical drop and axisymmetric flow regime. Different liquids are considered and the influence of evaporation is discussed, showing a good agreement between the experiments and the numerical simulations.

Marcello Lappa

Papers

Thermal Convection: Patterns, Evolution and Stability

Organic tissues in rotating bioreactors: fluid-mechanical aspects, dynamic growth models, and morphological evolution.

Marangoni flotation of liquid droplets

Three-dimensional numerical simulation of Marangoni instabilities in non-cylindrical liquid bridges in microgravity

Rotating Thermal Flows in Natural and Industrial Processes