MODERN CHEMISTRY AND ITS WONDERS: A POPULAR ACCOUNT OF RECENT ADVANCES IN CHEMICAL SCIENCE

By CHARLES CLARK

CONTENTS A REVIEW OF MULTISCALE ANALYSIS: EXAMPLES FROM SYSTEMS BIOLOGY, MATERIALS ENGINEERING, AND OTHER FLUID–SURFACE INTERACTING SYSTEMS I INTRODUCTION II DETERMINISTIC, CONTINUUM MODELS A HIERARCHY OF MODELS B SOLVING DETERMINISTIC, CONTINUUM DIFFERENTIAL EQUATION MODELS: TECHNIQUES AND STATUS III OVERVIEW OF DISCRETE, PARTICLE MODELS A HIERARCHY OF STOCHASTIC MODELS FOR WELL-MIXED, CHEMICALLY REACTING SYSTEMS B SOLVING MASTER EQUATIONS STOCHASTICALLY: MONTE CARLO METHODS IV CLASSI?CATION OF MULTISCALE SIMULATION APPROACHES V HYBRID MULTISCALE SIMULATION A ONION-TYPE HYBRID MULTISCALE SIMULATIONS AND ALGORITHMS B APPLICATION OF ONION-TYPE HYBRID MULTISCALE SIMULATION TO GROWTH OF MATERIALS C APPLICATIONS OF ONION-TYPE HYBRID MULTISCALE SIMULATION TO OTHER AREAS D MULTIGRID-TYPE HYBRID MULTISCALE SIMULATIONS E AN EXAMPLE OF MULTIGRID-TYPE HYBRID MULTISCALE SIMULATION FOR GROWTH UNDER LARGE LENGTH SCALE GRADIENTS F CHALLENGES IN HYBRID MULTISCALE SIMULATIONS VI COARSE GRAINING OF STOCHASTIC MODELS A TEMPORAL UPSCALING OF KMC SIMULATION IN WELL-MIXED SYSTEMS B SPATIAL UPSCALING OF DISTRIBUTED (LATTICE) KMC SIMULATION C SPATIOTEMPORAL ACCELERATION OF DISTRIBUTED (LATTICE) KMC SIMULATION VII MULTISCALE, STOCHASTIC MODELING OF BIOLOGICAL NETWORKS A SPATIALLY WELL-MIXED SYSTEMS B SPATIALLY DISTRIBUTED SYSTEMS VIII SYSTEMS TASKS A SENSITIVITY AND IDENTI?ABILITY ANALYSES B PARAMETER ESTIMATION FROM EXPERIMENTAL DATA AND FINER SCALE MODELS C MODEL REDUCTION AND CONTROL D BIFURCATION IX OUTLOOK ACKNOWLEDGMENTS REFERENCES QUANTIFYING PHYSICS AND CHEMISTRY AT MULTIPLE LENGTH-SCALES USING MAGNETIC RESONANCE TECHNIQUES I INTRODUCTION II PRINCIPLES OF MR MEASUREMENTS A SPATIALLY UNRESOLVED AND SPATIALLY RESOLVED EXPERIMENTS B NUCLEAR SPIN RELAXATION TIMES C TRANSPORT D TEMPERATURE E THE K-SPACE RASTER F FAST DATA ACQUISITION III RECENT DEVELOPMENTS IN MR AS A TOOL IN CHEMICAL ENGINEERING RESEARCH A ‘‘ULTRA-FAST’’ IMAGING OF VELOCITY FIELDS B MULTIPLE IMAGES FROM A SINGLE EXCITATION C IMAGING ROTATING SYSTEMS D ‘‘ULTRA-FAST’’ DIFFUSION MEASUREMENT E GAS-PHASE MR IV REACTION ENGINEERING: FROM CATALYST TO REACTOR A MR SPECTROSCOPY OF CATALYSTS B MICRO-IMAGING AND MOLECULAR DIFFUSION STUDIES OF FORMED CATALYST PELLETS C SINGLE-PHASE FLOW IN FIXED-BED REACTORS D MEASURING CHEMICAL COMPOSITION AND MASS TRANSFER IN FIXED-BED REACTORS: IN SITU STUDIES OF REACTIONS E TWO-PHASE FLOW IN FIXED-BED REACTORS F HYDRODYNAMIC TRANSITIONS IN FIXED-BED REACTORS V FUTURE PROSPECTS MODELING OF TRANSPORT AND TRANSFORMATION PROCESSES IN POROUS AND MULTIPHASE BODIES I INTRODUCTION II METHODOLOGY A REPRESENTATION OF MULTIPHASE MEDIA B STRUCTURE ACQUISITION C MORPHOLOGICAL CHARACTERIZATION D DIGITAL RECONSTRUCTION OF MULTIPHASE MEDIA E CALCULATION OF EFFECTIVE PROPERTIES F EFFECTIVE-SCALE TRANSPORT MODELS III TRANSFORMATIONS A SKELETONIZATION B PHASE TRANSITIONS C CHEMICALLY REACTIVE SYSTEMS IV APPLICATIONS A MULTI-SCALE RECONSTRUCTION OF A CATALYST PELLET B RECONSTRUCTION OF CLOSED-CELL POLYMER FOAM STRUCTURE C POLYMER PARTICLE MORPHOGENESIS D GRANULATION AND DISSOLUTION E SIMULATION OF CO OXIDATION ON RECONSTRUCTED CATALYTIC WASHCOAT V OUTLOOKS A BIOLOGICAL SYSTEMS B MATERIALS DESIGN VI CONCLUSIONS SPATIALLY AVERAGED MULTI-SCALE MODELS FOR CHEMICAL REACTORS I INTRODUCTION A A BRIEF HISTORY OF CHEMICAL REACTOR MODELS B MULTI-SCALE NATURE OF HOMOGENEOUS AND CATALYTIC REACTORS C DIFFERENT APPROACHES TO MULTI-SCALE AVERAGING OR DIMENSION REDUCTION II SPATIAL AVERAGING OF CONVECTION–DIFFUSION–REACTION MODELS USING THE L–S METHOD III SPATIALLY AVERAGED MODELS FOR DESCRIBING DISPERSION EFFECTS IN TUBES AND PACKED BEDS A A HYPERBOLIC-AVERAGED MODEL FOR DESCRIBING DISPERSION EFFECTS IN TUBES/CAPILLARIES B MULTI-MODE HYPERBOLIC AVERAGED MODELS FOR DESCRIBING DISPERSION EFFECTS IN CHROMATOGRAPHS C A HYPERBOLIC MODEL FOR DESCRIBING DISPERSION EFFECTS IN MONOLITHS WITH DIFFUSION INTO THE SOLID PHASE IV SPATIALLY AVERAGED MULTI-MODE (MULTI-SCALE) MODELS FOR HOMOGENEOUS REACTORS A ISOTHERMAL TUBULAR REACTORS B LOOP AND RECYCLE REACTORS C TANK REACTORS (CSTRS) D NON-ISOTHERMAL REACTOR MODELS E MULTIPLE REACTIONS F EXAMPLES ILLUSTRATING USE OF MULTI-MODE HOMOGENEOUS REACTOR MODELS V SPATIALLY AVERAGED MULTI-MODE (MULTI-SCALE) MODELS FOR CATALYTIC REACTORS A WALL-CATALYZED REACTIONS B COUPLED HOMOGENEOUS AND WALL-CATALYZED REACTIONS C NON-ISOTHERMAL REACTOR MODELS D EXAMPLES ILLUSTRATING USE OF MULTI-MODE CATALYTIC REACTOR MODELS VI ACCURACY, CONVERGENCE AND REGION OF VALIDITY OF MULTI-MODE/MULTI-SCALE AVERAGED MODELS A ACCURACY B CONVERGENCE C REGULARIZATION OF THE LOCAL EQUATION VII SUMMARY, CONCLUSIONS, AND RECOMMENDATIONS FOR FUTURE WORK A REVIEW OF MULTISCALE ANALYSIS: EXAMPLES FROM SYSTEMS BIOLOGY, MATERIALS ENGINEERING, AND OTHER FLUID–SURFACE INTERACTING SYSTEMS I INTRODUCTION B SOLVING DETERMINISTIC, CONTINUUM DIFFERENTIAL EQUA- TION MODELS: TECHNIQUES AND STATUS A ONION-TYPE HYBRID MULTISCALE SIMULATIONS AND AL- GORITHMS B APPLICATION OF ONION-TYPE HYBRID MULTISCALE SIMU- LATION TO GROWTH OF MATERIALS C APPLICATIONS OF ONION-TYPE HYBRID MULTISCALE SIM- ULATION TO OTHER AREAS A TEMPORAL UPSCALING OF KMC SIMULATION IN WELL- MIXED SYSTEMS ABSTRACT MULTISCALE SIMULATION IS AN EMERGING SCIENTIFIC ?ELD THAT SPANS MANY DISCIPLINES, INCLUDING PHYSICS, CHEMISTRY, MATHEMATICS, STATISTICS, CHEMICAL ENGINEERING, MECHANICAL ENGINEERING, AND MATERIALS SCIENCE THIS REVIEW PAPER ?RST DE?NES THIS NEW SCIENTIFIC ?ELD AND OUTLINES ITS OBJECTIVES AN OVERVIEW OF DETERMINISTIC, CONTINUUM MODELS AND DISCRETE, PARTICLE MODELS IS THEN GIVEN AMONG DISCRETE, PARTICLE MODELS, EMPHASIS IS PLACED ON MONTE CARLO STOCHASTIC SIMULATION METHODS IN WELL-MIXED AND SPATIALLY DISTRIBUTED SYSTEMS NEXT, A CLASSI?CATION OF MULTISCALE METHODS IS CARRIED OUT BASED ON SEPARATION OF LENGTH AND TIME SCALES AND THE COMPUTATIONAL AND MATHEMATICAL APPROACH TAKEN BROADLY SPEAKING, HYBRID SIMULATION AND COARSE GRAINING OR MESOSCOPIC MODELING ARE IDENTI?ED AS TWO GENERAL AND COMPLEMENTARY APPROACHES OF MULTISCALE MODELING THE FORMER IS FURTHER CLASSI?ED INTO ONION- AND MULTIGRID-TYPE SIMULATION DEPENDING ON LENGTH SCALES AND THE PRESENCE OR NOT OF GRADIENTS SEVERAL APPROACHES, SUCH AS THE NET EVENT, THE PROBABILITY WEIGHTED, THE POISSON AND BINOMIAL T-LEAP, AND THE HYBRID, ARE DISCUSSED FOR ACCELERATION OF STOCHASTIC SIM- ULATION IN ORDER TO DEMONSTRATE THE UNIFYING PRINCIPLES OF MULTISCALE SIMULATION, EXAMPLES FROM DIFFERENT AREAS ARE DISCUSSED, INCLUDING SYSTEMS BIOLOGY, MATERIALS GROWTH AND OTHER REACTING SYSTEMS, ?UIDS, AND STATISTICAL MECHANICS WHILE THE CLASSI?CATION IS GENERAL AND EXAMPLES FROM OTHER SCALES AND TOOLS ARE TOUCHED UPON, IN THIS REVIEW EMPHASIS IS PLACED ON STOCHASTIC MODELS, THEIR COARSE GRAINING, AND THEIR INTEGRATION WITH CON- TINUUM DETERMINISTIC MODELS, I E , ON THE COUPLING OF MESOSCOPIC AND MACROSCOPIC SCALES THE CONCEPT OF HIERARCHICAL MULTISCALE MODELING IS DISCUSSED IN SOME LENGTH FINALLY, THE IMPORTANCE OF SYSTEMS-LEVEL TOOLS SUCH AS SENSITIVITY ANALYSIS, PARAMETER ESTIMATION, OPTIMIZATION, CONTROL, MODEL REDUCTION, AND BIFURCATION IN MULTISCALE ANALYSIS IS UNDERSCORED I INTRODUCTION A DECADAL REPORT RECENTLY ISSUED BY THE NATIONAL RESEARCH COUNCIL (NRC), ENTITLED BEYOND THE MOLECULAR FRONTIER: CHALLENGES FOR CHEMISTRY AND CHEMICAL