Computational Approaches to Nanomineralogy

Nanomineralogy is concerned with the behavior of minerals on length scales between 10 A and 1 micron. Within the realm of computational science, molecular modeling methods have been working at the lower end of this scale for more than 50 years and comprise a relatively mature field even within the geosciences community (see Cygan and Kubicki 2001). Somewhere near the upper end of this scale, continuum approaches using bulk thermodyamics and homogeneous transport properties (diffusion, viscous flow and heat flow, and elastic moduli) can be used effectively (Turcotte and Schubert 1982). From one perspective, the nanoscale regime is the theoretical/ computational no-man’s land between atomistic and continuum scales, in which atoms cannot quite be ignored and continuum models cannot quite be applied. More generally, it is the simultaneous consideration of multiple scales, each requiring different methods, which, from the computational point of view, provides the driving force and makes this field exciting. The focus of this volume is on nanoscale phenomena in mineralogy and geochemistry in low-temperature, near-surface environments. This is indeed a rich area for multiscale investigations, as shown in Figure 1⇓. At the finest scales, one is interested in the spatio-temporal variability of the collective wave functions (or density) of electrons. At a simple level, this results in the formation of chemical bonds. Even at this scale, consideration of the detailed aspects of electron density topology is an emerging area (Bader 1990; Gibbs et al. 1998; Rescigno et al. 1999; Blanco et al. 2000; Espinosa and Molins 2000). As more than a few atoms begin to interact, complexity begins to be revealed in molecular arrangements as well as the electronic structure. In mineralogy, we have polynuclear clusters (such as discussed in detail by Casey and Furrer in this volume) and nanoporous minerals, …

[1]  U. Schwertmann,et al.  Iron Oxides , 2003, SSSA Book Series.

[2]  David A. Yuen,et al.  Geophysical Applications of Multidimensional Filtering with Wavelets , 2002 .

[3]  A. Wierzbicki,et al.  Formation of chiral morphologies through selective binding of amino acids to calcite surface steps , 2001, Nature.

[4]  Chung-Kung Lee Effect of Heating on the Surface Roughness and Pore Connectivity of TiO2: Fractal and Percolation Analysis , 2001 .

[5]  A. Falqui,et al.  Investigation of the precursors of γ-Fe2O3 in Fe2O3/SiO2 nanocomposites obtained through sol–gel , 2001 .

[6]  R. Purrello,et al.  Porphyrin binding and self-aggregation onto polymeric matrix: a combined spectroscopic and modelling approach , 2001 .

[7]  D. Veblen,et al.  Defects and Disorder: Probing the Surface Chemistry of Heterogenite (CoOOH) by Dissolution Using Hydroquinone and Iminodiacetic Acid , 2001 .

[8]  P. Searson,et al.  Epitaxial Assembly in Aged Colloids , 2001 .

[9]  C. Steefel,et al.  Multicomponent reactive transport in an in situ zero-valent iron cell. , 2001, Environmental science & technology.

[10]  L. Vecsey,et al.  Wavelet spectra and chaos in thermal convection modelling , 2001 .

[11]  David A. Yuen,et al.  Mixing Driven By Rayleigh–Taylor Instability In The Mesoscale Modeled With Dissipative Particle Dynamics , 2001 .

[12]  Z. Moktadir,et al.  Wavelet characterization of the submicron surface roughness of anisotropically etched silicon , 2000 .

[13]  Xixiang Zhang,et al.  High-resolution transmission electron microscopy study of epitaxial oxide shell on nanoparticles of iron , 2000 .

[14]  G. Henkelman,et al.  A climbing image nudged elastic band method for finding saddle points and minimum energy paths , 2000 .

[15]  Á. M. Pendás,et al.  Ions in crystals: The topology of the electron density in ionic materials. V. TheB1−B2phase transition in alkali halides , 2000 .

[16]  David A. Yuen,et al.  Capabilities of 3‐D wavelet transforms to detect plume‐like structures from seismic tomography , 2000 .

[17]  J. Khim,et al.  Kinetics of reductive denitrification by nanoscale zero-valent iron. , 2000, Chemosphere.

[18]  E. Molins,et al.  Retrieving interaction potentials from the topology of the electron density distribution: The case of hydrogen bonds , 2000 .

[19]  J. Banfield,et al.  Aggregation-based crystal growth and microstructure development in natural iron oxyhydroxide biomineralization products. , 2000, Science.

[20]  Tjerk P. Straatsma,et al.  NWChem: Exploiting parallelism in molecular simulations , 2000 .

[21]  Rajiv K. Kalia,et al.  Multiresolution algorithms for massively parallel molecular dynamics simulations of nanostructured materials , 2000 .

[22]  D. Dixon,et al.  Intrinsic acidity of aluminum, chromium (III) and iron (III) μ3-hydroxo functional groups from ab initio electronic structure calculations , 2000 .

[23]  Yuen,et al.  A Two-Level, Discrete-Particle Approach for Simulating Ordered Colloidal Structures. , 2000, Journal of colloid and interface science.

[24]  Patrick B. Warren,et al.  Mesoscopic Simulation of Drops in Gravitational and Shear Fields , 2000 .

[25]  J. Monaghan SPH without a Tensile Instability , 2000 .

[26]  P. Maurice,et al.  Dissolution of Al-substituted goethites by an aerobic Pseudomonas mendocina var. bacteria , 2000 .

[27]  J. Q. Broughton,et al.  Concurrent Coupling of Length Scales in Solid State Systems , 2000 .

[28]  Hashem Rafii-Tabar,et al.  Modelling the nano-scale phenomena in condensed matter physics via computer-based numerical simulations , 2000 .

[29]  David A. Yuen,et al.  Looking at the Inside of the Earth with 3-D Wavelets: A Pair of New Glasses for Geoscientists , 2000 .

[30]  David A. Yuen,et al.  Matching macroscopic properties of binary fluids to the interactions of dissipative particle dynamics , 2000 .

[31]  A. Varnek,et al.  Supramolecular Chemistry: Computer-Assisted Instruction in Undergraduate and Graduate Chemistry Courses , 2000 .

[32]  D. Yuen,et al.  A Two-Level, Discrete Particle Approach For Large-Scale Simulation Of Colloidal Aggregates , 2000 .

[33]  Sándor Suhai,et al.  A Self‐Consistent Charge Density‐Functional Based Tight‐Binding Method for Predictive Materials Simulations in Physics, Chemistry and Biology , 2000 .

[34]  Michael Ortiz,et al.  Hierarchical modeling in the mechanics of materials , 2000 .

[35]  Isaacs,et al.  Collisional breakup in a quantum system of three charged particles , 1999, Science.

[36]  P. Falaras,et al.  Preparation, fractal surface morphology and photocatalytic properties of TiO2 films , 1999 .

[37]  Wei-xian Zhang,et al.  Transformation of chlorinated methanes by nanoscale iron particles , 1999 .

[38]  G. Henkelman,et al.  A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives , 1999 .

[39]  T. Hiemstra,et al.  Effect of different crystal faces on experimental interaction force and aggregation of hematite , 1999 .

[40]  M. Abidi,et al.  Multi-scale analysis of shell growth increments using wavelet transform , 1999 .

[41]  David A. Yuen,et al.  Viewing seismic velocity anomalies with 3‐D continuous Gaussian wavelets , 1999 .

[42]  J. Q. Broughton,et al.  Concurrent coupling of length scales: Methodology and application , 1999 .

[43]  Rajiv K. Kalia,et al.  DYNAMICS OF OXIDATION OF ALUMINUM NANOCLUSTERS USING VARIABLE CHARGE MOLECULAR-DYNAMICS SIMULATIONS ON PARALLEL COMPUTERS , 1999 .

[44]  Jillian F. Banfield,et al.  Morphology development and crystal growth in nanocrystalline aggregates under hydrothermal conditions: insights from titania , 1999 .

[45]  A. Lepidi,et al.  Fractal analysis to discriminate between biotic and abiotic attacks on chalcopyrite and pyrolusite. , 1999, Journal of microbiological methods.

[46]  Aiichiro Nakano,et al.  A Rigid-Body-Based Multiple Time Scale Molecular Dynamics Simulation of Nanophase Materials , 1999, Int. J. High Perform. Comput. Appl..

[47]  Hut,et al.  Astrophysics on the GRAPE family of special-purpose computers , 1998, Science.

[48]  David A. Yuen,et al.  Dissipative Particle Dynamics of the Thin-Film Evolution in Mesoscale , 1999 .

[49]  A. Duparre,et al.  Hochauflösende Topometrie im Kontext globaler Makrostrukturen / High Resolution Topometry in Conjunction with Macro Structures , 1999 .

[50]  P. Huang,et al.  Atomic Force Microscopy and Surface Characteristics of Iron Oxides Formed in Citrate Solutions , 1999 .

[51]  Julio M. Ottino,et al.  Mixing and Dispersion of Viscous Liquids and Powdered Solids , 1999 .

[52]  U. Schwertmann,et al.  From Fe(III) Ions to Ferrihydrite and then to Hematite. , 1999, Journal of colloid and interface science.

[53]  Steven C. Smith,et al.  Bacterial reduction of crystalline Fe3+ oxides in single phase suspensions and subsurface materials , 1998 .

[54]  R. Larson The Structure and Rheology of Complex Fluids , 1998 .

[55]  M. Holschneider,et al.  Wavelet analysis of the Chandler wobble , 1998 .

[56]  J. Rustad,et al.  Interaction of water with the (1×1) and (2×1) surfaces of α-Fe2O3(012) , 1998 .

[57]  R. Downs,et al.  Power law relationships between bond length, bond strength and electron density distributions , 1998 .

[58]  John W. Mintmire,et al.  Universal Density of States for Carbon Nanotubes , 1998 .

[59]  Robert E. Rudd,et al.  COARSE-GRAINED MOLECULAR DYNAMICS AND THE ATOMIC LIMIT OF FINITE ELEMENTS , 1998 .

[60]  H. L. Resnikoff,et al.  Wavelet analysis: the scalable structure of information , 1998 .

[61]  Banfield,et al.  Imperfect oriented attachment: dislocation generation in defect-free nanocrystals , 1998, Science.

[62]  J. W. Halley,et al.  Self-consistent tight-binding atomic-relaxation model of titanium dioxide , 1998 .

[63]  P. Feibelman INTERLAYER SELF-DIFFUSION ON STEPPED PT(111) , 1998 .

[64]  V. Bulatov,et al.  Connecting atomistic and mesoscale simulations of crystal plasticity , 1998, Nature.

[65]  Paul Meakin,et al.  Fractals, scaling, and growth far from equilibrium , 1998 .

[66]  P. Español FLUID PARTICLE MODEL , 1997, cond-mat/9709024.

[67]  Alan C. Newell,et al.  Natural patterns and wavelets , 1998 .

[68]  Weidler,et al.  Surface Roughness Created by Acidic Dissolution of Synthetic Goethite Monitored with SAXS and N2-Adsorption Isotherms , 1998, Journal of colloid and interface science.

[69]  Bradford H. Hager,et al.  Localization of the gravity field and the signature of glacial rebound , 1997, Nature.

[70]  V. Loreto,et al.  A "Tetris-Like" Model for the Compaction of Dry Granular Media , 1997, cond-mat/9705195.

[71]  J. W. Halley,et al.  Ewald methods for polarizable surfaces with application to hydroxylation and hydrogen bonding on the (012) and (001) surfaces of α-Fe2O3 , 1997, cond-mat/9704070.

[72]  J. P. Lafemina,et al.  Kinetic Monte Carlo investigation of pit formation at the CaCO3(101̄4) surface-water interface , 1997 .

[73]  M. H. Ernst,et al.  Static and dynamic properties of dissipative particle dynamics , 1997, cond-mat/9702036.

[74]  G. I. Barenblatt Scaling: Self-similarity and intermediate asymptotics , 1996 .

[75]  H. Hettema,et al.  The direct Monte Carlo method applied to the homogeneous nucleation problem , 1996 .

[76]  Matthias Holschneider,et al.  Wavelets - an analysis tool , 1995, Oxford mathematical monographs.

[77]  Miguel Jose´-Yacama´n,et al.  Electron microscopy of catalysts; the present, the future and the hopes , 1995 .

[78]  A. Barabasi,et al.  Fractal concepts in surface growth , 1995 .

[79]  Shigeru Endo,et al.  Application of a high‐performance, special‐purpose computer, GRAPE‐2A, to molecular dynamics , 1994, J. Comput. Chem..

[80]  Jacopo Tomasi,et al.  Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent , 1994 .

[81]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[82]  R. W. Lof,et al.  CORRELATION EFFECTS IN SOLID C60 , 1992 .

[83]  J. Gao,et al.  A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations. , 1992, Science.

[84]  J. Bowles Iron Oxides in the Laboratory , 1992, Mineralogical Magazine.

[85]  J. Koelman,et al.  Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics , 1992 .

[86]  D. Turcotte Fractals and Chaos in Geology and Geophysics , 1992 .

[87]  Jh Harding,et al.  EMBEDDED CLUSTER CALCULATIONS OF DEFECT PROCESSES , 1992 .

[88]  C. Cramer,et al.  General parameterized SCF model for free energies of solvation in aqueous solution , 1991 .

[89]  William Smith,et al.  Molecular dynamics on hypercube parallel computers , 1991 .

[90]  G. Stucky,et al.  Low-temperature synthesis of hydrated zinco(beryllo)-phosphate and arsenate molecular sieves , 1991, Nature.

[91]  Andersen,et al.  10(6)-particle molecular-dynamics study of homogeneous nucleation of crystals in a supercooled atomic liquid. , 1990, Physical review. B, Condensed matter.

[92]  Kenneth Falconer,et al.  Fractal Geometry: Mathematical Foundations and Applications , 1990 .

[93]  R. Bader,et al.  Atoms in molecules , 1990 .

[94]  B. Wehrli Monte Carlo simulations of surface morphologies during mineral dissolution , 1989 .

[95]  Leslie Greengard,et al.  A fast algorithm for particle simulations , 1987 .

[96]  D. Papaconstantopoulos,et al.  Handbook of the Band Structure of Elemental Solids , 1986 .

[97]  A. Voter,et al.  Classically exact overlayer dynamics: Diffusion of rhodium clusters on Rh(100). , 1986, Physical review. B, Condensed matter.

[98]  Piet Hut,et al.  A hierarchical O(N log N) force-calculation algorithm , 1986, Nature.

[99]  Gerald V. Gibbs,et al.  Molecules as models for bonding in silicates , 1982 .

[100]  Donald L. Turcotte,et al.  Geodynamics : applications of continuum physics to geological problems , 1982 .

[101]  J. Dixon,et al.  Minerals in soil environments , 1990 .

[102]  C. Boiziau,et al.  Sublimation du krypton à basse température , 1973 .

[103]  J. C. Slater,et al.  Simplified LCAO Method for the Periodic Potential Problem , 1954 .