The Niagaran reef at Thornton, Illinois : guidebook for the field conference held in connection with the annual convention of the American Association of Petroleum Geologists and the Society of Economic Paleontologists and Mineralogists at Chicago, Illinois, April 22, 1956.

"Field Conference sponsored by Illinois State Geological Survey"Bibliography: leaf 3

Theoretical characterization of a model of aragonite crystal orientation in red abalone nacre

Nacre, commonly known as mother-of-pearl, is a remarkable biomineral that in red abalone consists of layers of 400-nm thick aragonite crystalline tablets confined by organic matrix sheets, with the $(001)$ crystal axes of the aragonite tablets oriented to within $\pm$ 12 degrees from the normal to the layer planes. Recent experiments demonstrate that this orientational order develops over a distance of tens of layers from the prismatic boundary at which nacre formation begins. Our previous simulations of a model in which the order develops because of differential tablet growth rates (oriented tablets growing faster than misoriented ones) yield patterns of tablets that agree qualitatively and quantitatively with the experimental measurements. This paper presents an analytical treatment of this model, focusing on how the dynamical development and eventual degree of order depend on model parameters. Dynamical equations for the probability distributions governing tablet orientations are introduced whose form can be determined from symmetry considerations and for which substantial analytic progress can be made. Numerical simulations are performed to relate the parameters used in the analytic theory to those in the microscopic growth model. The analytic theory demonstrates that the dynamical mechanism is able to achieve a much higher degree of order than naive estimates would indicate.Comment: 20 pages, 3 figure

Phosphonic Acid-Functionalized Diblock Copolymer Nano-Objects via Polymerization-Induced Self-Assembly: Synthesis, Characterization, and Occlusion into Calcite Crystals

Dialkylphosphonate-functionalized and phosphonic acid-functionalized macromolecular chain transfer agents (macro-CTAs) were utilized for the reversible addition–fragmentation chain transfer (RAFT) dispersion polymerization of benzyl methacrylate (BzMA) at 20% w/w solids in methanol at 64 °C. Spherical, worm-like and vesicular nano-objects could all be generated through systematic variation of the mean degree of polymerization of the core-forming PBzMA block when using relatively short macro-CTAs. Construction of detailed phase diagrams is essential for the reproducible targeting of pure copolymer morphologies, where these were characterized using transmission electron microscopy (TEM) and dynamic light scattering (DLS). For nano-objects prepared using the phosphonic acid-based macro-CTA, transfer from methanol dispersion to water leads to the development of anionic surface charge as a result of ionization of the stabilizer chains, but this does not adversely affect the copolymer morphology. Given the well-known strong affinity of phosphonic acid for calcium ions, selected nano-objects were evaluated for their in-situ occlusion within growing CaCO3 crystals. Scanning electron microscopy (SEM) studies provide convincing evidence for the occlusion of both worm-like and vesicular phosphonic acid-based nano-objects and hence the production of a series of interesting new organic-inorganic nanocomposites

Enamel-like apatite crown covering amorphous mineral in a crayfish mandible

Carbonated hydroxyapatite is the mineral found in vertebrate bones and teeth, whereas invertebrates utilize calcium carbonate in their mineralized organs. In particular, stable amorphous calcium carbonate is found in many crustaceans. Here we report on an unusual, crystalline enamel-like apatite layer found in the mandibles of the arthropod Cherax quadricarinatus (freshwater crayfish). Despite their very different thermodynamic stabilities, amorphous calcium carbonate, amorphous calcium phosphate, calcite and fluorapatite coexist in well-defined functional layers in close proximity within the mandible. The softer amorphous minerals are found primarily in the bulk of the mandible whereas apatite, the harder and less soluble mineral, forms a wear-resistant, enamel-like coating of the molar tooth. Our findings suggest a unique case of convergent evolution, where similar functional challenges of mastication led to independent developments of structurally and mechanically similar, apatite-based layers in the teeth of genetically remote phyla: vertebrates and crustaceans

CryoTEM as an Advanced Analytical Tool for Materials Chemists

Morphology plays an essential role in chemistry through the segregation of atoms and/or molecules into different phases, delineated by interfaces. This is a general process in materials synthesis and exploited in many fields including colloid chemistry, heterogeneous catalysis, and functional molecular systems. To rationally design complex materials, we must understand and control morphology evolution. Toward this goal, we utilize cryogenic transmission electron microscopy (cryoTEM), which can track the structural evolution of materials in solution with nanometer spatial resolution and a temporal resolution of <1 s. In this Account, we review examples of our own research where direct observations by cryoTEM have been essential to understanding morphology evolution in macromolecular self-assembly, inorganic nucleation and growth, and the cooperative evolution of hybrid materials. These three different research areas are at the heart of our approach to materials chemistry where we take inspiration from the myriad examples of complex materials in Nature. Biological materials are formed using a limited number of chemical components and under ambient conditions, and their formation pathways were refined during biological evolution by enormous trial and error approaches to self-organization and biomineralization. By combining the information on what is possible in nature and by focusing on a limited number of chemical components, we aim to provide an essential insight into the role of structure evolution in materials synthesis. Bone, for example, is a hierarchical and hybrid material which is lightweight, yet strong and hard. It is formed by the hierarchical self-assembly of collagen into a macromolecular template with nano- and microscale structure. This template then directs the nucleation and growth of oriented, nanoscale calcium phosphate crystals to form the composite material. Fundamental insight into controlling these structuring processes will eventually allow us to design such complex materials with predetermined and potentially unique properties

Importance of B4 medium in determining organomineralization potential of bacterial environmental isolates

B4 precipitation medium has been used as the preferred medium for studying mineral precipitation using bacterial strains in vitro since pioneer studies were performed by Boquet and coworkers in 1973. Using this medium, several authors have demonstrated that some environmental isolates were able to precipitate minerals, yet others did not. The main goal of the current study is to understand whether pH and buffer conditions would have a significant effect on mineral precipitation results for environmental isolates grown on B4. For this study, a total of 49 strains isolated from natural environments from Puerto Rico were grown on B4 plates, and their CaCO3 precipitation potential was investigated. Our findings revealed a strong correlation between a lack of CaCO3 precipitation and the acidification of the B4 plates by the colonies. The ability to precipitate CaCO3 could be restored by buffering the B4 medium to a pH of 8.2. Buffering capacity of the medium was proposed to be involved in CaCO3 precipitation: acid-base titrations conducted on the individual ingredients of B4 showed that yeast extract has a poor buffering capacity between pH 6.5?7.5. This pH range corresponds to the pH of B4 plates 6.87 (�±0.05)] prior to the inoculation. This might explain why B4 is such a good precipitation medium: a small variation in the H+/OH? balance during microbial growth and precipitation produces rapid changes in the pH of the medium. Finally, an amorphous matrix was distributed within 90% of the examined crystals generated on B4 medium by the environmental strains. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental file.; B4 precipitation medium has been used as the preferred medium for studying mineral precipitation using bacterial strains in vitro since pioneer studies were performed by Boquet and coworkers in 1973. Using this medium, several authors have demonstrated that some environmental isolates were able to precipitate minerals, yet others did not. The main goal of the current study is to understand whether pH and buffer conditions would have a significant effect on mineral precipitation results for environmental isolates grown on B4. For this study, a total of 49 strains isolated from natural environments from Puerto Rico were grown on B4 plates, and their CaCO3 precipitation potential was investigated. Our findings revealed a strong correlation between a lack of CaCO3 precipitation and the acidification of the B4 plates by the colonies. The ability to precipitate CaCO3 could be restored by buffering the B4 medium to a pH of 8.2. Buffering capacity of the medium was proposed to be involved in CaCO3 precipitation: acid-base titrations conducted on the individual ingredients of B4 showed that yeast extract has a poor buffering capacity between pH 6.5?7.5. This pH range corresponds to the pH of B4 plates 6.87 (�±0.05)] prior to the inoculation. This might explain why B4 is such a good precipitation medium: a small variation in the H+/OH? balance during microbial growth and precipitation produces rapid changes in the pH of the medium. Finally, an amorphous matrix was distributed within 90% of the examined crystals generated on B4 medium by the environmental strains. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental file

Identification of Genes Directly Involved in Shell Formation and Their Functions in Pearl Oyster, Pinctada fucata

Mollusk shell formation is a fascinating aspect of biomineralization research. Shell matrix proteins play crucial roles in the control of calcium carbonate crystallization during shell formation in the pearl oyster, Pinctada fucata. Characterization of biomineralization-related genes during larval development could enhance our understanding of shell formation. Genes involved in shell biomineralization were isolated by constructing three suppression subtractive hybridization (SSH) libraries that represented genes expressed at key points during larval shell formation. A total of 2,923 ESTs from these libraries were sequenced and gave 990 unigenes. Unigenes coding for secreted proteins and proteins with tandem-arranged repeat units were screened in the three SSH libraries. A set of sequences coding for genes involved in shell formation was obtained. RT-PCR and in situ hybridization assays were carried out on five genes to investigate their spatial expression in several tissues, especially the mantle tissue. They all showed a different expression pattern from known biomineralization-related genes. Inhibition of the five genes by RNA interference resulted in different defects of the nacreous layer, indicating that they all were involved in aragonite crystallization. Intriguingly, one gene (UD_Cluster94.seq.Singlet1) was restricted to the ‘aragonitic line’. The current data has yielded for the first time, to our knowledge, a suite of biomineralization-related genes active during the developmental stages of P.fucata, five of which were responsible for nacreous layer formation. This provides a useful starting point for isolating new genes involved in shell formation. The effects of genes on the formation of the ‘aragonitic line’, and other areas of the nacreous layer, suggests a different control mechanism for aragonite crystallization initiation from that of mature aragonite growth

Environmental and diagenetic controls on the morphology and calcification of the Ediacaran metazoan Cloudina

Abstract Cloudina is a globally distributed Ediacaran metazoan, with a tubular, funnel-in-funnel form built of thin laminae (ca. 1–10 μm). To what degree local environmental controlled morphology, and whether early diagenesis controlled the degree of calcification of Cloudina, is debated. Here we test these hypotheses by considering assemblages from four, coeval localities from the Upper Omkyk Member, Nama Group, Namibia, from inner ramp to mid-ramp reef across the Zaris Subbasin. We show that sinuosity of the Cloudina tube is variable between sites, as is the relative thickness of the tube wall, suggesting these features were environmentally controlled. Walls are thickest in high-energy reef settings, and thinnest in the low-energy, inner ramp. While local diagenesis controls preservation, all diagenetic expressions are consistent with the presence of weakly calcified, organic-rich laminae, and lamina thicknesses are broadly constant. Finally, internal ‘cements’ within Cloudina are found in all sites, and pre-date skeletal breakage, transport, as well as syn-sedimentary botryoidal cement precipitation. Best preservation shows these to be formed by fine, pseudomorphed aragonitic acicular crystals. Sr concentrations and Mg/Ca show no statistically significant differences between internal Cloudina cements and botryoidal cements, but we infer all internal cements to have precipitated when Cloudina was still in-situ and added considerable mechanical strength, but may have formed post-mortem or in abandoned parts of the skeleton

Cationic Amino Acids Specific Biomimetic Silicification in Ionic Liquid: A Quest to Understand the Formation of 3-D Structures in Diatoms

The intricate, hierarchical, highly reproducible, and exquisite biosilica structures formed by diatoms have generated great interest to understand biosilicification processes in nature. This curiosity is driven by the quest of researchers to understand nature's complexity, which might enable reproducing these elegant natural diatomaceous structures in our laboratories via biomimetics, which is currently beyond the capabilities of material scientists. To this end, significant understanding of the biomolecules involved in biosilicification has been gained, wherein cationic peptides and proteins are found to play a key role in the formation of these exquisite structures. Although biochemical factors responsible for silica formation in diatoms have been studied for decades, the challenge to mimic biosilica structures similar to those synthesized by diatoms in their natural habitats has not hitherto been successful. This has led to an increasingly interesting debate that physico-chemical environment surrounding diatoms might play an additional critical role towards the control of diatom morphologies. The current study demonstrates this proof of concept by using cationic amino acids as catalyst/template/scaffold towards attaining diatom-like silica morphologies under biomimetic conditions in ionic liquids

Homogenized stiffness matrices for mineralized collagen fibrils and lamellar bone using unit cell finite element models

Mineralized collagen fibrils have been usually analyzed like a two phase composite material where crystals are considered as platelets that constitute the reinforcement phase. Different models have been used to describe the elastic behavior of the material. In this work, it is shown that, when Halpin-Tsai equations are applied to estimate elastic constants from typical constituent properties, not all crystal dimensions yield a model that satisfy thermodynamic restrictions. We provide the ranges of platelet dimensions that lead to positive definite stiffness matrices. On the other hand, a finite element model of a mineralized collagen fibril unit cell under periodic boundary conditions is analyzed. By applying six canonical load cases, homogenized stiffness matrices are numerically calculated. Results show a monoclinic behavior of the mineralized collagen fibril. In addition, a 5-layer lamellar structure is also considered where crystals rotate in adjacent layers of a lamella. The stiffness matrix of each layer is calculated applying Lekhnitskii transformations and a new finite lement model under periodic boundary conditions is analyzed to calculate the homogenized 3D anisotropic stiffness matrix of a unit cell of lamellar bone. Results are compared with the rule-of-mixtures showing in general good agreement.The authors acknowledge the Ministerio de Economia y Competitividad the financial support given through the project DPI2010-20990 and the Generalitat Valenciana through the Programme Prometeo 2012/023. The authors thank Ms. Carla Gonzalez Carrillo by her help in the development of some of the numerical models.Vercher Martínez, A.; Giner Maravilla, E.; Arango Villegas, C.; Tarancón Caro, JE.; Fuenmayor Fernández, FJ. (2014). Homogenized stiffness matrices for mineralized collagen fibrils and lamellar bone using unit cell finite element models. Biomechanics and Modeling in Mechanobiology. 13(2):1-21. https://doi.org/10.1007/s10237-013-0507-yS121132Akiva U, Wagner HD, Weiner S (1998) Modelling the three-dimensional elastic constants of parallel-fibred and lamellar bone. J Mater Sci 33:1497–1509Ascenzi A, Bonucci E (1967) The tensile properties of single osteons. Anat Rec 158:375–386Ascenzi A, Bonucci E (1968) The compressive properties of single osteons. Anat Rec 161:377–392Ashman RB, Cowin SC, van Buskirk WC, Rice JC (1984) A continuous wave technique for the measurement of the elastic properties of cortical bone. J Biomech 17:349–361Bar-On B, Wagner HD (2012) Elastic modulus of hard tissues. J Biomech 45:672–678Bondfield W, Li CH (1967) Anisotropy of nonelastic flow in bone. J Appl Phys 38:2450–2455Cowin SC (2001) Bone mechanics handbook, 2nd edn. CRC Press Boca Raton, FloridaCowin SC, van Buskirk WC (1986) Thermodynamic restrictions on the elastic constant of bone. J Biomech 19:85–86Currey JD (1962) Strength of bone. Nature 195:513Cusack S, Miller A (1979) Determination of the elastic constants of collagen by brillouin light scattering. J Mol Biol 135:39–51Doty S, Robinson RA, Schofield B (1976) Morphology of bone and histochemical staining characteristics of bone cells. In: Aurbach GD (ed) Handbook of physiology. American Physiology Soc, Washington, pp 3–23Erts D, Gathercole LJ, Atkins EDT (1994) Scanning probe microscopy of crystallites in calcified collagen. J Mater Sci Mater Med 5:200–206Faingold A, Sidney RC, Wagner HD (2012) Nanoindentation of osteonal bone lamellae. J Mech Biomech Materials 9:198–206Franzoso G, Zysset PK (2009) Elastic anisotropy of human cortical bone secondary osteons measured by nanoindentation. J Biomech Eng 131:021001Gebhardt W (1906) Über funktionell wichtige Anordnungsweisen der eineren und grösseren Bauelemente des Wirbeltierknochens. II. Spezieller Teil. Der Bau der Haversschen Lamellensysteme und seine funktionelle Bedeutung. Arch Entwickl Mech Org 20:187–322Gibson RF (1994) Principles of composite material mechanics. McGraw-Hill, New YorkGiraud-Guille M (1988) Twisted plywood architecture of collagen fibrils in human compact bone osteons. Calcif Tissue Int 42:167–180Gurtin ME (1972) The linear theory of elasticity. Handbuch der Physik VIa/ 2:1–296Halpin JC (1992) Primer on composite materials: analysis, 2nd edn. CRC Press, Taylor & Francis, Boca Raton, FloridaHassenkam T, Fantner GE, Cutroni JA, Weaver JC, Morse DE, Hanma PK (2004) High-resolution AFM imaging of intact and fractured trabecular bone. Bone 35:4–10Hohe J (2003) A direct homogenization approach for determination of the stiffness matrix for microheterogeneous plates with application to sandwich panels. Composites Part B 34:615–626Hulmes DJS, Wess TJ, Prockop DJ, Fratzl P (1995) Radial packing, order, and disorder in collagen fibrils. Biophys J 68:1661–1670Jäger I, Fratzl P (2000) Mineralized collagen fibrils: a mechanical model with a staggered arrangement of mineral particles. Biophys J 79:1737–1746Ji B, Gao H (2004) Mechanical properties of nanostructure of biological materials. J Mech Phy Sol 52:1963–1990Landis WJ, Hodgens KJ, Aerna J, Song MJ, McEwen BF (1996) Structural relations between collagen and mineral in bone as determined by high voltage electron microscopic tomography. Microsc Res Tech 33:192–202Lekhnitskii SG (1963) Theory of elasticity of an anisotropic elastic body. Holden-Day, San FranciscoLempriere BM (1968) Poisson’s ratio in orthotropic materials. Am Inst Aeronaut Astronaut J J6:2226–2227Lowenstam HA, Weiner S (1989) On biomineralization. Oxford University, New YorkLusis J, Woodhams RT, Xhantos M (1973) The effect of flake aspect ratio on flexural properties of mica reinforced plastics. Polym Eng Sci 13:139–145Martínez-Reina J, Domínguez J, García-Aznar JM (2011) Effect of porosity and mineral content on the elastic constants of cortical bone: a multiscale approach. Biomech Model Mechanobiol 10:309–322Orgel JPRO, Miller A, Irving TC, Fischetti RF, Hammersley AP, Wess TJ (2001) The in situ supermolecular structure of type I collagen. Structure 9:1061–1069Padawer GE, Beecher N (1970) On the strength and stiffness of planar reinforced plastic resins. Polym Eng Sci 10:185–192Pahr DH, Rammerstofer FG (2006) Buckling of honeycomb sandwiches: periodic finite element considerations. Comput Model Eng Sci 12:229–242Reisinger AG, Pahr DH, Zysset PK (2010) Sensitivity analysis and parametric study of elastic properties of an unidirectional mineralized bone fibril-array using mean field methods. Biomech Model Mechanobiol 9:499–510Reisinger AG, Pahr DH, Zysset PK (2011) Elastic anisotropy of bone lamellae as a function of fibril orientation pattern. Biomech Model Mechanobiol 10:67–77Rezkinov N, Almany-Magal R, Shahar R, Weiner S (2013) Three-dimensional imaging of collagen fibril organization in rat circumferential lamellar bone using a dual beam electron microscope reveals ordered and disordered sub-lamellar structures. Bone 52(2):676–683Rho JY, Kuhn-Spearing L, Zioupos P (1998) Mechanical properties and the hierarchical structure of bone. Med Eng Phys 20:92–102Rubin MA, Jasiuk I, Taylor J, Rubin J, Ganey T, Apkarian RP (2003) TEM analysis of the nanostructure of normal and osteoporotic human trabecular bone. Bone 33:270–282Suquet P (1987) Lecture notes in physics-homogenization techniques for composite media. Chapter IV. Springer, BerlinWagermaier W, Gupta HS, Gourrier A, Burghammer M, Roschger P, Fratzl P (2006) Spiral twisting of fiber orientation inside bone lamellae. Biointerphases 1:1–5Wagner HD, Weiner S (1992) On the relationship between the microstructure of bone and its mechanical stiffness. J Biomech 25:1311–1320Weiner S, Wagner HD (1998) The material bone: structure-mechanical function relations. Annu Rev Mater Sci 28:271–298Weiner S, Traub W, Wagner H (1999) Lamellar bone: structure-function relations. J Struct Biol 126:241–255Yao H, Ouyang L, Ching W (2007) Ab initio calculation of elastic constants of ceramic crystals. J Am Ceram 90:3194–3204Yoon YJ, Cowin SC (2008b) The estimated elastic constants for a single bone osteonal lamella. Biomech Model Mechanobiol 7:1–11Yuan F, Stock SR, Haeffner DR, Almer JD, Dunand DC, Brinson LC (2011) A new model to simulate the elastic properties of mineralized collagen fibril. Biomech Model Mechanobiol 10:147–160Zhang Z, Zhang YWF, Gao H (2010) On optimal hierarchy of load-bearing biological materials. Proc R Soc B 278:519–525Zuo S, Wei Y (2007) Effective elastic modulus of bone-like hierarchical materials. Acta Mechanica Solida Sinica 20:198–20