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

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.

/pdf/the-oyster-genome-reveals-stress-adaptation-and-complexity-21k1krsbun.pdf

The oyster genome reveals stress adaptation and complexity of shell formation

2.3. Amorphous Minerals 4354 3. Biological Routes to Controlling Morphology 4354 3.1. General Mechanisms 4356 3.1.1. Soluble and Insoluble Organic Molecules 4356 3.1.2. Control over Crystal Polymorph 4357 3.1.3. Control over Crystal Orientation 4359 3.2. Single-Crystal Biominerals 4359 3.2.1. Organic and Inorganic Soluble Additives 4360 3.2.2. Templating of Single-Crystal Morphologies 4361 3.3. Polycrystalline Biominerals 4366 3.3.1. Nacre Formation in Mollusks 4366 3.3.2. ForaminiferasA Biogenic Mesocrystal 4368 3.4. Amorphous Biominerals 4370 3.4.1. Silicification in Diatoms 4370 3.4.2. In Vitro Studies of Silicification in Diatoms 4371 4. Bioinspired Routes to Controlling Crystal Morphologies 4371

Controlling Mineral Morphologies and Structures in Biological and Synthetic Systems

The biological approach to forming crystals is proving to be most surprising. Mollusks build their shells by using a hydrophobic silk gel, very acidic aspartic acid rich proteins, and apparently also an amorphous precursor phase from which the crystals form. All this takes place in a highly structured chitinous framework. Here we present ideas on how these disparate components work together to produce the highly structured pearly nacreous layer of the mollusk shell.

/pdf/mollusk-shell-formation-a-source-of-new-concepts-for-4d1anmsagc.pdf

Mollusk shell formation: a source of new concepts for understanding biomineralization processes.

Biologically-formed hard tissues, referred to as biominerals, have intrigued the materials engineering community for years because of the high degree of crystallographic control that is exerted during the precipitation of the bioinorganic crystals. In recent years, there has been a shift in attention, from prior studies that focused on specific organic-inorganic interactions that modulate the crystal morphology via the conventional crystallization pathway, to recent studies that find that many biominerals are formed via an amorphous precursor pathway. It has become clear that the things we thought we had learned about biominerals before, may or may not be relevant to truly understanding the mechanisms involved in biomineralization. Having witnessed this paradigm shift first hand, I am inclined to provide a review from this historical perspective, where I hope to belay some ideas about where we were, where we are, and where we are going, with respect to understanding how these shells and other biominerals are formed. Therefore, one goal of this review is to try and provide a link between the prior literature and the new literature, which might be useful to newcomers in the field, whom I suspect may find it confusing and difficult to integrate the findings in these different types of studies across this time period. A second goal is to try and integrate some of the knowledge obtained from in vitro model systems, which can be more amenable to obtaining mechanistic information, with the in vivo and ex vivo observational studies on biominerals. A third goal is to demonstrate that there may be certain unifying principles found in biomineral systems that seem widely diverse, such as from diatoms, to mollusk shells, to vertebrate bones and teeth. A final goal (the not so hidden agenda), is to demonstrate that not only is there as strong likelihood that many biominerals are formed by an amorphous precursor, but that the amorphous phase may possess fluidic properties that impart new processing capabilities to the system. Of course those who know my work will readily assess that I am referring to the polymer-induced liquid-precursor (PILP) process, which has been a primary focus in my lab. Along these lines, some new hypotheses are presented regarding the morphogenesis of certain biominerals, such as mollusk nacre, kidney stones, and bones and teeth, along with a review of the literature that provides support to these new ideas. The intent is to stimulate thoughtful discussions in this rapidly emerging area, which seemingly provides a unifying principle in biomineralization.

1.1. Biomineral Overview
Biominerals that have intrigued the materials engineer for years. The diversity of biominerals became particularly evident by the variety of books on biominerals that emerged in the late 80’s to 90’s,1–11 which has continued with a few more recent additions to this nice collection.12–16 Many people are probably not even aware of the diversity of biologically formed minerals, so a sampling is provided in Table 1 to illustrate some of the different chemistries that evolved in the formation of various biological hard tissues. The calcium carbonate (CaCO3) biominerals of invertebrates, such as mollusk shells and sea urchin spines, have been particularly well studied due to their accessibility, and because of the high degree of crystallographic control that is achieved in these biologically formed crystals. The calcium phosphate (CaP) biominerals of the vertebrates, such as bones and teeth, have also been extensively investigated because of their remarkable structure and mechanical properties, and for the more obvious reasons of health related issues.14 Calcium oxalate (CaOx) biominerals can be found in plants, but the majority of studies have focused on the pathological form of CaOx that is found in kidney stones, which often occurs in conjunction with CaP deposits.8,14

Table 1

Examples of the diversity of biominerals. This list is by no means comprehensive, where some 70 different mineral phases have been identified to date.1–11

Biomimetic Model Systems for Investigating the Amorphous Precursor Pathway and Its Role in Biomineralization

In the last few years, the field of molluscan biomineralization has known a tremendous mutation, regarding fundamental concepts on biomineralization regulation as well as regarding the methods of investigation. The most recent advances deal more particularly with the structure of shell biominerals at nanoscale and the identification of an increasing number of shell matrix protein components. Although the matrix is quantitatively a minor constituent in the shell of mollusks (less than 5% w/w), it is, however, the major component that controls different aspects of the shell formation processes: synthesis of transient amorphous minerals and evolution to crystalline phases, choice of the calcium carbonate polymorph (calcite vs aragonite), organization of crystallites in complex shell textures (microstructures). Until recently, the classical paradigm in molluscan shell biomineralization was to consider that the control of shell synthesis was performed primarily by two antagonistic mechanisms: crystal nucleation and growth inhibition. New concepts and emerging models try now to translate a more complex reality, which is remarkably illustrated by the wide variety of shell proteins, characterized since the mid-1990s, and described in this chapter. These proteins cover a broad spectrum of pI, from very acidic to very basic. The primary structure of a number of them is composed of different modules, suggesting that these proteins are multifunctional. Some of them exhibit enzymatic activities. Others may be involved in cell signaling. The oldness of shell proteins is discussed, in relation with the Cambrian appearance of the mollusks as a mineralizing phylum and with the Phanerozoic evolution of this group. Nowadays, the extracellular calcifying shell matrix appears as a whole integrated system, which regulates protein-mineral and protein-protein interactions as well as feedback interactions between the biominerals and the calcifying epithelium that synthesized them. Consequently, the molluscan shell matrix may be a source of bioactive molecules that would offer interesting perspectives in biomaterials and biomedical fields.

Molluscan shell proteins: primary structure, origin, and evolution.

Molluscan shell proteins

In the last years, the field of mollusk biomineralization has known a tremendous mutation. The most recent advances deal with the nanostructure of shell biominerals, and with the identification of several shell matrix proteins: on one hand, the complex hierarchical organization of shell biominerals has been deciphered in few models, like nacre. On the other hand, although proteins represent a minor shell component, they are the major macromolecules that control biocrystal synthesis. Until recently, the paradigm was to consider that this control occurs by two antagonist mechanisms: crystal nucleation and growth inhibition. Emerging models try to translate a more complex reality, illustrated by the huge variety of shell proteins, characterized so far. The primary structure of many of them is composed of different functional domains, some of which exhibit enzymatic activity, while others may be involved in cell signalling. Many of them have unknown functions. Today, the shell matrix appears as a whole system, which regulates protein-mineral, protein-protein, and epithelium-mineral interactions. These aspects should be taken in account for the future models of shell formation.

The formation and mineralization of mollusk shell.

Mollusca evolutionary success can be attributed partly to their efficiency to sustain and protect their soft body with an external biomineralized structure, the shell. Current knowledge of the protein set responsible for the formation of the shell microstructural polymorphism and unique properties remains largely patchy. In Pinctada margaritifera and Pinctada maxima, we identified 80 shell matrix proteins, among which 66 are entirely unique. This is the only description of the whole "biomineralization toolkit" of the matrices that, at least in part, is thought to regulate the formation of the prismatic and nacreous shell layers in the pearl oysters. We unambiguously demonstrate that prisms and nacre are assembled from very different protein repertoires. This suggests that these layers do not derive from each other.

https://www.pnas.org/content/pnas/109/51/20986.full.pdf

Different secretory repertoires control the biomineralization processes of prism and nacre deposition of the pearl oyster shell

Clinical experiments aimed at reducing bone loss in jaws raise a raft of interdisciplinary issues. Those investigating biomineralization, early evolutionary history and biological signal transduction might take an interest.

Frédéric Marin

Papers

Molluscan shell proteins: primary structure, origin, and evolution.

Molluscan shell proteins

The formation and mineralization of mollusk shell.

Different secretory repertoires control the biomineralization processes of prism and nacre deposition of the pearl oyster shell

A marriage of bone and nacre.