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

General principles - historical background and overview saccharide structure and nomenclature evolution of glycan diversity protein-glycan Interactions exploring the biological roles of glycans biosynthesis, metabolism, and function - monosaccharide metabolism N-glycans O-glycans glycosphingolipids glycophospholipid anchors proteoglycans and glycosaminoglycans other classes of golgi-derived glycans nuclear and cytoplasmic glycosylation the O-GlcNAc modification sialic acids structures common to different types of glycans glycosyltransferases degradation and turnover of glycans glycosylation in "model" organisms glycobiology of plant cells bacterial polysaccharides proteins that recognize glycans - discovery and classification of animal lectins P-type lectins I-type lectins C-type lectins selectins S-type lectins (galectins) microbial glycan-binding proteins glycosaminoglycan-binding proteins plant lectins glycans in genetic disorders and disease - genetic disorders of glycosylation in cultured cells naturally occurring genetic disorders of glycosylation in animals determining glycan function using genetically modified mice glycosylation changes in ontogeny and cell activation glycosylation changes in cancer glycobiology of protozoal and helminthic parasites acquired glycosylation changes in human disease methods and applications - structural analysis and sequencing of glycans chemical and enzymatic synthesis of glycans natural and synthetic inhibitors of glycosylation glycobiology in biotechnology and medicine.

Essentials of Glycobiology

Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S. A. S. Nagar,Mohali, Punjab-160 062, India, Institute of Biochemistry, Faculty of Medicine, Polytechnic University, Via Ranieri 67, IT-60100 Ancona, Italy,Green Biotechnology Research Group, The Special Division for Human Life Technology, National Institute of Advanced Industrial Science andTechnology, 1-8-31 Midorigaoka, Ikeda, Osaka-563-8577, Japan, and Department of Medicinal Chemistry & Natural Products,The Hebrew University of Jerusalem, School of Pharmacy-Faculty of Medicine, Jerusalem 91120, IsraelReceived March 2, 2004

Chitosan chemistry and pharmaceutical perspectives.

The innate immune system evolved several strategies of self/nonself discrimination that are based on the recognition of molecular patterns demarcating infectious nonself, as well as normal and abnormal self. These patterns are deciphered by receptors that either induce or inhibit an immune response, depending on the meaning of these signals.

/pdf/decoding-the-patterns-of-self-and-nonself-by-the-innate-4e31h5xiv0.pdf

Decoding the patterns of self and nonself by the innate immune system.

Endospores of Bacillus spp., especially Bacillus subtilis, have served as experimental models for exploring the molecular mechanisms underlying the incredible longevity of spores and their resistance to environmental insults. In this review we summarize the molecular laboratory model of spore resistance mechanisms and attempt to use the model as a basis for exploration of the resistance of spores to environmental extremes both on Earth and during postulated interplanetary transfer through space as a result of natural impact processes.

/pdf/resistance-of-bacillus-endospores-to-extreme-terrestrial-and-2qp3zxqicl.pdf

Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments.

Publisher Summary This chapter discusses the chemistry, metabolism, and biological functions of sialic acids. Interest in the sialic acids has rapidly increased in recent years, especially because of the reorganization of their involvement in the regulation of a great variety of biological phenomena. The occurrence of sialic acids in plants has never unequivocally been established, although some positive reports exist. The acylneuraminic acids can be released from their glycosidic linkages either by dilute (aqueous or methanolic) acids or sialidases. The unequivocal determination of sialic acids occurring in low concentrations in many biological materials is rather difficult, and this explains the many errors that have been made in this field. The biosynthesis of N-acetylneuraminic acid (Neu5Ac) is briefly reported in this chapter and more attention is given to the enzyme reactions modifying this compound. Little information is available about the role of the modifications of sialic acid resulting in a species- and tissue-specific distribution of different N,O-acylated and O-methylated sialic acids.

Chemistry, Metabolism, and Biological Functions of Sialic Acids

https://www.uni-kiel.de/Biochemie/AGSch/pdf/reviews/82_Schauer_2009_Current-Opinion-in-Structural-Biology.pdf

Sialic Acids as Regulators of Molecular and Cellular Interactions

Sialic acids are one of the most important molecules of life, since they occupy the terminal position on macromolecules and cell membranes and are involved in many biological and pathological phenomena. The structures of sialic acids, comprising a family of over 40 neuraminic acid derivatives, have been elucidated. However, many aspects of the regulation of their metabolism at the enzyme and gene levels, as well as of their functions remain mysterious. Sialic acids play a dual role, not only are they indispensable for the protection to and adaptation of life, but are also utilised by life-threatening infectious microorganisms. In this article the present state of knowledge in sialobiology, with an emphasis on my personal experience in this research area, is outlined including a discussion of necessary future work in this fascinating field of cell biology.

/pdf/achievements-and-challenges-of-sialic-acid-research-4ya9a4cpft.pdf

Achievements and challenges of sialic acid research.

Sialic acids and their role as biological masks

Sialic acids (Sias) are terminal components of many glycoproteins and glycolipids especially of higher animals. In this exposed position they contribute significantly to the structural properties of these molecules, both in solution and on cell surfaces. Therefore, it is not surprising that Sias are important regulators of cellular and molecular interactions, in which they play a dual role. They can either mask recognition sites or serve as recognition determinants. Whereas the role of Sias in masking and in binding of pathogens to host cells has been documented over many years, their role in nonpathological cellular interaction has only been shown recently. The aim of this chapter is to summarize our knowledge about Sias in masking, for example, galactose residues, and to review the progress made during the past few years with respect to Sias as recognition determinants in the adhesion of pathogenic viruses, bacteria, and protozoa, and particularly as binding sites for endogenous cellular interaction molecules. Finally, perspectives for future research on these topics are discussed.

Roland Schauer

Papers

Chemistry, Metabolism, and Biological Functions of Sialic Acids

Sialic Acids as Regulators of Molecular and Cellular Interactions

Achievements and challenges of sialic acid research.

Sialic acids and their role as biological masks

Sialic Acids in Molecular and Cellular Interactions