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

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

Wetting phenomena are ubiquitous in nature and technology. A solid substrate exposed to the environment is almost invariably covered by a layer of fluid material. In this review, the surface forces that lead to wetting are considered, and the equilibrium surface coverage of a substrate in contact with a drop of liquid. Depending on the nature of the surface forces involved, different scenarios for wetting phase transitions are possible; recent progress allows us to relate the critical exponents directly to the nature of the surface forces which lead to the different wetting scenarios. Thermal fluctuation effects, which can be greatly enhanced for wetting of geometrically or chemically structured substrates, and are much stronger in colloidal suspensions, modify the adsorption singularities. Macroscopic descriptions and microscopic theories have been developed to understand and predict wetting behavior relevant to microfluidics and nanofluidics applications. Then the dynamics of wetting is examined. A drop, placed on a substrate which it wets, spreads out to form a film. Conversely, a nonwetted substrate previously covered by a film dewets upon an appropriate change of system parameters. The hydrodynamics of both wetting and dewetting is influenced by the presence of the three-phase contact line separating "wet" regions from those that are either dry or covered by a microscopic film only. Recent theoretical, experimental, and numerical progress in the description of moving contact line dynamics are reviewed, and its relation to the thermodynamics of wetting is explored. In addition, recent progress on rough surfaces is surveyed. The anchoring of contact lines and contact angle hysteresis are explored resulting from surface inhomogeneities. Further, new ways to mold wetting characteristics according to technological constraints are discussed, for example, the use of patterned surfaces, surfactants, or complex fluids.

/pdf/wetting-and-spreading-56ditqbfmj.pdf

Wetting and Spreading

Polysaccharide protein interactions

Preface 1 Introduction 1.1 Colloidal interactions 1.2 The Von Guericke force 1.3 Depletion 1.4 Manifestations of depletion effects in colloid + polymer mixtures 1.5 Historical overview on depletion 1.5.1 Experimental observations before the 1950s 1.5.2 Attractive forces in Nagoya 1.5.3 Systematic studies after AO 1.6 Outline of this book 2 Depletion Interaction 2.1 Depletion interaction due to penetrable spheres 2.1.1 Depletion interaction between two flat plates 2.1.2 Depletion interaction between two spheres 2.2 Depletion interaction due to ideal polymers 2.2.1 Depletion interaction between two flat plates 2.2.2 Interaction between two spheres 2.3 Depletion interaction due to excluded volume polymers 2.3.1 Characteristic length scales in polymer solutions 2.3.2 Osmotic pressure of polymer solutions 2.3.3 Depletion thickness due to excluded volume polymers 2.3.4 Evaluation of the depletion interaction due to excluded volume polymers 2.4 Depletion interaction due to spheres 2.4.1 Concentration profiles near a hard wall and between two hard walls 2.4.2 Depletion interaction between two flat plates 2.4.3 Depletion interaction between two (big) spheres 2.5 Depletion interaction due to rods 2.5.1 Depletion interaction between two flat plates 2.5.2 Interaction between two (big) colloidal spheres using the Derjaguin approximation 2.6 Depletion interaction due to disks 2.6.1 Depletion interaction between two flat plates 2 .6.2 Interaction bet ween two (big) colloidal spheres using the Derjaguin approximation 2.7 Measurements of depletion interactions 2.7.1 Atomic force microscope 2.7.2 Total internal eflection microscopy 2.7.3 Optical tweezers 3 Phase transitions of hard spheres plus depletants basics 3.1 Introduction -colloid/atom analogy 3.2 The hard sphere fluid-crystal transition 3.3 Free volume theory Appendix 3.1. Statistical Mechanical derivation of the Free Volume Theory 4 Stability of colloid-polymer mixtures 4.1 Experimental state diagrams of colloid-polymer mixtures 4.2 Phase behaviour of colloid + ideal polymer mixtures 4.3 Phase behaviour of sphere plus interacting polymer mixtures GFVT 4.3.1 Depletion thickness and osmotic pressure 4.3.2 Protein Limit 4.4 Non-equilibrium phenomena 4.4.1 Unmixing kinetics 4.4.2 Aggregation and gelation 4.4.3 Depletion effects on colloidal glasses 5 Phase transitions of hard spheres plus colloids 5.1 Free volume theory for big plus small hard spheres 5.2 Phase behavior of mixed spheres 5.2.1 Phase separation in binary mixtures differing only in diameter 5.2.2 Mixtures of latex particles and micelles 5.2.3 Oil-in-water emulsion particles and micelles of the stabilizing surfactant 5.3 free volume theory for sphere-rod mixtures 5.4 Phase behaviour of sphere-rod mixtures 6 Suspensions of rod-like colloids plus polymers 6.1 Onsager theory of the isotropic-nematic transition 6.2 Scaled particle theory of the isotropic-nematic transition 6.3 Isotropic-nematic phase behaviour of rods plus phs 6.4 I-N phase behaviour of rods plus polymers 6.4.1 Rod-like colloids plus ideal polymers 6.4.2 Rod-like colloids plus interacting polymers 6.5 Experiments on rod/polymer mixtures 6.5.1 Stiff virusparticles + polymer 6.5.2 Cellulose nanocrystals + polymer 6.5.3 Sterically stabilized colloidal boehmite rods + polymer 6.6 Rod/polymer mixtures: full phase diagrams. 6.7 Concluding remarks. List of symbols Index

/pdf/colloids-and-the-depletion-interaction-3i9xtcbr8e.pdf

Colloids and the Depletion Interaction

https://dspace.library.uu.nl/bitstream/handle/1874/14355/1434.pdf?sequence=1

Depletion-induced phase separation in colloid-polymer mixtures.

Deep eutectic solvents (DESs) based on terpenes are identified and characterized. 507 combinations of solid components are tested, which results in the identification of 17 new hydrophobic DESs. Four criteria are introduced to assess the sustainability of these hydrophobic DESs from a chemical engineering point of view. These criteria include a viscosity smaller than 100 mPa·s, a density difference between DES and water of at least 50 kg·m–3 upon mixing of the DES and water, low transfer of the DES to the water phase and minor to no pH change. The results show that five new hydrophobic DESs based on natural components satisfy these criteria; thymol and coumarin (2:1), thymol and menthol (1:1), thymol and coumarin (1:1), thymol and menthol (1:2) and 1-tetradecanol and menthol (1:2), and thus are promising DESs. These new DESs can be considered as natural deep eutectic solvents, which have the potential to be environmentally friendly. A selected group of the hydrophobic DESs were used for the extraction of ...

/pdf/a-search-for-natural-hydrophobic-deep-eutectic-solvents-1z436orz63.pdf

A Search for Natural Hydrophobic Deep Eutectic Solvents Based on Natural Components

Casein micelles in milk are proteinaceous colloidal particles and are essential for the production of flocculated and gelled products such as yogurt, cheese, and ice-cream. The colloidal stability of casein micelles is described here by a calculation of the pair potential, containing the essential contributions of brush repulsion, electrostatic repulsion, and van der Waals attraction. The parameters required are taken from the literature. The results are expressed by the second osmotic virial coefficient and are quite consistent with experimental findings. It appears that the stability is mainly attributable to a steric layer of κ-casein, which can be described as a salted polyelectrolyte brush.

/pdf/stability-of-casein-micelles-in-milk-18ripysho8.pdf

Remco Tuinier

Papers

Polysaccharide protein interactions

Colloids and the Depletion Interaction

Depletion-induced phase separation in colloid-polymer mixtures.

A Search for Natural Hydrophobic Deep Eutectic Solvents Based on Natural Components

Stability of casein micelles in milk