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

An introduction to heat transfer

Capillarity and Wetting Phenomena: Drops, Bubbles, Pearls, Waves

The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too hydrophobic, and dimers formed by polar residues in apolar solvents did not bind strongly enough. Here, we reparametrize these residues either through reassignment of particle types or by introducing embedded charges. The new parameters are tested with respect to partitioning across a lipid bilayer, membrane binding of Wimley–White peptides, and dimerization free energy in solvents of different polarity. In addition, we improve some of the bonded terms in the Martini protein force field that lead to a more realistic length of α-helices and to improved numerical stability for polyalanine and glycine repeats. The new parameter set is denoted Martini version 2.2.

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Improved Parameters for the Martini Coarse-Grained Protein Force Field

The Martini model, a coarse-grained force field for biomolecular simulations, has found a broad range of applications since its release a decade ago. Based on a building block principle, the model combines speed and versatility while maintaining chemical specificity. Here we review the current state of the model. We describe recent highlights as well as shortcomings, and our ideas on the further development of the model.

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Perspective on the Martini model.

In molecular dynamics (MD) simulations, interactions between water molecules and graphitic surfaces are often modeled as a simple Lennard-Jones potential between oxygen and carbon atoms. A possible method for tuning this parameter consists of simulating a water nanodroplet on a flat graphitic surface, measuring the equilibrium contact angle, extrapolating it to the limit of a macroscopic droplet, and finally matching this quantity to experimental results. Considering recent evidence demonstrating that the contact angle of water on a graphitic plane is much higher than what was previously reported, we estimate the oxygen-carbon interaction for the recent SPC/Fw water model. Results indicate a value of about 0.2 kJ/mol, much lower than previous estimations. We then perform simulations of cylindrical water filaments on graphitic surfaces, in order to compare and correlate contact angles resulting from these two different systems. Results suggest that a modified Young's equation does not describe the relation between contact angle and drop size in the case of extremely small systems and that contributions different from the one deriving from contact line tension should be taken into account.

Wetting and contact-line effects for spherical and cylindrical droplets on graphene layers: a comparative molecular-dynamics investigation.

A systematic study of the additive manufacturing of complex ceramic objects was carried out using two different Digital Light Processing (DLP) approaches, the "bottom-up" and "top-down" ones, employing the same projector as light source and a photosensitive Al2O3-based ceramic slurry. Cylindrical periodic architectures having different macro-porosity, as well a bulk (dense) component in the form of a disk, were designed and additively manufactured with the two printers employing similar printing conditions. In the "bottom-up" approach, the periodic detachment of the part being manufactured from the bottom surface of the vat, to enable the insertion of a fresh layer of slurry, introduced stresses and deformations in the component, leading to several problems. In the "top-down" approach, the main issue is that the thickness of the printed slices is not precise and constant, due to the difficulty of the viscous slurry to uniformly wet and coat the already printed layers.

Additive Manufacturing of ceramic components by Digital Light Processing: A comparison between the “bottom-up” and the “top-down” approaches

Cellular ceramics produced by rapid prototyping and replication

In the field of thermal shielding for aerospace applications C f /SiC composites are raising great interest, provided that they are protected from oxidation by suitable coatings. Conversely, ultra high temperature ceramics, and in particular HfB 2 , are among the best oxidation resistant materials known. A coating made of a HfB 2 /SiC composite (20% weight SiC) was tested as an oxidation protection on a C f /SiC composite. The composite was produced by Polymer Impregnation Pyrolysis (PIP), which is a simple and low cost method; the coating was applied by painting a slurry on the surface of the composite and by heat treating. The thermal behaviour was studied by thermo-gravimetric analysis, and mechanical tests were conducted before and after oxidation. The HfB 2 /SiC composite seems to effectively protect the underlying C f /SiC composite, with a mechanical strength reduction of only 20% after 30 min at 1600 °C, even if some weight loss due to partial carbon fibre damage is observed. A first analysis of thermal cycling in oxidizing environment suggested that the HfB 2 /SiC coating reduces continual damage thanks to the sealing effect of the glassy surface layer.

Alberto Ortona

Papers

Wetting and contact-line effects for spherical and cylindrical droplets on graphene layers: a comparative molecular-dynamics investigation.

Additive Manufacturing of ceramic components by Digital Light Processing: A comparison between the “bottom-up” and the “top-down” approaches

Cellular ceramics produced by rapid prototyping and replication

HfB2/SiC as a protective coating for 2D Cf/SiC composites: Effect of high temperature oxidation on mechanical properties

Molecular dynamics simulations of the contact angle between water droplets and graphite surfaces