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

Responsive polymer materials can adapt to surrounding environments, regulate transport of ions and molecules, change wettability and adhesion of different species on external stimuli, or convert chemical and biochemical signals into optical, electrical, thermal and mechanical signals, and vice versa. These materials are playing an increasingly important part in a diverse range of applications, such as drug delivery, diagnostics, tissue engineering and 'smart' optical systems, as well as biosensors, microelectromechanical systems, coatings and textiles. We review recent advances and challenges in the developments towards applications of stimuli-responsive polymeric materials that are self-assembled from nanostructured building blocks. We also provide a critical outline of emerging developments.

Emerging applications of stimuli-responsive polymer materials

An all-atom protein force field, CHARMM36m, offers improved accuracy for simulating intrinsically disordered peptides and proteins. The all-atom additive CHARMM36 protein force field is widely used in molecular modeling and simulations. We present its refinement, CHARMM36m (
 http://mackerell.umaryland.edu/charmm_ff.shtml
 ), with improved accuracy in generating polypeptide backbone conformational ensembles for intrinsically disordered peptides and proteins.

/pdf/charmm36m-an-improved-force-field-for-folded-and-hi2fge7lt7.pdf

CHARMM36m: An improved force field for folded and intrinsically disordered proteins

http://www.uniroma2.it/didattica/tbs2/deposito/Manufacture,_characterisation_and_application_of_cellular_metals_and_metal_foams.pdf

Manufacture, characterisation and application of cellular metals and metal foams

Many biologically interesting phenomena occur on a time scale that is too long to be studied by atomistic simulations. These phenomena include the dynamics of large proteins and self-assembly of biological materials. Coarse-grained (CG) molecular modeling allows computer simulations to be run on length and time scales that are 2–3 orders of magnitude larger compared to atomistic simulations, providing a bridge between the atomistic and the mesoscopic scale. We developed a new CG model for proteins as an extension of the MARTINI force field. Here, we validate the model for its use in peptide-bilayer systems. In order to validate the model, we calculated the potential of mean force for each amino acid as a function of its distance from the center of a dioleoylphosphatidylcholine (DOPC) lipid bilayer. We then compared amino acid association constants, the partitioning of a series of model pentapeptides, the partitioning and orientation of WALP23 in DOPC lipid bilayers and a series of KALP peptides in dimyris...

The MARTINI Coarse-Grained Force Field: Extension to Proteins

https://pure.rug.nl/ws/files/3103420/2001IntJMechSciAndrews.pdf

Size effects in ductile cellular solids. Part II : experimental results

This paper describes the spontaneous formation of patterns of aligned buckles in a thin film of gold deposited on the surface of an elastomer [poly(dimethylsiloxane), PDMS]. The surface of the elastomer is patterned photochemically into areas differing in stiffness and coefficient of thermal expansion. The gold is deposited while the surface of the patterned elastomer is warm (T ∼ 100 °C). On cooling, shrinkage in the elastomer places the gold film under compressive stress. The buckles relieve this compressive stress. The distribution of stresses and buckle patterns is described during the pre- and postbuckling regimes using solutions from calculations describing a model comprising a thin stiff plate resting on a thick elastic foundation.

Ordering of Spontaneously Formed Buckles on Planar Surfaces

Strain stiffening of filamentous protein networks is explored by means of a finite strain analysis of a two-dimensional network model of cross-linked semiflexible filaments The results show that stiffening is caused by nonaffine network rearrangements that govern a transition from a bending-dominated response at small strains to a stretching-dominated response at large strains Filament undulations, which are key in the existing explanation of stiffening, merely postpone the transition

https://pure.rug.nl/ws/files/2887609/2005PhysRevLettOnck.pdf

Alternative Explanation of Stiffening in Cross-Linked Semiflexible Networks

https://pure.rug.nl/ws/files/3106995/2001IntJMechSciOnck1.pdf

Size effects in ductile cellular solids. Part I: modeling

In the mechanical testing of metallic foams, an important issue is the e!ect of the specimen size, relative to the cell size, on the measured properties. Here we analyze size e!ects for the modulus and strength of regular, hexagonal honeycombs under uniaxial and shear loadings. Size e!ects for indentation of a honeycomb are evaluated using "nite element analysis. Finally, the results for honeycombs are extrapolated to foams. The results are compared with data for metallic foams in the following, companion paper. ( 2000 Elsevier Science Ltd. All rights reserved.

Patrick Onck

Papers

Size effects in ductile cellular solids. Part II : experimental results

Ordering of Spontaneously Formed Buckles on Planar Surfaces

Alternative Explanation of Stiffening in Cross-Linked Semiflexible Networks

Size effects in ductile cellular solids. Part I: modeling

Size e!ects in ductile cellular solids. Part I: modeling