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 term photonic crystals appears because of the analogy between electron waves in crystals and the light waves in artificial periodic dielectric structures. During the recent years the investigation of one-, two-and three-dimensional periodic structures has attracted a widespread attention of the world optics community because of great potentiality of such structures in advanced applied optical fields. The interest in periodic structures has been stimulated by the fast development of semiconductor technology that now allows the fabrication of artificial structures, whose period is comparable with the wavelength of light in the visible and infrared ranges.

http://ieeexplore.ieee.org/iel5/6354/16969/00781867.pdf

Photonic crystals

In this review, the authors discuss the properties of chemokines and their receptors and highlight the roles of these chemoattractants in selected clinical disorders.

The Many Roles of Chemokines and Chemokine Receptors in Inflammation

MSCs are nonhematopoietic stromal cells that are capable of differentiating into, and contribute to the regeneration of, mesenchymal tissues such as bone, cartilage, muscle, ligament, tendon, and adipose. MSCs are rare in bone marrow, representing approximately 1 in 10,000 nucleated cells. Although not immortal, they have the ability to expand manyfold in culture while retaining their growth and multilineage potential. MSCs are identified by the expression of many molecules including CD105 (SH2) and CD73 (SH3/4) and are negative for the hematopoietic markers CD34, CD45, and CD14. The properties of MSCs make these cells potentially ideal candidates for tissue engineering. It has been shown that MSCs, when transplanted systemically, are able to migrate to sites of injury in animals, suggesting that MSCs possess migratory capacity. However, the mechanisms underlying the migration of these cells remain unclear. Chemokine receptors and their ligands and adhesion molecules play an important role in tissue-specific homing of leukocytes and have also been implicated in trafficking of hematopoietic precursors into and through tissue. Several studies have reported the functional expression of various chemokine receptors and adhesion molecules on human MSCs. Harnessing the migratory potential of MSCs by modulating their chemokine-chemokine receptor interactions may be a powerful way to increase their ability to correct inherited disorders of mesenchymal tissues or facilitate tissue repair in vivo. The current review describes what is known about MSCs and their capacity to home to tissues together with the associated molecular mechanisms involving chemokine receptors and adhesion molecules.

https://stemcellsjournals.onlinelibrary.wiley.com/doi/epdf/10.1634/stemcells.2007-0197

Concise review: mesenchymal stem cells: their phenotype, differentiation capacity, immunological features, and potential for homing.

Multiple sclerosis (MS) develops in young adults with a complex predisposing genetic trait and probably requires an inciting environmental insult such as a viral infection to trigger the disease. The activation of CD4+ autoreactive T cells and their differentiation into a Th1 phenotype are a crucial events in the initial steps, and these cells are probably also important players in the long-term evolution of the disease. Damage of the target tissue, the central nervous system, is, however, most likely mediated by other components of the immune system, such as antibodies, complement, CD8+ T cells, and factors produced by innate immune cells. Perturbations in immunomodulatory networks that include Th2 cells, regulatory CD4+ T cells, NK cells, and others may in part be responsible for the relapsing-remitting or chronic progressive nature of the disease. However, an important paradigmatic shift in the study of MS has occurred in the past decade. It is now clear that MS is not just a disease of the immune system, but that factors contributed by the central nervous system are equally important and must be considered in the future.

Immunology of multiple sclerosis

Materials with good vibration damping properties and high stiffness are of great industrial interest. In this paper the bounds for viscoelastic composites are investigated and material microstructures that realize the upper bound are obtained by topology optimization. These viscoelastic composites can be realized by additive manufacturing technologies followed by an infiltration process. Viscoelastic composites consisting of a relatively stiff elastic phase, e.g. steel, and a relatively lossy viscoelastic phase, e.g. silicone rubber, have non-connected stiff regions when optimized for maximum damping. In order to ensure manufacturability of such composites the connectivity of the matrix is ensured by imposing a conductivity constraint and the influence on the bounds is discussed.

https://orbit.dtu.dk/files/81738290/viscoelastic_composites.pdf

On the realization of the bulk modulus bounds for two-phase viscoelastic composites

Wave motion in a continuous elastic rod with a periodically attached inertial-amplification mechanism is investigated. The mechanism has properties similar to an "inerter" typically used in vehicle suspensions, however here it is constructed and utilized in a manner that alters the intrinsic properties of a continuous structure. The elastodynamic band structure of the hybrid rod-mechanism structure yields band gaps that are exceedingly wide and deep when compared to what can be obtained using standard local resonators, while still being low in frequency. With this concept, a large band gap may be realized with as much as twenty times less added mass compared to what is needed in a standard local resonator configuration. The emerging inertially enhanced continuous structure also exhibits unique qualitative features in its dispersion curves. These include the existence of a characteristic double-peak in the attenuation constant profile within gaps and the possibility of coalescence of two neighbouring gaps creating a large contiguous gap.

/pdf/inertial-amplification-of-continuous-structures-large-band-whxn6ecn6k.pdf

Inertial amplification of continuous structures: Large band gaps from small masses

Acoustical topology optimization for Zwicker’s loudness model – Application to noise barriers

Inverse design of photonic crystals by topology optimization

Much is known about the nonlinear resonant response of mechanical systems, but methods for the systematic design of structures that optimize aspects of these responses have received little attention. Progress in this area is particularly important in the area of micro-systems, where nonlinear resonant behaviour is being used for a variety of applications in sensing and signal conditioning. In this work, we describe a computational method that provides a systematic means for manipulating and optimizing features of nonlinear resonant responses of mechanical structures that are described by a single vibrating mode, or by a pair of internally resonant modes. The approach combines techniques from nonlinear dynamics, computational mechanics and optimization, and it allows one to relate the geometric and material properties of structural elements to terms in the normal form for a given resonance condition, thereby providing a means for tailoring its nonlinear response. The method is applied to the fundamental nonlinear resonance of a clamped-clamped beam and to the coupled mode response of a frame structure, and the results show that one can modify essential normal form coefficients by an order of magnitude by relatively simple changes in the shape of these elements. We expect the proposed approach, and its extensions, to be useful for the design of systems used for fundamental studies of nonlinear behaviour as well as for the development of commercial devices that exploit nonlinear behaviour.

https://royalsocietypublishing.org/doi/pdf/10.1098/rsta.2014.0408

Jakob Søndergaard Jensen

Papers

On the realization of the bulk modulus bounds for two-phase viscoelastic composites

Inertial amplification of continuous structures: Large band gaps from small masses

Acoustical topology optimization for Zwicker’s loudness model – Application to noise barriers

Inverse design of photonic crystals by topology optimization

Structural optimization for nonlinear dynamic response