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

Chemokines direct tissue invasion by specific leukocyte populations. Thus, chemokines may play a role in multiple sclerosis (MS), an idiopathic disorder in which the central nervous system (CNS) inflammatory reaction is largely restricted to mononuclear phagocytes and T cells. We asked whether specific chemokines were expressed in the CNS during acute demyelinating events by analyzing cerebrospinal fluid (CSF), whose composition reflects the CNS extracellular space. During MS attacks, we found elevated CSF levels of three chemokines that act toward T cells and mononuclear phagocytes: interferon-γ–inducible protein of 10 kDa (IP-10); monokine induced by interferon-γ (Mig); and regulated on activation, normal T-cell expressed and secreted (RANTES). We then investigated whether specific chemokine receptors were expressed by infiltrating cells in demyelinating MS brain lesions and in CSF. CXCR3, an IP-10/Mig receptor, was expressed on lymphocytic cells in virtually every perivascular inflammatory infiltrate in active MS lesions. CCR5, a RANTES receptor, was detected on lymphocytic cells, macrophages, and microglia in actively demyelinating MS brain lesions. Compared with circulating T cells, CSF T cells were significantly enriched for cells expressing CXCR3 or CCR5. Our results imply pathogenic roles for specific chemokine–chemokine receptor interactions in MS and suggest new molecular targets for therapeutic intervention.

https://dm5migu4zj3pb.cloudfront.net/manuscripts/5000/5150/JCI9905150.pdf

Expression of specific chemokines and chemokine receptors in the central nervous system of multiple sclerosis patients

Phononic band-gap materials prevent elastic waves in certain frequency ranges from propagating, and they may therefore be used to generate frequency filters, as beam splitters, as sound or vibration protection devices, or as waveguides. In this work we show how topology optimization can be used to design and optimize periodic materials and structures exhibiting phononic band gaps. Firstly, we optimize infinitely periodic band-gap materials by maximizing the relative size of the band gaps. Then, finite structures subjected to periodic loading are optimized in order to either minimize the structural response along boundaries (wave damping) or maximize the response at certain boundary locations (waveguiding).

Systematic design of phononic band-gap materials and structures by topology optimization.

Topology optimization is a computational tool that can be used for the systematic design of photonic crystals, waveguides, resonators, filters and plasmonics. The method was originally developed for mechanical design problems but has within the last six years been applied to a range of photonics applications. Topology optimization may be based on finite element and finite difference type modeling methods in both frequency and time domain. The basic idea is that the material density of each element or grid point is a design variable, hence the geometry is parameterized in a pixel-like fashion. The optimization problem is efficiently solved using mathematical programming-based optimization methods and analytical gradient calculations. The paper reviews the basic procedures behind topology optimization, a large number of applications ranging from photonic crystal design to surface plasmonic devices, and lists some of the future challenges in non-linear applications.

Topology optimization for nano‐photonics

Phononic band gaps and vibrations in one- and two-dimensional mass-spring structures

Topology optimized architectures are designed and printed with programmable Poisson's ratios ranging from -0.8 to 0.8 over large deformations of 20% or more.

/pdf/topology-optimized-architectures-with-programmable-poisson-s-5909nf4kwg.pdf

Jakob Søndergaard Jensen

Papers

Expression of specific chemokines and chemokine receptors in the central nervous system of multiple sclerosis patients

Systematic design of phononic band-gap materials and structures by topology optimization.

Topology optimization for nano‐photonics

Phononic band gaps and vibrations in one- and two-dimensional mass-spring structures

Topology Optimized Architectures with Programmable Poisson's Ratio over Large Deformations