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

Vector beams, and in particular vector vortex beams, have found many applications in recent times, both as classical fields and as quantum states. While much attention has focused on the creation and detection of scalar optical fields, it is only recently that vector beams have found their place in the modern laboratory. In this review, we outline the fundamental concepts of vector beams, summarise the various approaches to control them in the laboratory, and give a concise overview of the many applications they have spurned.

https://iopscience.iop.org/article/10.1088/2040-8986/aaeb7d/pdf

A review of complex vector light fields and their applications

Microbial fuel cell performance with non-Pt cathode catalysts

Currently, cylindrical beams with radial or azimuthal polarization are being used successfully for the optical manipulation of micro- and nano-particles as well as in microscopy, lithography, nonlinear optics, materials processing, and telecommunication applications. The creation of these laser beams is carried out using segmented polarizing plates, subwavelength gratings, interference, or light modulators. Here, we demonstrate the conversion of cylindrically polarized laser beams from a radial to an azimuthal polarization, or vice versa, by introducing a higher-order vortex phase singularity. To simultaneously generate several vortex phase singularities of different orders, we utilized a multi-order diffractive optical element. Both the theoretical and the experimental results regarding the radiation transmitted through the diffractive optical element show that increasing the order of the phase singularity leads to more efficient conversation of the polarization from radial to azimuthal. This demonstrates a close connection between the polarization and phase states of electromagnetic beams, which has important implications in many optical experiments.

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Polarization conversion when focusing cylindrically polarized vortex beams.

Engineering efficient, directional electronic communication between living and nonliving systems has the potential to combine the unique characteristics of both materials for advanced biotechnological applications. However, the cell membrane is designed by nature to be an insulator, restricting the flow of charged species; therefore, introducing a biocompatible pathway for transferring electrons across the membrane without disrupting the cell is a significant challenge. Here we describe a genetic strategy to move intracellular electrons to an inorganic extracellular acceptor along a molecularly defined route. To do so, we reconstitute a portion of the extracellular electron transfer chain of Shewanella oneidensis MR-1 into the model microbe Escherichia coli. This engineered E. coli can reduce metal ions and solid metal oxides ∼8× and ∼4× faster than its parental strain. We also find that metal oxide reduction is more efficient when the extracellular electron acceptor has nanoscale dimensions. This work demonstrates that a genetic cassette can create a conduit for electronic communication from living cells to inorganic materials, and it highlights the importance of matching the size scale of the protein donors to inorganic acceptors.

/pdf/engineering-of-a-synthetic-electron-conduit-in-living-cells-55gjztvs09.pdf

Engineering of a synthetic electron conduit in living cells

The generation of cylindrical vector beams in birefringent crystals is studied analytically and experimentally in paraxial and non-paraxial regimes. At sharp focusing (in the non-paraxial case), two foci corresponding ordinary and extraordinary beams are formed along the crystal’s axis. There is the radially polarized distribution in one focus and the azimuthally polarized distribution in the other focus when the incident beam has the vortex phase of the first order and circular polarization of the opposite direction. The results are extended to the generation of higher-order radially and azimuthally polarized laser beams. The physical experiments with an Iceland spar crystal have been conducted.

https://iopscience.iop.org/article/10.1088/2040-8978/17/6/065001/pdf

Generation of cylindrical vector beams of high orders using uniaxial crystals

We study the sharp focusing of differently polarized low-order and high-order beams, including Bessel and Laguerre-Gaussian (LG) modes, to compare them using several criteria: the size of a light spot, the intensity ratio of the central peak and sidelobes, and the intensity of the longitudinal electric field component. The experiments performed using the near-field microscopy techniques are in general agreement with the results of the numerical simulation. We have validated the growth of the longitudinal component in the focus for high-order modes at moderate NA=0.6-0.8, and essential lower sidelobes of Bessel modes, in comparison with LG modes.

Strengthening the longitudinal component of the sharply focused electric field by means of higher-order laser beams

We analytically and numerically show that by introducing asymmetry into axicon design it becomes possible to generate the longitudinal E-field component on the optical axis for linearly and circularly polarized incident beams. Binary axicons with high numerical aperture (NA) are fabricated in three configurations?axisymmetric and spiral, and bi-axicon?by electron beam lithography. Experimental measurements for the near-field diffraction of the most common and easy to implement incident beams?linearly and circularly polarized?are conducted. The experimental results agree with the theoretical analysis.

https://iopscience.iop.org/article/10.1088/2040-8978/15/8/085704/pdf

Experimental demonstration of the generation of the longitudinal E-field component on the optical axis with high-numerical-aperture binary axicons illuminated by linearly and circularly polarized beams

Yeast-based self-organized hybrid bio-silica sol-gels for the design of biosensors

We propose a new approach to generating a pair of initial beams for a polarization converter that operates by summing up two opposite-sign circularly polarized beams. The conjugated pairs of vortex beams matched with laser modes are generated using binary diffractive optical elements (DOEs). The same binary element simultaneously serves two functions: a beam shaper and a beam splitter. Two proposed optical arrangements are compared in terms of alignment complexity and energy efficiency. The DOEs in question have been designed and fabricated. Natural experiments that demonstrate the generation of vector higher-order cylindrical beams have been conducted.

S. V. Alferov

Papers

Generation of cylindrical vector beams of high orders using uniaxial crystals

Strengthening the longitudinal component of the sharply focused electric field by means of higher-order laser beams

Experimental demonstration of the generation of the longitudinal E-field component on the optical axis with high-numerical-aperture binary axicons illuminated by linearly and circularly polarized beams

Yeast-based self-organized hybrid bio-silica sol-gels for the design of biosensors

Polarization converter for higher-order laser beams using a single binary diffractive optical element as beam splitter