There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

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

基礎講座 電気泳動(Electrophoresis)

A review is presented of the present status of the theory, the developed technology and the current applications of dielectrophoresis (DEP). Over the past 10 years around 2000 publications have addressed these three aspects, and current trends suggest that the theory and technology have matured sufficiently for most effort to now be directed towards applying DEP to unmet needs in such areas as biosensors, cell therapeutics, drug discovery, medical diagnostics, microfluidics, nanoassembly, and particle filtration. The dipole approximation to describe the DEP force acting on a particle subjected to a nonuniform electric field has evolved to include multipole contributions, the perturbing effects arising from interactions with other cells and boundary surfaces, and the influence of electrical double-layer polarizations that must be considered for nanoparticles. Theoretical modelling of the electric field gradients generated by different electrode designs has also reached an advanced state. Advances in the technology include the development of sophisticated electrode designs, along with the introduction of new materials (e.g., silicone polymers, dry film resist) and methods for fabricating the electrodes and microfluidics of DEP devices (photo and electron beam lithography, laser ablation, thin film techniques, CMOS technology). Around three-quarters of the 300 or so scientific publications now being published each year on DEP are directed towards practical applications, and this is matched with an increasing number of patent applications. A summary of the US patents granted since January 2005 is given, along with an outline of the small number of perceived industrial applications (e.g., mineral separation, micropolishing, manipulation and dispensing of fluid droplets, manipulation and assembly of micro components). The technology has also advanced sufficiently for DEP to be used as a tool to manipulate nanoparticles (e.g., carbon nanotubes, nano wires, gold and metal oxide nanoparticles) for the fabrication of devices and sensors. Most efforts are now being directed towards biomedical applications, such as the spatial manipulation and selective separation/enrichment of target cells or bacteria, high-throughput molecular screening, biosensors, immunoassays, and the artificial engineering of three-dimensional cell constructs. DEP is able to manipulate and sort cells without the need for biochemical labels or other bioengineered tags, and without contact to any surfaces. This opens up potentially important applications of DEP as a tool to address an unmet need in stem cell research and therapy.

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Review Article—Dielectrophoresis: Status of the theory, technology, and applications

Driven by functionality and purity demand for applications of inorganic nanoparticle colloids in optics, biology, and energy, their surface chemistry has become a topic of intensive research interest. Consequently, ligand-free colloids are ideal reference materials for evaluating the effects of surface adsorbates from the initial state for application-oriented nanointegration purposes. After two decades of development, laser synthesis and processing of colloids (LSPC) has emerged as a convenient and scalable technique for the synthesis of ligand-free nanomaterials in sealed environments. In addition to the high-purity surface of LSPC-generated nanoparticles, other strengths of LSPC include its high throughput, convenience for preparing alloys or series of doped nanomaterials, and its continuous operation mode, suitable for downstream processing. Unscreened surface charge of LSPC-synthesized colloids is the key to achieving colloidal stability and high affinity to biomolecules as well as support materials,...

Laser Synthesis and Processing of Colloids: Fundamentals and Applications

The use of femtosecond laser pulses allows precise and thermal-damage-free removal of material (ablation) with wide-ranging scientific, medical and industrial applications. However, its potential is limited by the low speeds at which material can be removed and the complexity of the associated laser technology. The complexity of the laser design arises from the need to overcome the high pulse energy threshold for efficient ablation. However, the use of more powerful lasers to increase the ablation rate results in unwanted effects such as shielding, saturation and collateral damage from heat accumulation at higher laser powers. Here we circumvent this limitation by exploiting ablation cooling, in analogy to a technique routinely used in aerospace engineering. We apply ultrafast successions (bursts) of laser pulses to ablate the target material before the residual heat deposited by previous pulses diffuses away from the processing region. Proof-of-principle experiments on various substrates demonstrate that extremely high repetition rates, which make ablation cooling possible, reduce the laser pulse energies needed for ablation and increase the efficiency of the removal process by an order of magnitude over previously used laser parameters. We also demonstrate the removal of brain tissue at two cubic millimetres per minute and dentine at three cubic millimetres per minute without any thermal damage to the bulk.

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Ablation-cooled material removal with ultrafast bursts of pulses

Dielectrophoresis (DEP) is the movement of a particle in a non-uniform electric field due to the interaction of the particle's dipole and spatial gradient of the electric field. DEP is a subtle solution to manipulate particles and cells at microscale due to its favorable scaling for the reduced size of the system. DEP has been utilized for many applications in microfluidic systems. In this review, a detailed analysis of the modeling of DEP-based manipulation of the particles is provided, and the recent applications regarding the particle manipulation in microfluidic systems (mainly the published works between 2007 and 2010) are presented.

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Dielectrophoresis in microfluidics technology

Continuous particle separation with localized AC-dielectrophoresis using embedded electrodes and an insulating hurdle

The Joule heating (JH) is a ubiquitous phenomenon in electrokinetic flow due to the presence of electrical potential gradient and electrical current. JH may become pronounced for applications with high electrical potential gradients or with high ionic concentration buffer solutions. In this review, an in-depth look at the effect of JH on electrokinetic processes is provided. Theoretical modeling of EOF and electrophoresis (EP) with the presence of JH is presented and the important findings from the previous studies are examined. A numerical study of a fused-silica capillary PCR reactor powered by JH is also presented to extend the discussion of favorable usage of JH.

Effect of Joule heating on electrokinetic transport.

In this paper, we present a novel, simple lab-on-a-chip device for continuous separation of particles by size. The device is composed of a straight rectangular microchannel connecting two inlet reservoirs and two exit reservoirs. Two asymmetric, 3-D electrodes are embedded along the channel wall to generate a non-uniform electrical field for dielectrophoresis. Particles with different sizes are collected at the different exit reservoirs. Main flow is induced by pressure difference between the inlet and the exit reservoirs. The device is used successfully for the separation of the 5 and 10 mum latex particles and for the separation of yeast cells and white blood cells. A numerical simulation based on Lagrangian tracking method is used to simulate the particle motion and the results showed a good agreement with the experimental data.

Barbaros Çetin

Papers

Ablation-cooled material removal with ultrafast bursts of pulses

Dielectrophoresis in microfluidics technology

Continuous particle separation with localized AC-dielectrophoresis using embedded electrodes and an insulating hurdle

Effect of Joule heating on electrokinetic transport.

Continuous particle separation by size via AC-dielectrophoresis using a lab-on-a-chip device with 3-D electrodes