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

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Titanium Dioxide Nanomaterials: Synthesis, Properties, Modifications, and Applications

The interest in nanoscale materials stems from the fact that new properties are acquired at this length scale and, equally important, that these properties * To whom correspondence should be addressed. Phone, 404-8940292; fax, 404-894-0294; e-mail, mostafa.el-sayed@ chemistry.gatech.edu. † Case Western Reserve UniversitysMillis 2258. ‡ Phone, 216-368-5918; fax, 216-368-3006; e-mail, burda@case.edu. § Georgia Institute of Technology. 1025 Chem. Rev. 2005, 105, 1025−1102

Chemistry and properties of nanocrystals of different shapes.

We present a comprehensive, up-to-date compilation of band parameters for the technologically important III–V zinc blende and wurtzite compound semiconductors: GaAs, GaSb, GaP, GaN, AlAs, AlSb, AlP, AlN, InAs, InSb, InP, and InN, along with their ternary and quaternary alloys. Based on a review of the existing literature, complete and consistent parameter sets are given for all materials. Emphasizing the quantities required for band structure calculations, we tabulate the direct and indirect energy gaps, spin-orbit, and crystal-field splittings, alloy bowing parameters, effective masses for electrons, heavy, light, and split-off holes, Luttinger parameters, interband momentum matrix elements, and deformation potentials, including temperature and alloy-composition dependences where available. Heterostructure band offsets are also given, on an absolute scale that allows any material to be aligned relative to any other.

Band parameters for III–V compound semiconductors and their alloys

This study investigates the dependence of the luminescence linewidth from thin quantum wells grown by molecular beam epitaxy on misorientated substrates with (110) terraces of different widths. The narrow luminescence linewidths observed from quantum wells grown on exactly orientated (001) surfaces, 6.7 meV for a five-monolayer well, make them particularly suited to sensing changes in interface roughness associated with either substrate misorientation or growth interruption. An increased luminescence linewidth was found to occur during growth interruption, for example 2.2 meV to 7.2 meV for a 20-monolayer well. This was due to the scale of the roughness at the interface becoming similar in size to that of the sensing exciton wavefunction. The authors suggest this may be related to an increase of the island size at the inverted interface along the (110) direction.

http://iopscience.iop.org/article/10.1088/0268-1242/7/7/004/pdf

The optical properties of thin Al0.3Ga0.7As-GaAs quantum wells on misorientated substrates with (110) terraces. A study of interface roughness using photoluminescence

Using contactless photoreflectance at 300K and 77K we have investigated the intersubband transitions from two modulation-doped GaAs/GaAlAs quantum dot (QD) arrays fabricated by reactive-ion etching (RIE). The samples consisted of 8 nm decoupled GaAs/GaAlAs quantum wells with dot sizes (lateral dimensions) of 60 and 100 nm. The lineshapes of the “1C-1H” and “1C-1L” features were indicative of a screened exciton, i.e., the derivative of a broadened two-dimensional density of states (step function), due to the presence of the electron gas. On the other hand, even at 300K the “2C-2H” features exhibited a well-defined sharp excitonic lineshape, i.e., derivative of a Gaussian profile. Even at room temperature it is possible to detect the effects of the lateral quantum confinement. We have observed a 2 meV blue shift of the “2C-2H” feature of the 60 nm QD array in relation to the 100 nm QD array. At 77K we have found evidence for a “parabolic-like” in-plane confining potential on the smaller QD array. This experiment demonstrates the considerable utility of PR in studying these reduced dimensional systems.

Photoreflectance Study of Modulation-Doped GaAs/GaAlAs Quantum Dots Fabricated by Reactive-Ion Etching

We present experimental and theoretical results on the low temperature luminescence intensity of dry etched GaAs-AlxGa1−x As quantum dots. The luminescence intensity was found to decrease by two orders of magnitude with the decrease of dot sizes from 1µm to 60nm. Our intrinsic model of the emission yield invokes slower momentum and energy relaxation mechanisms as the lateral dimensions decrease. The extrinsic effect, which we include in our interpretation of the luminescence intensity, involves carrier diffusion with a surface nonradiative recombination velocity. The combined effect (intrinsic and extrinsic) gives a good fit to our data. The surface recombination velocity needed for the fit was ~105cm/s. Raman studies of quantum dot arrays showed enhanced surface phonons with the decrease of the nanostructure sizes. “GaAs”-like and “AlAs”-like surface phonons were also observed for the first time in etched nanostructures, in good agreement with theoretical predications.

Luminescence and Raman Scattering Studies of Ga-As-AlGaAs Quantum Dots

Enhanced exciton binding energy in InAs monolayers grown on (311)A GaAs substrates

We report resonant Raman scattering and ‘hot’ carrier luminescence from deep dry etched GaAs-AlGaAs quantum dots. Up to 4th-order multiphonon processes were observed for the first time via photoluminescence (PL) and excitation of PL (PLE) in quantum dots. Quantum confinement effects were also found with various dot sizes. Confined and interface phonons play an important role in the carrier relaxation process. It demonstrates that Raman scattering is mediated by the zero dimensional (0D) electronic states. The measured GaAs mode frequencies are found to agree well with the theoretical bulk LO phonon dispersion curve.

C. M. Sotomayor Torres

Papers

The optical properties of thin Al0.3Ga0.7As-GaAs quantum wells on misorientated substrates with (110) terraces. A study of interface roughness using photoluminescence

Photoreflectance Study of Modulation-Doped GaAs/GaAlAs Quantum Dots Fabricated by Reactive-Ion Etching

Luminescence and Raman Scattering Studies of Ga-As-AlGaAs Quantum Dots

Enhanced exciton binding energy in InAs monolayers grown on (311)A GaAs substrates

Phonon Confinement and Electron-Phonon Interactions in Semiconductor Nanostructures