nMoldyn 3: Using task farming for a parallel spectroscopy‐oriented analysis of molecular dynamics simulations

We present a new version of the program package nMoldyn, which has been originally developed for a neutron‐scattering oriented analysis of molecular dynamics simulations of macromolecular systems (Kneller et al., Comput. Phys. Commun. 1995, 91, 191) and was later rewritten to include in‐depth time series analyses and a graphical user interface (Rog et al., J. Comput. Chem. 2003, 24, 657). The main improvement in this new version and the focus of this article are the parallelization of all the analysis algorithms for use on multicore desktop computers as well as distributed‐memory computing clusters. The parallelization is based on a task farming approach which maintains a simple program structure permitting easy modification and extension of the code to integrate new analysis methods. © 2012 Wiley Periodicals, Inc.     

Reconfigurable three-dimensional DNA nanostructures for the construction of intracellular logic sensors

Right out of the (logic) gate: Logic gates made from 3D DNA nanotetrahedra were constructed that are responsive to various ions, small molecules, and short strands of DNA. By including dynamic sequences in one or more edges of the tetrahedra, a FRET signal can be generated in the manner of AND, OR, XOR, and INH logic gates, as well as a half-adder circuit. These DNA logic gates were also applied to intracellular detection of ATP.     

组合材料学研究进展

综述了近年来组合材料学的研究进展. 首先简介了组合材料学的基本概念和历史传承, 然后重点介绍了组合材料学中的并行合成方法和高通量表征技术, 最后展示了一些用组合方法筛选新材料的成功范例. 并行合成方面包括：液滴喷射技术、阵列燃烧法、结合薄膜沉积的四元掩模技术和结合薄膜沉积的原位掩模技术等；高通量表征部分包括：针对发光表征的照相术, 扫描X射线结构/成分分析技术, 介电/铁电表征技术等. 在范例中, 给出一个发光材料, 一个磁电材料和一个电催化材料组合研究的例子. 最后, 对组合材料学的现状和未来进行了分析和展望.     

Intramolecular Hamiltonian logic gates

An intramolecular computing model is presented that is based on the quantum time evolution of a single molecule driven by the preparation of a non-stationary single-electron state. In our scheme, the input bits are encoded into the coupling constants of the Hamiltonian that governs the molecular quantum dynamics. The results of the computation are obtained by carrying out a quantum measurement on the molecule. We design reliable , , and logic gates. This opens new avenues for the design of more complex logic circuits at a single-molecular scale.     

Balanced steady-state free precession with parallel imaging gives distortion-free fMRI with high temporal resolution

Research on the functions of the human brain requires that functional magnetic resonance imaging (MRI) moves towards producing images with less distortion and higher temporal and spatial resolution. This study compares passband balanced steady-state free precession (bSSFP) acquisitions with and without parallel imaging (PI) to investigate whether combining PI with this pulse sequence is a viable option for functional MRI. Such a novel combination has the potential to offer the distortion-free advantages of bSSFP with the reduced acquisition time of PI. Scans were done on a Philips 3T Intera, using the installed bSSFP pulse sequence, both with and without the sensitivity encoding (SENSE) PI option. The task was a visual flashing checkerboard, and the viewing window covered the visual cortex. Sensitivity comparisons with and without PI were done using the same manually drawn region of interest for each time course of the subject, and comparing the z-score summary statistics: number of voxels with z>2.3, the mean of those voxels, their 90th percentile and their maximum value. We show that PI greatly improves the temporal resolution in bSSFP, reducing the volume acquisition time by more than half in this study to 0.67 s with 3-mm isotropic voxels. At the same time, a statistically significant increase was found for the maximum z-score using bSSFP with PI as compared to without it (P=.02). This improvement can be understood in terms of physiological noise, as demonstrated by noise measurements. This produces observed increases in the overall temporal signal to noise of the functional time series, giving greater sensitivity to functional activations with PI. This study demonstrates for the first time the possibility of combining PI with bSSFP to achieve distortion-free functional images without loss of sensitivity and with high temporal resolution.     

Note on Shim and Kim’s lower bounds for scheduling on identical parallel machines to minimize total tardiness

This note introduces a new lower bound for the problem of scheduling on parallel identical machines to minimize total tardiness that is based on the concepts used in the two lower bounds developed by Shim and Kim [Shim, S.O., Kim, Y.D., 2007. Scheduling on parallel identical machines to minimize total tardiness. European Journal of Operational Research 177, 135–146]. The note shows that the new lower bound dominates the three lower bounds used in Shim and Kim’s branch-and-bound algorithm and can be used in place of these lower bounds to lower the enumeration required.     

Spin Ensembles Coupled to Superconducting Resonators: A Scalable Architecture for Solid-State Quantum Computing

A design is proposed for scalable solid-state quantum computing, which is based on collectively enhanced magnetic coupling between nitrogen-vacancy center ensembles and superconducting transmission line resonators interconnected by current-biased Josephson junction superconducting phase qubit. In this hybrid system, we realize distant multi-qubit controlled phase gate operations and generate distant multi-qubit entangled W-like states, being indispensable resource to quantum computation. Our proposed architecture consists of solid-state spin ensembles and circuit QED, and could achieve quantum computing in a solid-state environment with high-fidelity and scalable way. The experimental feasibility is discussed, and the implementation efficiency is demonstrated numerically.     

Parallel two-step phase-shifting microscopic interferometry based on a cube beamsplitter

Parallel two-step phase-shifting interferometry for microscopy is presented, and the recording condition for generalized two-step phase-shifting interferometry is discussed. A 45° tilted cube beamsplitter enables to replicate the orthogonally linear polarized object and reference waves into two parallel beams, respectively. As a consequence, two interferograms with quadrature phase shift are obtained along the two beams, and phase reconstructed with an improved algorithm. To reconstruct the phase distribution from the two-step phase-shifting interferograms, a certain recording condition should be satisfied. However, the recording condition has not ever been discussed before. In this paper, the recording condition for the two-step phase-shifting interferometry is derived and that is: the intensity of reference wave should be no less than two times object wave intensity.     

On the convergence of parallel chaotic nonlinear multisplitting Newton-type methods

A class of parallel chaotic nonlinear multisplitting Newton-type methods for solving the nonlinear system of equations F(x) = 0(F : D Rⁿ → Rⁿ) is established and its local convergence theory is presented.