Accelerating molecular dynamic simulation on the cell processor and Playstation 3

Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3). In particular, we discuss issues regarding memory access versus computation and the types of calculations which are best suited for streaming processors such as the Cell, focusing on implicit solvation models. We conclude with a comparison of improved performance on the PS3's Cell processor over more traditional processors.     

Exact solution of the excited-state geminate A*+B <==> C*+D reaction with two different lifetimes and quenching

The authors obtain, in the Laplace transform space, the exact analytic solution for the Green function and survival probabilities for the excited-state diffusion-influenced reversible geminate reaction, A*+B <==> C*+D, with two different lifetimes and in the presence of an added quenching process. This extends a previous investigation by Popov and Agmon [J. Chem. Phys. 117, 5770 (2002)] of the ground-state reaction without quenching. The long-time asymptotic behavior of the survival probabilities is obtained in the time domain. It is found to be different from the equal-lifetime case. This paper also provides a useful short-time approximation for the kinetics.     

A novel homogeneous immunoassay for anthrax detection based on the AlphaLISA method: detection of B. anthracis spores and protective antigen (PA) in complex samples

Amplified Luminescent Proximity Homogeneous Assay (AlphaLISA) technology is an energy-transfer-based assay, utilizing singlet oxygen as an energy donor to a fluorescent acceptor. The long singlet oxygen migration distance allows the energy transfer mechanism to go up to ～200 nm, facilitating flexible and sensitive homogeneous immunoassays. While soluble protein detection using AlphaLISA was previously described, the detection of particles such as bacteria and viruses was not reported. In this work, we show for the first time the implementation of the AlphaLISA technology for the detection of a particulate antigen, i.e., Bacillus anthracis spores. Here, we show that an efficient particle immunoassay requires a high acceptor-to-donor ratio (>4:1). The results suggested that the high acceptor/donor ratio is required to avoid donor aggregation (“islands”) on the spore surface, hence facilitating donor/acceptor interaction. The developed assay enabled the detection of 10⁶ spores/mL spiked in PBS. We also demonstrate the development of a highly sensitive AlphaLISA assay for the detection of the main toxin component of anthrax, protective antigen (PA). The assay enabled the detection of 10 and 100 pg/mL PA in buffer and spiked naïve rabbit sera, respectively, and was successfully implemented in sera of anthrax-infected rabbits. To summarize, this study demonstrates that AlphaLISA enables detection of anthrax spores and toxin, utilizing short homogeneous assays. Moreover, it is shown for the first time that this technology facilitates the detection of particulate entities and might be suitable for the detection of other bacteria or viruses.     

Overcoming apparent susceptibility-induced anisotropy (aSIA) by bipolar double-pulsed-field-gradient NMR

Double-Pulsed-Field-Gradient (d-PFG) MR is emerging as a powerful new means for obtaining unique microstructural information in opaque porous systems that cannot be obtained by conventional single-PFG (s-PFG) methods. The angular d-PFG MR methodology is particularly important since it can utilize the effects of microscopic anisotropy (μA) and compartment shape anisotropy (csA) in the E(ψ) profile at the different t_m regimes to provide detailed information on compartment size and eccentricity. An underlying assumption is that the PFGs that are imparted to weigh diffusion are the only gradients present; however, in realistic systems and especially where there are randomly oriented anisotropic pores, susceptibility effects may induce strong internal gradients. In this study, the effects of such internal gradients on E(ψ) plots obtained from angular d-PFG MR and on microstructural information that can be obtained from s-PFG and d-PFG MR were investigated. First, it was found that internal gradients induce a bias in the s-PFG MR results, thus creating an anisotropy that is not related to microstructure, termed apparent-Susceptibility-Induced-Anisotropy (aSIA). We then show that aSIA effects are also manifest in different ways in the angular d-PFG MR experiment in controlled phantoms and in realistic systems such as quartz sand, emulsions, and biological systems. The effects of aSIA in some cases completely masked the effects of μA and csA; however, we subsequently show that by introducing bipolar gradients to the d-PFG MR (bp-d-PFG), the effects of aSIA can be largely suppressed, restoring the E(ψ) plots that are expected from the theory along with the microstructural information that it conveys. We conclude that when specimens are characterized by strong internal gradients, the novel information on μA and csA that is manifest in the E(ψ) plots can indeed be inferred when bp-d-PFG MR is used, i.e. when bipolar gradients are applied.     

Effective Polynomial Ballisticity Conditions for Random Walk in Random Environment

The conditions (T)_γ, γ ? (0,1), which were introduced by Sznitman in 2002, have had a significant impact on research in random walk in a random environment. Among others, these conditions entail a ballistic behavior as well as an invariance principle. They require the stretched exponential decay of certain slab exit probabilities for the random walk under the averaged measure and are asymptotic in nature. The main goal of this paper is to show that in all relevant dimensions (i.e., d ≥ 2), in order to establish the conditions (T)_γ, it is actually enough to check a corresponding condition (??) of polynomial type. In addition to only requiring an a priori weaker decay of the corresponding slab exit probabilities than (T)_γ, another advantage of the condition (??) is that it is effective in the sense that it can be checked on finite boxes. In particular, this extends the conjectured equivalence of the conditions (T)_γ, γ ? (0,1), to all relevant dimensions. © 2014 Wiley Periodicals, Inc.     

Photocurrent Generation and Polarity Switching in Electrochemical Cells through Light-induced Excited State Proton Transfer of Photoacids and Photobases**

Light is a common source of energy in sustainable technologies for photocurrent generation. To date, in such light-harvesting applications, the excited electrons generate the photocurrent. Here, we introduce a new mechanism for photocurrent generation that is based on excited state proton transfer (ESPT) of photoacids and photobases that can donate or accept a proton, respectively, but only after excitation. We show that the formed ions following ESPT can either serve as electron donors or acceptors with the electrodes, or modify the kinetics of mass transport across the diffuse layer, both resulting in photocurrent generation. We further show that control of the current polarity is obtained by switching the irradiation between the photoacid and the photobase. Our study represents a new approach in photoelectrochemistry by introducing ESPT processes, which can be further utilized in light-responsive energy production or energy storage.     

Origin of Radiation Reaction

The emission of radiation from an accelerated charge is analyzed. It is foundthat at zero velocity, the radiation emitted from the charge imparts no countermomentum to the emitting charge, and no radiation reaction force is created bythe radiation. A reaction force is created by the stress force that exists in thecurved electric field of the charge, and the work done in overcoming this forceis the source of the energy carried by the radiation.     

Mordell–Weil lattices in characteristic 2 II: The Leech lattice as a Mordell–Weil lattice

Sans résumé Oblatum 10-VIII-1994     

Transience, Recurrence and Critical Behavior¶for Long-Range Percolation

We study the behavior of the random walk on the infinite cluster of independent long-range percolation in dimensions d= 1,2, where x and y are connected with probability . We show that if d<s<2d, then the walk is transient, and if s≥ 2d, then the walk is recurrent. The proof of transience is based on a renormalization argument. As a corollary of this renormalization argument, we get that for every dimension d≥ 1, if d>s>2d, then there is no infinite cluster at criticality. This result is extended to the free random cluster model. A second corollary is that when d≥& 2 and d>s>2d we can erase all long enough bonds and still have an infinite cluster. The proof of recurrence in two dimensions is based on general stability results for recurrence in random electrical networks. In particular, we show that i.i.d. conductances on a recurrent graph of bounded degree yield a recurrent electrical network. Received: 27 October 2000 / Accepted: 29 November 2001     

On rank vs. communication complexity

This paper concerns the open problem of Lovász and Saks regarding the relationship between the communication complexity of a boolean function and the rank of the associated matrix. We first give an example exhibiting the largest gap known. We then prove two related theorems.A preliminary version of this paper appeared in [10].This work was supported by USA-Israel BSF grant 92-00043 and by a Wolfeson research award administered by the Israeli Academy of Sciences.This work was supported by USA-Israel BSF grant 92-00106 and by a Wolfeson research award administered by the Israeli Academy of Sciences.