The Berkeley Center for Structural Biology at the Advanced Light Source

The Berkeley Center for Structural Biology (BCSB) operates and develops a suite of protein crystallography beamlines at the Advanced Light Source (ALS) located at Lawrence Berkeley National Laboratory (LBNL). Although the ALS was conceived as a low-energy (1.9-GeV), third-generation synchrotron source of vacuum ultraviolet (VUV) and soft X-ray radiation, it was realized during the development of the facility in the mid-1990s that a multipole wiggler coupled with brightness-preserving optics would result in a beamline whose performance in the energy range of 5 to 15 keV would be sufficient for most protein crystallographic experiments. Later, the hard X-ray capabilities of the ALS were expanded by the addition of three superconducting bending magnets, resulting in additional protein crystallography facilities at the ALS [1 A.A. MacDowell, J Synchrotron Radiation 11(6), 447–55 (2004).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]].     

Parity-violating electron deuteron scattering and the proton's neutral weak axial vector form factor

We report on a new measurement of the parity-violating asymmetry in quasielastic electron scattering from the deuteron at backward angles at Q2=0.038 (GeV/c)2. This quantity provides a determination of the neutral weak axial vector form factor of the nucleon, which can potentially receive large electroweak corrections. The measured asymmetry A=-3.51+/-0.57 (stat)+/-0.58 (syst) ppm is consistent with theoretical predictions. We also report on updated results of the previous experiment at Q2=0.091 (GeV/c)2, which are also consistent with theoretical predictions.     

Tail behavior of conditional sojourn times in Processor-Sharing queues

We investigate the tail behavior of the sojourn-time distribution for a request of a given length in an M/G/1 Processor-Sharing (PS) queue. An exponential asymptote is proven for general service times in two special cases: when the traffic load is sufficiently high and when the request length is sufficiently small. Furthermore, using the branching process technique we derive exact asymptotics of exponential type for the sojourn time in the M/M/1 queue. We obtain an equation for the asymptotic decay rate and an exact expression for the asymptotic constant. The decay rate is studied in detail and is compared to other service disciplines. Finally, using numerical methods, we investigate the accuracy of the exponential asymptote. AMS 2000 Subject Classifications Primary:60K25,Secondary: 60F10,68M20,90B22     

Large deviations of sojourn times in processor sharing queues

This paper presents a large deviation analysis of the steady-state sojourn time distribution in the GI/G/1 PS queue. Logarithmic estimates are obtained under the assumption of the service time distribution having a light tail, thus supplementing recent results for the heavy-tailed setting. Our proof gives insight into the way a large sojourn time occurs, enabling the construction of an (asymptotically efficient) importance sampling algorithm. Finally our results for PS are compared to a number of other service disciplines, such as FCFS, LCFS, and SRPT. 2000 mathematics subject classification: 60K25.     

Nonlinear programming: Global use of the Lagrangian

In some constrained nonlinear programming problems possessing several local optima, a local optimum can be recognized as the global optimum by looking closely at the Lagrangian, the augmented function. Similarly, classes of constrained optimization problems, such as geometric programming problems, can be recognized as possessing at most a single local optimum.This research was supported in part by the Atomic Energy Commission under Research Contract No. A(11-1)-1493 and by the Department of Defense under Themis Grant No. F44620-69-C-0116.     

A sparse octree gravitational N-body code that runs entirely on the GPU processor

We present the implementation and performance of a new gravitational N-body tree-code that is specifically designed for the graphics processing unit (GPU).¹ All parts of the tree-code algorithm are executed on the GPU. We present algorithms for parallel construction and traversing of sparse octrees. These algorithms are implemented in CUDA and tested on NVIDIA GPUs, but they are portable to OpenCL and can easily be used on many-core devices from other manufacturers. This portability is achieved by using general parallel-scan and sort methods. The gravitational tree-code outperforms tuned CPU code during the tree-construction and shows a performance improvement of more than a factor 20 overall, resulting in a processing rate of more than 2.8 million particles per second.     

Sojourn time asymptotics in the M/G/1 processor sharing queue

We show for the M/G/1 processor sharing queue that the service time distribution is regularly varying of index -ν, ν non-integer, iff the sojourn time distribution is regularly varying of index -ν. This result is derived from a new expression for the Laplace–Stieltjes transform of the sojourn time distribution. That expression also leads to other new properties for the sojourn time distribution. We show how the moments of the sojourn time can be calculated recursively and prove that the kth moment of the sojourn time is finite iff the kth moment of the service time is finite. In addition, we give a short proof of a heavy traffic theorem for the sojourn time distribution, prove a heavy traffic theorem for the moments of the sojourn time, and study the properties of the heavy traffic limiting sojourn time distribution when the service time distribution is regularly varying. Explicit formulas and multiterm expansions are provided for the case that the service time has a Pareto distribution. This revised version was published online in June 2006 with corrections to the Cover Date.     

On the invertibility and bounded extension of C 0 -semigroups

A well-known necessary and sufficient condition for the operator A to be the infinitesimal generator of a strongly continuous (C ₀ -) group is that both A and -A generate a C ₀ -semigroup. This seems to imply that one has to check the conditions in the Hille-Yosida Theorem for both A and -A . In this paper we show that this is not necessary. Given that A generates a C ₀ -semigroup we prove that a (weak) growth bound on the resolvent on a left half plane is sufficient to guarantee that A generates a group. This extends the recent result found by Liu, see [6]. Furthermore, we study when a generator of a bounded C ₀ -semigroup is the generator of a bounded group. The condition that we obtain is the same as found by Van Casteren in [2, 3], but we present a direct proof.     

Steady state approximations of limited processor sharing queues in heavy traffic

We investigate steady state properties of limited processor sharing queues in heavy traffic. Our analysis builds on previously obtained process limit theorems, and requires the interchange of steady state and heavy traffic limits, which are established by a coupling argument. The limit theorems yield explicit approximations of the steady state queue length and response time distribution in heavy traffic, of which the quality is supported by simulation experiments.