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]].     

Cut sharing for multistage stochastic linear programs with interstage dependency

Multistage stochastic programs with interstage independent random parameters have recourse functions that do not depend on the state of the system. Decomposition-based algorithms can exploit this structure by sharing cuts (outer-linearizations of the recourse function) among different scenario subproblems at the same stage. The ability to share cuts is necessary in practical implementations of algorithms that incorporate Monte Carlo sampling within the decomposition scheme. In this paper, we provide methodology for sharing cuts in decomposition algorithms for stochastic programs that satisfy certain interstage dependency models. These techniques enable sampling-based algorithms to handle a richer class of multistage problems, and may also be used to accelerate the convergence of exact decomposition algorithms. Research leading to this work was partially supported by the Department of Energy Contract DE-FG03-92ER25116-A002; the Office of Naval Research Contract N00014-89-J-1659; the National Science Foundation Grants ECS-8906260, DMS-8913089; and the Electric Power Research Institute Contract RP 8010-09, CSA-4O05335. This author's work was supported in part by the National Research Council under a Research Associateship at the Naval Postgraduate School, Monterey, California.     

Evolution Galerkin methods for hyperbolic systems in two space dimensions

The subject of the paper is the analysis of three new evolution Galerkin schemes for a system of hyperbolic equations, and particularly for the wave equation system. The aim is to construct methods which take into account all of the infinitely many directions of propagation of bicharacteristics. The main idea of the evolution Galerkin methods is the following: the initial function is evolved using the characteristic cone and then projected onto a finite element space. A numerical comparison is given of the new methods with already existing methods, both those based on the use of bicharacteristics as well as commonly used finite difference and finite volume methods. We discuss the stability properties of the schemes and derive error estimates.

     

Assessing solution quality in stochastic programs

Determining whether a solution is of high quality (optimal or near optimal) is fundamental in optimization theory and algorithms. In this paper, we develop Monte Carlo sampling-based procedures for assessing solution quality in stochastic programs. Quality is defined via the optimality gap and our procedures' output is a confidence interval on this gap. We review a multiple-replications procedure that requires solution of, say, 30 optimization problems and then, we present a result that justifies a computationally simplified single-replication procedure that only requires solving one optimization problem. Even though the single replication procedure is computationally significantly less demanding, the resulting confidence interval might have low coverage probability for small sample sizes for some problems. We provide variants of this procedure that require two replications instead of one and that perform better empirically. We present computational results for a newsvendor problem and for two-stage stochastic linear programs from the literature. We also discuss when the procedures perform well and when they fail, and we propose using ɛ-optimal solutions to strengthen the performance of our procedures.     

On the motion of a phase interface by surface diffusion

Mullins, in a series of papers, developed a surface dynamics for phase interfaces whose evolution is controlled by mass diffusion within the interface. It is our purpose here to embed Mullins's theory within a general framework based on balance laws for mass and capillary forces in conjunction with a version of the second law, appropriate to a purely mechanical theory, which asserts that the rate at which the free energy increases cannot be greater than the energy inflow plus the power supplied. We develop an appropriate constitutive theory, and deduce general and approximate equations for the evolution of the interface.

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Sommario Mullins, in una serie di articoli inerenti la morfologia delle superfici di interfaccia tra fasi, ha sviluppato una dinamica delle superfici la cui evoluzione è governata dal fenomeno di diffusione di massa all'interno dell'interfaccia. Scopo di questo articolo è inscrire la teoria di Mullins in uno schema più generale basato su leggi di bilancio della massa e delle azioni capillari nonchè su una formulazione puramente meccanica del secondo principio della termodinamica, asserente ehe l'incremento di energia libera non possa essere superiore al flusso di energia ed alla potenza fornite all'interfaccia. Viene successivamente sviluppata una appropriata teoria costitutiva, e vengono dedotte le equazioni di evoluzione sia in forma generale che approssimata.

     

Fourier series of half-range functions by smooth extension

This paper considers Fourier series approximations of one- and two-dimensional functions over the half-range, that is, over the sub-interval [0, L] of the interval [−L, L] in one-dimensional problems and over the sub-domain [0, L_x] × [0, L_y] of the domain [−L_x, L_x] × [−L_y, L_y] in two-dimensional problems. It is shown how to represent these functions using a Fourier series that employs a smooth extension. The purpose of the smooth extension is to improve the convergence characteristics otherwise obtained using the even and odd extensions. Significantly improved convergence characteristics are illustrated in one-dimensional and two-dimensional problems.     

Thermomechanics of the interface between a body and its environment

We formulate integral statements of force balance, energy balance, and entropy imbalance for an interface between a body and its environment. These statements account for interfacial energy, entropy, and stress but neglect the inertia of the interface. Our final results consist of boundary conditions describing thermomechanical interactions between the body and its environment. In their most general forms, these results are partial differential equations that account for dissipation and encompass as special cases Navier’s slip law, Newton’s law of cooling, and Kirchhoff’s law of radiation. When dissipation is neglected, our results reduce to the well-known zero-slip, free-surface, zero-shear, prescribed temperature, and flux-free conditions. Dedicated to James K. Knowles: teacher, colleague, friend     

A theory of strain-gradient plasticity for isotropic, plastically irrotational materials. Part I: Small deformations

This study develops a small-deformation theory of strain-gradient plasticity for isotropic materials in the absence of plastic rotation. The theory is based on a system of microstresses consistent with a microforce balance; a mechanical version of the second law that includes, via microstresses, work performed during viscoplastic flow; a constitutive theory that allows:

•

the microstresses to depend on , the gradient of the plastic strain-rate, and

•

the free energy ψ to depend on the Burgers tensor .

The microforce balance when augmented by constitutive relations for the microstresses results in a nonlocal flow rule in the form of a tensorial second-order partial differential equation for the plastic strain. The microstresses are strictly dissipative when ψ is independent of the Burgers tensor, but when ψ depends on G the gradient microstress is partially energetic, and this, in turn, leads to a back stress and (hence) to Bauschinger-effects in the flow rule. It is further shown that dependencies of the microstresses on lead to strengthening and weakening effects in the flow rule.Typical macroscopic boundary conditions are supplemented by nonstandard microscopic boundary conditions associated with flow, and, as an aid to numerical solutions, a weak (virtual power) formulation of the nonlocal flow rule is derived.     

Effect of defect energy on strain-gradient predictions of confined single-crystal plasticity

Gurtin recently proposed a strain-gradient theory for crystal plasticity in which the gradient effect originates from a defect energy that characterizes energy storage due to the presence of a net Burgers vector. Here we consider a number of different possibilities for this energy: specifically, working within a simple two-dimensional framework, we compare predictions of the theory with results of discrete-dislocation simulations of stress relaxation in thin films. Our objective is to investigate which specific defect energies are capable of capturing the size-dependent response of such systems for different crystal orientations.     

Dependence of nonlinear elasticity on filler size in composite polymer systems

Nanosized filler particles enhance the mechanical properties of polymer composites in a size-dependent fashion. This is puzzling, because classical elasticity is inherently scale-free, and models for the elasticity of composite systems never predict a filler-size dependence. Here, we study the industrially important system of silica-filled rubbers, together with a well-characterized model-filled crosslinked gel and show that at high filler content both the linear and nonlinear elastic properties of these systems exhibit a unique scaling proportional to the cube of the volume fraction divided by the particle size. This remarkable behavior makes it possible to predict the full mechanical response of particle-filled rubbers for small but finite deformations based solely on the rheology of the matrix and the size and modulus of the filler particles.