A clonal selection algorithm for dynamic facility layout problems

The dynamic facility layout problem (DFLP) aims to minimize the sum of handling and re-layout costs by devising an individual layout for each distinctive production period. It is a complex combinatorial optimization problem. This paper proposes a clonal selection algorithm (CSA) for DFLP. The algorithm is capable of being extended to more general cases although equal area machines and standardized handling equipments with identical unit costs are assumed for the time being. The performance of the proposed algorithm is examined by using three test problems from the literature. CSA reached the best known solutions–even found better solutions for large sized problems–in 88% of the instances, while each of the former methods was successful only in a small fraction of those 50 problems. CSA also outperformed all the present methods as regards solution times.     

General distributed economic framework for dynamic spectrum allocation

The emergence of novel radio techniques enables the application of advantageous revolutionary spectrum policies. An important body of research has appeared about possible frequency management schemes, but none of them proposes solutions that meet every related criteria. In this paper we present our work on dynamic spectrum allocation and pricing that offers a distributed mechanism design, well-suited to practical employment issues. Our model handles interference effects without any restricting assumptions, provides universal scalable and incentive-compatible allocation and pricing mechanisms. We provide both analytical and numerical evaluation of the proposed framework, and in either case we prove this latter to be a suitable approach to efficient and flexible spectrum utilization.     

Models wagging the dog: are circuits constructed with disparate parameters?

In a recent article, Prinz, Bucher, and Marder (2004) addressed the fundamental question of whether neural systems are built with a fixed blueprint of tightly controlled parameters or in a way in which properties can vary largely from one individual to another, using a database modeling approach. Here, we examine the main conclusion that neural circuits indeed are built with largely varying parameters in the light of our own experimental and modeling observations. We critically discuss the experimental and theoretical evidence, including the general adequacy of database approaches for questions of this kind, and come to the conclusion that the last word for this fundamental question has not yet been spoken.     

Efficient computation of Morse-Smale complexes for three-dimensional scalar functions

The Morse-Smale complex is an efficient representation of the gradient behavior of a scalar function, and critical points paired by the complex identify topological features and their importance. We present an algorithm that constructs the Morse-Smale complex in a series of sweeps through the data, identifying various components of the complex in a consistent manner. All components of the complex, both geometric and topological, are computed, providing a complete decomposition of the domain. Efficiency is maintained by representing the geometry of the complex in terms of point sets.     

Interactive Ray Tracing of Large Models Using Voxel Hierarchies

We propose an efficient approach for interactive visualization of massive models with CPU ray tracing. A voxel‐based hierarchical level‐of‐detail (LOD) framework is employed to minimize rendering time and required system memory. In a pre‐processing phase, a compressed out‐of‐core data structure is constructed, which contains the original primitives of the model and the LOD voxels, organized into a kd‐tree. During rendering, data is loaded asynchronously to ensure a smooth inspection of the model regardless of the available I/O bandwidth. With our technique, we are able to explore data sets consisting of hundreds of millions of triangles in real‐time on a desktop PC with a quad‐core CPU.     

An implementation of the coupled perturbed Kohn-Sham equations: perturbation due to nuclear displacements

The Coupled Perturbed Kohn-Sham equations have been implemented in the Amsterdam Density Functional program package. Our implementation differs from previous ones in many ways. This program uses density fitting to calculate the Coulomb and exchange integrals. Further, all matrix elements of the Fock type matrix and its derivatives are calculated by numerical integration. The frozen core approximation is also implemented. Our implementation is approximately 10 times faster than a finite difference algorithm, and the absolute CPU times also compare favorably with other reported implementations.     

Incident Light Metering in Computer Graphics

Every rendering process consists of two steps. The first is the computing of luminance values by methods like ray tracing or radiosity, and the second step is the mapping of the computed values to values appropriate for displaying. In the last years, as alternative to simple linear scaling which maps the average value to the medium luminance, some new ways of mapping were introduced. These new methods are based on photography analogies and on human vision models. All existing methods follow, implicitly or explicitly, the reflected light metering principle. The method introduced in this paper is the first that follows the incident light metering used in professional photography and in the movie industry. Actually the irradiances are measured using a set of diffusors, which are placed automatically in the scene, and a linear scale factor based on these measurements is used to map the computed radiances to the display device. The diffusors act as half space integrators, they collect the light energy from all half space directions. The light comes from the primary light sources, or it is the result of various interreflections. The newly introduced method reproduces original colors faithfully even for scenes with very low or very high average reflectivity.     

The Phagocytosis of Lacticaseibacillus casei and Its Immunomodulatory Properties on Human Monocyte-Derived Dendritic Cells Depend on the Expression of Lc-p75, a Bacterial Peptidoglycan Hydrolase

The human gut symbiont Lacticaseibacillus (L.) casei (previously Lactobacillus casei) is under intense research due to its wide range of immunomodulatory effects on the human host. Dendritic cells (DCs) are crucial players in the direct and indirect communication with lactobacilli in the gastrointestinal tract. Here, we demonstrate that human monocyte-derived DCs (moDCs) are able to engulf L. casei BL23, in which the intact bacterial cell wall and morphology have a key role. The absence of the bacterial cell-wall-degrading enzyme, Lc-p75, in L. casei cells causes remarkable morphological changes, which have important consequences in the phagocytosis of L. casei by moDCs. Our results showed that the Lc-p75 mutation induced defective internalization and impaired proinflammatory and T-cell-polarizing cytokine secretion by bacteria-exposed moDCs. The T helper (Th) 1 and Th17 cell activating capacity of moDCs induced by the mutant L. casei was consequently reduced. Moreover, inhibition of the phagocytosis of wild-type bacteria showed similar results. Taken together, these data suggested that formation of short bacterial chains helps to exert the potent immunomodulatory properties of L. casei BL23.     

Model complexity reduction of chemical reaction networks using mixed-integer quadratic programming

The model complexity reduction problem of large chemical reaction networks under isobaric and isothermal conditions is considered. With a given detailed kinetic mechanism and measured data of the key species over a finite time horizon, the complexity reduction is formulated in the form of a mixed-integer quadratic optimization problem where the objective function is derived from the parametric sensitivity matrix. The proposed method sequentially eliminates reactions from the mechanism and simultaneously tunes the remaining parameters until the pre-specified tolerance limit in the species concentration space is reached. The computational efficiency and numerical stability of the optimization are improved by a pre-reduction step followed by suitable scaling and initial conditioning of the Hessian involved. The proposed complexity reduction method is illustrated using three well-known case studies taken from reaction kinetics literature.     

Response dynamics of phosphorelays suggest their potential utility in cell signalling

Phosphorelays are extended two-component signalling systems found in diverse bacteria, lower eukaryotes and plants. Only few of these systems are characterized, and we still lack a full understanding of their signalling abilities. Here, we aim to achieve a global understanding of phosphorelay signalling and its dynamical properties. We develop a generic model, allowing us to systematically analyse response dynamics under different assumptions. Using this model, we find that the steady-state concentration of phosphorylated protein at the final layer of a phosphorelay is a linearly increasing, but eventually saturating function of the input. In contrast, the intermediate layers can display ultrasensitivity. We find that such ultrasensitivity is a direct result of the phosphorelay biochemistry; shuttling of a single phosphate group from the first to the last layer. The response dynamics of the phosphorelay results in tolerance of cross-talk, especially when it occurs as cross-deactivation. Further, it leads to a high signal-to-noise ratio for the final layer. We find that a relay length of four, which is most commonly observed, acts as a saturating point for these dynamic properties. These findings suggest that phosphorelays could act as a mechanism to reduce noise and effects of cross-talk on the final layer of the relay and enforce its input–response relation to be linear. In addition, our analysis suggests that middle layers of phosphorelays could embed thresholds. We discuss the consequence of these findings in relation to why cells might use phosphorelays along with enzymatic kinase cascades.