A robust scheme for free surface and pressurized flows in channels with arbitrary cross-sections

Flows in closed channels, such as rain storm sewers, often contain transitions from free surface flows to pressurized flows, or viceversa. These phenomena usually require two different sets of equations to model the two different flow regimes. Actually, a few specifications for the geometry of the channel and for the discretization choices can be sufficient to model closed channel flows using only the open channel flow equations. Transitions can also occur in open channels, like those from super- to subcritical flow, or vice versa. These particular flows are usually difficult to reproduce numerically and strong restrictions are imposed on the numerical scheme to simulate them. In this paper, an implicit finite-difference conservative algorithm is proposed to deal properly with these problems. In addition, a special flux limiter is described and implemented to allow accurate flow simulations near hydraulic structures such as weirs. A few computational examples are given to illustrate the properties of the scheme and the numerical solutions are compared with experimental data, when possible

Stelling Bill- Callison College One Pager

https://scholarlycommons.pacific.edu/callison-college-sis/1023/thumbnail.jp

Creation of False Memories and Beliefs: Expectancy Consistent Errors Based on Gender Stereotypes

This study was a series of three experiments which examined the effects of gender stereotypes on the creation of false-memories. Participants were undergraduate students who viewed a short one-scene video depicting a couple on a date. The video featured a man and a woman displaying a mixture of typical, atypical, or a combination of both gender stereotypical behaviors. Following the video, participants completed a quiz to determine whether they created false memories consistent with gender stereotypes. Participants completed an attitudinal scale to gauge their views on gender stereotypes. It was hypothesized that participants would create stereotype- consistent false memories and that memories would be altered to be stereotype-consistent with the behavior of the man than with the behavior of the woman. This hypothesis was partially supported by the data. Participants were more likely to create stereotype-consistent false memories when quizzed about the men’s atypical behavior

Large-scale computation of elementary flux modes with bit pattern trees

Motivation: Elementary flux modes (EFMs)—non-decomposable minimal pathways—are commonly accepted tools for metabolic network analysis under steady state conditions. Valid states of the network are linear superpositions of elementary modes shaping a polyhedral cone (the flux cone), which is a well-studied convex set in computational geometry. Computing EFMs is thus basically equivalent to extreme ray enumeration of polyhedral cones. This is a combinatorial problem with poorly scaling algorithms, preventing the large-scale analysis of metabolic networks so far. Results: Here, we introduce new algorithmic concepts that enable large-scale computation of EFMs. Distinguishing extreme rays from normal (composite) vectors is one critical aspect of the algorithm. We present a new recursive enumeration strategy with bit pattern trees for adjacent rays—the ancestors of extreme rays—that is roughly one order of magnitude faster than previous methods. Additionally, we introduce a rank updating method that is particularly well suited for parallel computation and a residue arithmetic method for matrix rank computations, which circumvents potential numerical instability problems. Multi-core architectures of modern CPUs can be exploited for further performance improvements. The methods are applied to a central metabolism network of Escherichia coli, resulting in ≈26 Mio. EFMs. Within the top 2% modes considering biomass production, most of the gain in flux variability is achieved. In addition, we compute ≈5 Mio. EFMs for the production of non-essential amino acids for a genome-scale metabolic network of Helicobacter pylori. Only large-scale EFM analysis reveals the >85% of modes that generate several amino acids simultaneously. Availability: An implementation in Java, with integration into MATLAB and support of various input formats, including SBML, is available at http://www.csb.ethz.ch in the tools section; sources are available from the authors upon request. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Signaling cascades as cellular devices for spatial computations

Signaling networks usually include protein-modification cycles. Cascades of such cycles are the backbones of multiple signaling pathways. Protein gradients emerge from the spatial separation of opposing enzymes, such as kinases and phosphatases, or guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs) for GTPase cycles. We show that different diffusivities of an active protein form and an inactive form leads to spatial gradients of protein abundance in the cytoplasm. For a cascade of cycles, using a discrete approximation of the space, we derive an analytical expression for the spatial gradients and show that it converges to an exact solution with decreasing the size of the quantization. Our results facilitate quantitative analysis of the dependence of spatial gradients on the network topology and reaction kinetics. We demonstrate how different cascade designs filter and process the input information to generate precise, complex spatial guidance for multiple GTPase effector processes. Thus, protein-modification cascades may serve as devices to compute complex spatial distributions of target proteins within intracellular spac

Computational design of synthetic gene circuits with composable parts

Motivation: In principle, novel genetic circuits can be engineered using standard parts with well-understood functionalities. However, no model based on the simple composition of these parts has become a standard, mainly because it is difficult to define signal exchanges between biological units as unambiguously as in electrical engineering. Corresponding concepts and computational tools for easy circuit design in biology are missing. Results: Taking inspiration from (and slightly modifying) ideas in the ‘MIT Registry of Standard Biological Parts', we developed a method for the design of genetic circuits with composable parts. Gene expression requires four kinds of signal carriers: RNA polymerases, ribosomes, transcription factors and environmental ‘messages' (inducers or corepressors). The flux of each of these types of molecules is a quantifiable biological signal exchanged between parts. Here, each part is modeled independently by the ordinary differential equations (ODE) formalism and integrated into the software ProMoT (Process Modeling Tool). In this way, we realized a ‘drag and drop' tool, where genetic circuits are built just by placing biological parts on a canvas and by connecting them through ‘wires' that enable flow of signal carriers, as it happens in electrical engineering. Our simulations of well-known synthetic circuits agree well with published computational and experimental results. Availability: The code is available on request from the authors. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin