Whole-cell model simulations for medicine and bioengineering

Whole-cell models predict cell behaviors by modeling all molecular components and their interactions. Recently, we and other developed the first whole-cell model. The model represents the functionality of all 409 characterized genes and 725 metabolites throughout one life cycle of the reduced bacterium Mycoplasma genitalium. This model was validated against a broad range of data and provided insights into many previously unobserved cellular behaviors. Simulating the behavior of a single cell required modest computing resources – 1 core-day of an Intel E5520 CPU, capable of 3.3×1015 double-precision floating-point operations during the computation. Sampling the organism’s behavior required 128 simulations. Nevertheless, we anticipate that exascale computing resources will be required to use more comprehensive and more accurate whole-cell models to personalize medicine and engineer bacteria

Numerical approach to the Schrodinger equation in momentum space

The treatment of the time-independent Schrodinger equation in real-space is an indispensable part of introductory quantum mechanics. In contrast, the Schrodinger equation in momentum space is an integral equation that is not readily amenable to an analytical solution and is rarely taught. We present a numerical approach to the Schrodinger equation in momentum space. After a suitable discretization process, we obtain the Hamiltonian matrix and diagonalize it numerically. By considering a few examples, we show that this approach is ideal for exploring bound-states in a localized potential and complements the traditional (analytical or numerical) treatment of the Schrodinger equation in real-space.Comment: 14 pages, 4 figures, several changes and one figure correctio

Emission-line Helium Abundances in Highly Obscured Nebulae

This paper outlines a way to determine the ICF using only infrared data. We identify four line pairs, [NeIII] 36\micron/[NeII] 12.8\micron, [NeIII]~15.6\micron /[NeII] 12.8\micron, [ArIII] 9\micron/[ArII] 6.9\micron, and [ArIII] 21\micron/[ArII] 6.9\micron, that are sensitive to the He ICF. This happens because the ions cover a wide range of ionization, the line pairs are not sensitive to electron temperature, they have similar critical densities, and are formed within the He$^+$/H$^+$ region of the nebula. We compute a very wide range of photoionization models appropriate for galactic HII regions. The models cover a wide range of densities, ionization parameters, stellar temperatures, and use continua from four very different stellar atmospheres. The results show that each line pair has a critical intensity ratio above which the He ICF is always small. Below these values the ICF depends very strongly on details of the models for three of the ratios, and so other information would be needed to determine the helium abundance. The [Ar III] 9\micron/[ArII] 6.9\micron ratio can indicate the ICF directly due to the near exact match in the critical densities of the two lines. Finally, continua predicted by the latest generation of stellar atmospheres are sufficiently hard that they routinely produce significantly negative ICFs.Comment: Accepted by PASP. Scheduled for the October 1999 issue. 11 pages, 5 figure

A bone grease processing station at the Mitchell Prehistoric Indian Village: archaeological evidence for the exploitation of bone fats

© Association for Environmental Archaeology 2015. Author's accepted manuscript version deposited in accordance with SHERPA RoMEO guidelines. The definitive version is available at http://www.maneyonline.com/doi/abs/10.1179/1749631414Y.0000000035.Recent excavations at the Mitchell Prehistoric Indian Village, an Initial Middle Missouri site in Mitchell, South Dakota have revealed a large, clay-lined feature filled with fractured and fragmented bison bones. Fracture and fragmentation analysis, along with taphonomic evidence, suggests that the bones preserved within the feature represent evidence of prehistoric bone marrow and bone grease exploitation. Further, the character of the feature suggests that it served as a bone grease processing station. Bone fat exploitation is an activity that is frequently cited as a causal explanation for the nature of many fractured and fragmented bone assemblages in prehistory, and zooarchaeological assemblages have frequently been studied as evidence of bone fat exploitation. The Mitchell example provides some of the first direct, in-situ archaeological evidence of a bone grease processing feature, and this interpretation is sustained by substantial analytical evidence suggesting bone fat exploitation. This new evidence provides a clearer concept of the nature of bone fat exploitation in prehistory as well as an indication of the scale and degree to which bone grease exploitation occurred at the Mitchell site. Finally, this research demonstrates the importance of careful zooarchaeological and taphonomic analysis for the interpretation of both artifactual remains as well as archaeological features

Interval Slopes as Numerical Abstract Domain for Floating-Point Variables

The design of embedded control systems is mainly done with model-based tools such as Matlab/Simulink. Numerical simulation is the central technique of development and verification of such tools. Floating-point arithmetic, that is well-known to only provide approximated results, is omnipresent in this activity. In order to validate the behaviors of numerical simulations using abstract interpretation-based static analysis, we present, theoretically and with experiments, a new partially relational abstract domain dedicated to floating-point variables. It comes from interval expansion of non-linear functions using slopes and it is able to mimic all the behaviors of the floating-point arithmetic. Hence it is adapted to prove the absence of run-time errors or to analyze the numerical precision of embedded control systems

Static Safety for an Actor Dedicated Process Calculus by Abstract Interpretation

The actor model eases the definition of concurrent programs with non uniform behaviors. Static analysis of such a model was previously done in a data-flow oriented way, with type systems. This approach was based on constraint set resolution and was not able to deal with precise properties for communications of behaviors. We present here a new approach, control-flow oriented, based on the abstract interpretation framework, able to deal with communication of behaviors. Within our new analyses, we are able to verify most of the previous properties we observed as well as new ones, principally based on occurrence counting