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At least 361 records · Page 20

Elucidating Microbial Adaptation Dynamics via Autonomous Exposure and Sampling

The adaptation of micro-organisms to their environments is a complex process of interaction between the pressures of the environment and of competition. Reducing this multifactorial process to environmental exposure in the laboratory is a common tool for elucidating individual mechanisms of evolution, such as mutation rates. Although such studies inform fundamental questions about the way adaptation and even speciation occur, they are often limited by labor-intensive manual techniques. Current methods for controlled study of microbial adaptation limit the length of time, the depth of collected data, and the breadth of applied environmental conditions. Small idiosyncrasies in manual techniques can have large effects on outcomes; for example, there are significant variations in induced radiation resistances following similar repeated exposure protocols. We describe here a project under development to allow rapid cycling of multiple types of microbial environmental exposure. The system allows continuous autonomous monitoring and data collection of both single species and sampled communities, independently and concurrently providing multiple types of controlled environmental pressure (temperature, radiation, chemical presence or absence, and so on) to a microbial community in dynamic response to the ecosystem's current status. When combined with DNA sequencing and extraction, such a controlled environment can cast light on microbial functional development, population dynamics, inter- and intra-species competition, and microbe-environment interaction. The project's goal is to allow rapid, repeatable iteration of studies of both natural and artificial microbial adaptation. As an example, the same system can be used both to increase the pH of a wet soil aliquot over time while periodically sampling it for genetic activity analysis, or to repeatedly expose a culture of bacteria to the presence of a toxic metal, automatically adjusting the level of toxicity based on the number or growth rate of surviving cells. We are on our second prototype iteration, with demonstrated functions of microbial growth monitoring and dynamic exposure to UV-C radiation and temperature. We plan to add functionality for general chemical presence or absence by Nov. 2013. By making the project low-cost and open-source, we hope to encourage others to use it as a basis for future development of a common microbial environmental adaptation testbed.

Microbiology↗

Incorporation of Failure Into an Orthotropic Three-Dimensional Model with Tabulated Input Suitable for Use in Composite Impact Problems

The need for accurate material models to simulate the deformation, damage and failure of polymer matrix composites under impact conditions is becoming critical as these materials are gaining increased use in the aerospace and automotive communities. The aerospace community has identified several key capabilities which are currently lacking in the available material models in commercial transient dynamic finite element codes. To attempt to improve the predictive capability of composite impact simulations, a next generation material model is being developed for incorporation within the commercial transient dynamic finite element code LS-DYNA. The material model, which incorporates plasticity, damage and failure, utilizes experimentally based tabulated input to define the evolution of plasticity and damage and the initiation of failure as opposed to specifying discrete input parameters such as modulus and strength. The plasticity portion of the orthotropic, three-dimensional, macroscopic composite constitutive model is based on an extension of the Tsai-Wu composite failure model into a generalized yield function with a non-associative flow rule. For the damage model, a strain equivalent formulation is used to allow for the uncoupling of the deformation and damage analyses. In the damage model, a semi-coupled approach is employed where the overall damage in a particular coordinate direction is assumed to be a multiplicative combination of the damage in that direction resulting from the applied loads in various coordinate directions. For the failure model, a tabulated approach is utilized in which a stress or strain based invariant is defined as a function of the location of the current stress state in stress space to define the initiation of failure. Failure surfaces can be defined with any arbitrary shape, unlike traditional failure models where the mathematical functions used to define the failure surface impose a specific shape on the failure surface. In the current paper, the complete development of the failure model is described and the generation of a tabulated failure surface for a representative composite material is discussed.

Impact↗

Implementation of a Tabulated Failure Model Into a Generalized Composite Material Model Suitable for Use in Impact Problems

The need for accurate material models to simulate the deformation, damage and failure of polymer matrix composites under impact conditions is becoming critical as these materials are gaining increased use in the aerospace and automotive communities. The aerospace community has identified several key capabilities which are currently lacking in the available material models in commercial transient dynamic finite element codes. To attempt to improve the predictive capability of composite impact simulations, a next generation material model is being developed for incorporation within the commercial transient dynamic finite element code LS-DYNA. The material model, which incorporates plasticity, damage and failure, utilizes experimentally based tabulated input to define the evolution of plasticity and damage and the initiation of failure as opposed to specifying discrete input parameters such as modulus and strength. The plasticity portion of the orthotropic, three-dimensional, macroscopic composite constitutive model is based on an extension of the Tsai-Wu composite failure model into a generalized yield function with a non-associative flow rule. For the damage model, a strain equivalent formulation is used to allow for the uncoupling of the deformation and damage analyses. For the failure model, a tabulated approach is utilized in which a stress or strain based invariant is defined as a function of the location of the current stress state in stress space to define the initiation of failure. Failure surfaces can be defined with any arbitrary shape, unlike traditional failure models where the mathematical functions used to define the failure surface impose a specific shape on the failure surface. In the current paper, the complete development of the failure model is described and the generation of a tabulated failure surface for a representative composite material is discussed.

polymer matrix composites↗

Observing the Full Spectrum of the Rain Drop Size Distribution

GPM DSD retrievals exhibit inconsistencies between GV, DPR and Combined algorithm retrievals. Development of positive bias in convective Dm rain DSD noted, and strongest in KuPR retrieval. Associated epsilons are too low and result in markedly reduced convective rain rates (a current issue in the retrievals). Source may be NUBF. Issues with the large end of the DSD not withstanding, on the small end of the DSD, combined MPS and 2DVD measurements fit with generalized gamma functions exhibit strong potential for representing the entire spectrum of the DSD and subsequently the whole rain rate spectrum.

Hydrology↗

Verification and Validation of a Three-Dimensional Composite Impact Model with Tabulated Input

A material model which incorporates several key capabilities which have been identified by the aerospace community as lacking in the composite impact models currently available in the commercial transient dynamic finite element code LS-DYNA® has been developed. The material model utilizes experimentally based tabulated input to define the evolution of plasticity and damage as opposed to specifying discrete input parameters (such as modulus and strength. The plasticity portion of the orthotropic, three-dimensional, macroscopic composite constitutive model is based on an extension of the Tsai-Wu composite failure model into a generalized yield function with a non-associative flow rule. The capability to account for the rate and temperature dependent deformation response of composites has also been incorporated into the material model. For the damage model, a strain equivalent formulation is utilized to allow for the uncoupling of the deformation and damage analyses. In the damage model, a diagonal damage tensor is defined to account for the directionally dependent variation of damage. However, the terms in the damage matrix are semi-coupled such that the damage in a particular coordinate direction is a function of the stresses and plastic strains in all of the coordinate directions. For the failure model, a tabulated approach is utilized in which a stress or strain based invariant is defined as a function of the location of the current stress state in stress space to define the initiation of failure, which allows an arbitrarily shaped failure surface to be defined. A systematic series of validation and verification studies, at a variety of length scales ranging from single element simulations to simulations of a flat panel impact test, have been performed to fully exercise and evaluate the capabilities of the developed model.

Impact↗

A Parametric Assessment of Lunar and Mars Ascent Vehicle Synergy

The National Aeronautics and Space Administration has long had a focus on the human exploration of space, starting with Earth orbit, progressing to the Moon, and looking forward to Mars and other deep space destinations. With current priorities aiming toward a return to the Lunar surface in 2024 as part of an extended exploration campaign that will prepare the way for the first crewed mission to Mars, it is timely to examine possible commonalities between the Lunar and Martian mission architectures, particularly in the vehicle systems. One area of potential similarity lies within the ascent phase of the missions; at a first look, the initial Artemis missions to return to the Moon and a short-duration surface stay option for a Mars mission appear similar in several regards, especially in regards to the selection of the crew size, duration of crewed flight, and general subsystem functionality. This paper will take a closer look at these similarities as they apply to the respective ascent vehicles for each planetary body and how those similarities could enable synergies between the Lunar and Mars ascent vehicles of both missions.

Human Exploration↗

Excited State Orbital Optimization via Minimizing the Square of the Gradient: General Approach and Application to Singly and Doubly Excited States via Density Functional Theory

We present a general approach to converge excited state solutions to any quantum chemistry orbital optimization process, without the risk of variational collapse. The resulting square gradient minimization (SGM) approach only requires analytic energy/Lagrangian orbital gradients and merely costs 3 times as much as ground state orbital optimization (per iteration), when implemented via a finite difference approach. SGM is applied to both single determinant ΔSCF and spin-purified restricted open-shell Kohn-Sham (ROKS) approaches to study the accuracy of orbital optimized DFT excited states. It is found that SGM can converge challenging states where the maximum overlap method (MOM) or analogues either collapse to the ground state or fail to converge. We also report that ΔSCF/ROKS predict highly accurate excitation energies for doubly excited states (which are inaccessible via TDDFT). Singly excited states obtained via ROKS are also found to be quite accurate, especially for Rydberg states that frustrate (semi)local TDDFT. Our results suggest that orbital optimized excited state DFT methods can be used to push past the limitations of TDDFT to doubly excited, charge-transfer, or Rydberg states, making them a useful tool for the practical quantum chemist's toolbox for studying excited states in large systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Importance of imposing gauge invariance in time-dependent density functional theory calculations with meta-generalized gradient approximations

It has been known for more than a decade that the gauge variance of the kinetic energy density τ leads to additional terms in the magnetic orbital rotation Hessian used in linear-response time-dependent density functional theory (TDDFT), affecting excitation energies obtained with τ-dependent exchange–correlation functionals. While previous investigations found that a correction scheme based on the paramagnetic current density has a small effect on benchmark results, we report more pronounced effects here, in particular, for the popular M06-2X functional and for some other meta-generalized gradient approximations (mGGAs). In the first part of this communication, this is shown by a reassessment of a set of five Ni(II) complexes for which a previous benchmark study that did not impose gauge invariance has found surprisingly large errors for excitation energies obtained with M06-2X. These errors are more than halved by restoring gauge invariance. The variable importance of imposing gauge invariance for different mGGA-based functionals can be rationalized by the derivative of the mGGA exchange energy integrand with respect to τ. In the second part, a large set of valence excitations in small main-group molecules is analyzed. For M06-2X, several selected n → π* and π→π$^{*}_{⊥}$ excitations are heavily gauge-dependent with average changes of –0.17 and –0.28 eV, respectively, while π→π$^{*}_{∥}$ excitations are marginally affected (–0.04 eV). Similar patterns, but of the opposite signs, are found for SCAN0. Here, the results suggest that reevaluation of previous gauge variant TDDFT results based on M06-2X and other mGGA functionals is warranted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Finite difference grid generation by multivariate blending function interpolation

The General Interpolants Method (GIM) code which solves the multidimensional Navier-Stokes equations for arbitrary geometric domains is described. The geometry module in the GIM code generates two and three dimensional grids over specified flow regimes, establishes boundary condition information and computes finite difference analogs for use in the GIM code numerical solution module. The technique can be classified as an algebraic equation approach. The geometry package uses multivariate blending function interpolation of vector-values functions which define the shapes of the edges and surfaces bounding the flow domain. By employing blending functions which conform to the cardinality conditions the flow domain may be mapped onto a unit square (2-D) or unit cube (3-D), thus producing an intrinsic coordinate system for the region of interest. The intrinsic coordinate system facilitates grid spacing control to allow for optimum distribution of nodes in the flow domain.

Anderson, P. G.↗

Canonical fluid thermodynamics

The space-time integral of the thermodynamic pressure plays the role of the thermodynamic potential for compressible, adiabatic flow in the sense that the pressure integral for stable flow is less than for all slightly different flows. This stability criterion can be converted into a variational minimum principle by requiring the molar free-enthalpy and the temperature, which are the arguments of the pressure function, to be generalized velocities, that is, the proper-time derivatives of scalar spare-time functions which are generalized coordinates in the canonical formalism. In a fluid context, proper-time differentiation must be expressed in terms of three independent quantities that specify the fluid velocity. This can be done in several ways, all of which lead to different variants (canonical transformations) of the same constraint-free action integral whose Euler-Lagrange equations are just the well-known equations of motion for adiabatic compressible flow.

Schmid, L. A.↗

A procedure for obtaining explicit solutions to a class of Fredholm integral equations

A Fredholm integral equation is solved in closed form by reducing it to a standard boundary value problem for a sectionally analytic function. The procedure maybe extended to more general classes of functions whose Fourier transforms only exist along certain lines in the complex k-plane. Examples are used to illustrate the results.

Goldstein, M. E.↗

Design of efficient stiffened shells of revolution

A method to produce efficient piecewise uniform stiffened shells of revolution is presented. The approach uses a first order differential equation formulation for the shell prebuckling and buckling analyses and the necessary conditions for an optimum design are derived by a variational approach. A variety of local yielding and buckling constraints and the general buckling constraint are included in the design process. The local constraints are treated by means of an interior penalty function and the general buckling load is treated by means of an exterior penalty function. This allows the general buckling constraint to be included in the design process only when it is violated. The self-adjoint nature of the prebuckling and buckling formulations is used to reduce the computational effort. Results for four conical shells and one spherical shell are given.

Majumder, D. K.↗

Advanced Digital Avionics System for general aviation

Objectives and functions of the Advanced Digital Avionics System (ADAS) for general aviation are outlined with particular reference to navigation, flight control, engine management, ATC surveillance, flight management, communications, and the pilot controls and displays. The resulting ADAS design comprises the selection of off-the-shelf avionics to be integrated with ADAS-unique elements including new pilot displays and controls along with a microcomputer control complex (MCC). Reasons for which the ADAS achieves increased avionics capability are mentioned, including overall system integration through the MCC and pilot orientation from navigation map display.

Smyth, R. K.↗

Application of multivariable search techniques to structural design optimization

Multivariable optimization techniques are applied to a particular class of minimum weight structural design problems: the design of an axially loaded, pressurized, stiffened cylinder. Minimum weight designs are obtained by a variety of search algorithms: first- and second-order, elemental perturbation, and randomized techniques. An exterior penalty function approach to constrained minimization is employed. Some comparisons are made with solutions obtained by an interior penalty function procedure. In general, it would appear that an interior penalty function approach may not be as well suited to the class of design problems considered as the exterior penalty function approach. It is also shown that a combination of search algorithms will tend to arrive at an extremal design in a more reliable manner than a single algorithm. The effect of incorporating realistic geometrical constraints on stiffener cross-sections is investigated. A limited comparison is made between minimum weight cylinders designed on the basis of a linear stability analysis and cylinders designed on the basis of empirical buckling data. Finally, a technique for locating more than one extremal is demonstrated.

Jones, R. T.↗

Inverse methods for assessing ship-of-opportunity networks and estimating circulation and winds from tropical expendable bathythermograph data

Inverse methods for estimating the surface ciculation of the equatorial Pacific by combining a linear reduced-gravity shallow-water model with the Tropical Ocean-Global Atmosphere ship-of-opportunity expendable bathythermograph (TOGA SOP XBT) observing program are examined. It is demonstrated that a simple linear model of the upper circulation of the equatorial Pacific can be successfully used as a weak constraint when smoothing the TOGA SOP XBT data. A circulation is sought as the weighted least squares fit to the dynamics and the data. The solution method is an expansion in representer functions, and the generalized inverse problem is thereby reduced from a functional problem to an algebraic problem for the coefficients of the representer. A specific inverse calculation using synthetic forcing and data is presented.

Bennett, Andrew F.↗

Thermal hybrid exchange-correlation density functional for improving the description of warm dense matter

Finite-temperature density functional theory (FT-DFT) has become a standard tool for first principles calculations of the properties of warm dense matter (WDM) relevant to high-energy density physics (HEDP) applications. In this work we introduce theoretical grounds of thermal hybrid exchange-correlation (XC) functionals within the generalized Mermin-Kohn-Sham scheme for an improved description of WDM. Building on the previously developed KSDT (Karasiev-Sjostrom-Dufty-Trickey) [Karasiev et al., Phys. Rev. Lett. 112, 076403 (2014)] local density approximation (LDA) and the KDT16 (Karasiev-Dufty-Trickey 2016) [Karasiev et al., Phys. Rev. Lett. 120, 076402 (2018)] generalized-gradient approximation (GGA) XC free-energy density functionals, we construct a new thermal hybrid XC functional, referred to here as KDT0. The KDT0 model at low temperature reduces to the popular ground-state PBE0 hybrid due to properties of the used KDT16 density functional approximation. Application to static calculations of electronic band gap and band structure at a wide range of temperatures for various systems of interest to HEDP show that KDT0 provides a significant improvement to the lower LDA and GGA rung XC functionals and to the ground-state PBE0 hybrid.

36 MATERIALS SCIENCE↗