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At least 325 records · Page 18

Life in the Clouds of Venus? An Experimental Synthetic Biology Approach

The surface of Venus constitutes the most hellish and biologically inhospitable planetary surface in our solar system, boasting a pH of 0, blistering winds that can melt lead, and pressures of 60 atm. However, during the earlier years of the solar system, without the runaway greenhouse effect that has plagued the planet, Venus potentially housed oceans and perhaps even life. There is a possibility that microbes could have retreated into hospitable niches in the atmosphere, as suggested by Carl Sagan as early as 1967 [1]. For example, 50 km above the raging hell of the Venusian surface, exists a relatively temperate environment that might serve as reservoir for life. This astrobiology project seeks to explore life at the extremes and to theorize whether microbial communities could not only survive but also reproduce in the Venusian atmosphere. Specifically, we ask: are aerosols viable microbial environments? But before we can test for life in the clouds, we have to develop a proper reporter to visualize cell growth in situ. For this purpose, we aimed to develop cell-growth dependent reporters to serve as remote biosensors for cell growth. We developed two using the polA promoter, a DNA-replication dependent promoter, and nrd operon promoter, a cell-cycle dependent promoter. Using these cell-growth reporters, the next step is to aerosolize microbes expressing these reporters in a suspension chamber adapted from a Millikan Drop Apparatus to assay reproduction in an aerosolized environment. Better yet is to test the reproduction of microbes in a microgravity regime such as on ISS.Approach: We engineered two cell-cycle dependent genetic reporters. One was the polA promoter which codes for DNA Polymerase I, a gene active in DNA replication [2]. The other was the nrdP. The activation of ribonucleotide reductase reduces ribonucleotides into deoxyribonucleotides and is involved in the bacterial cell cycle [3]. This promoter began activation during the initiation of DNA replication and is cell-cycle dependent [4]. These promoters were fused to a GFP reporter, transformed into E. coli. The constructs were deposited in the iGEM registry as K847210: Escherichia coli DNA-replication dependent polA promoter K847211: Escherichia coli cell-division dependent nrd promoter Results: Our constructs displayed fluorescence when transformed into NEB-5alpha competent cells. While nrdP-E0840 displayed sufficient fluorescence as verified by fluorescent microscopy, the original polAP-E0840 construct (which uses mut3b GFP) exhibited low expression; while fluorescence was visible under the microscope, the signal was too weak for the camera to recognize. The polA promoter was therefore digest-ed with EcoRI and SpeI then ligated into plasmid pNCS containing a RBS, Clover, and a terminator. Clover is a highly engineered green fluorescent protein that exhibits extreme brightness [5] Fluoresence time course data demonsrated that the genes were induced in a cell cycle dependant manner [6]. Our assays via microscopy and the bulk assay shows that our promoters are functional as cell cycle reporters.Conclusions: The application of such tools are widespread and not limited to astrobiology; nrdP could be used to determine doubling times empirically and could possibly extrapolate DNA content from intensity of signals expressed by polAP. However, we are pri-marily interested in its use in astrobiology.

Escherichia↗

Direct Reconstruction of Ablative Thermal Protection System Aeroheating Using A Green's Function Approach

A Green’s function inverse heat transfer (IHT) approach is used to reconstruct the surface heating conditions on ablative thermal protection system (TPS) materials from embedded heat flux sensor and temperature probe measurements. The approach models the temperature time-history at the measurement location as a discrete linear system, allowing for the heat flux boundary condition to be recovered directly without the need for time-marching schemes. The effects of material decomposition and pyrolysis gas transport are modeled using an energy source/sink analogue. The performance of the reconstruction approach is analyzed on a 1D test case representative of an atmospheric entry heating scenario. The approach can recover the TPS surface heat flux to within 4% of the input heating condition with a computation time of 2-3 seconds (>3 orders of magnitude faster than current time-marching IHT methods). As a byproduct of the surface heating reconstruction, the algorithm also captures the surface pyrolysis gas mass flux and solid decomposition at multiple through-thickness locations within the TPS.

Kenneth McAfee↗

The small-voxel tracking algorithm for simulating chemical reactions among diffusing molecules

Simulating the evolution of a chemically reacting system using the bimolecular propensity function, as is done by the stochastic simulation algorithm and its reaction-diffusion extension, entails making statistically inspired guesses as to where the reactant molecules are at any given time. Those guesses will be physically justified if the system is dilute and well-mixed in the reactant molecules. Otherwise, an accurate simulation will require the extra effort and expense of keeping track of the positions of the reactant molecules as the system evolves. One molecule-tracking algorithm that pays careful attention to the physics of molecular diffusion is the enhanced Green's function reaction dynamics (eGFRD) of Takahashi, Tănase-Nicola, and ten Wolde [Proc. Natl. Acad. Sci. U.S.A. 107, 2473 (2010)]. We introduce here a molecule-tracking algorithm that has the same theoretical underpinnings and strategic aims as eGFRD, but a different implementation procedure. Called the small-voxel tracking algorithm (SVTA), it combines the well known voxel-hopping method for simulating molecular diffusion with a novel procedure for rectifying the unphysical predictions of the diffusion equation on the small spatiotemporal scale of molecular collisions. Indications are that the SVTA might be more computationally efficient than eGFRD for the problematic class of non-dilute systems. A widely applicable, user-friendly software implementation of the SVTA has yet to be developed, but we exhibit some simple examples which show that the algorithm is computationally feasible and gives plausible results.

97 MATHEMATICS AND COMPUTING↗

A Computer Program for the Computation of Running Gear Temperatures Using Green's Function

A new technique has been developed to study two dimensional heat transfer problems in gears. This technique consists of transforming the heat equation into a line integral equation with the use of Green's theorem. The equation is then expressed in terms of eigenfunctions that satisfy the Helmholtz equation, and their corresponding eigenvalues for an arbitrarily shaped region of interest. The eigenfunction are obtalned by solving an intergral equation. Once the eigenfunctions are found, the temperature is expanded in terms of the eigenfunctions with unknown time dependent coefficients that can be solved by using Runge Kutta methods. The time integration is extremely efficient. Therefore, any changes in the time dependent coefficients or source terms in the boundary conditions do not impose a great computational burden on the user. The method is demonstrated by applying it to a sample gear tooth. Temperature histories at representative surface locatons are given.

GREENS FUNCTIONS↗

Vapor concentration measurement with photothermal deflectometry

Theoretical and experimental results for using the photothermal deflection technique to measure vapor species concentration, while minimizing the disturbance of the transport (material) parameters due to vapor heating, are developed and described. In contrast to common practice, the above constraints require using a pump-beam duty cycle of less than 50 percent. The theoretical description of the shortened heating time is based on a step-function formulation of the pumping cycle. The results are obtained as closed-form solutions of the energy equation for many chopping cycles until steady state is reached, by use of a Green's-function method. The Euler formulation of the Fermat principle is used to calculate the deflection angle. The equations are expanded to include the effects of vapor velocity on both the temperature and temperature gradient profiles. The effects of finite (unfocused) pump and probe beams and thermal (Soret) diffusion are also accounted for. Excellent agreement between theory and experiment is obtained.

Banish, R. Michael↗

Spectral Characteristics of Wake Vortex Sound During Roll-Up

This report presents an analysis of the sound spectra generated by a trailing aircraft vortex during its rolling-up process. The study demonstrates that a rolling-up vortex could produce low frequency (less than 100 Hz) sound with very high intensity (60 dB above threshold of human hearing) at a distance of 200 ft from the vortex core. The spectrum then drops o rapidly thereafter. A rigorous analytical approach has been adopted in this report to derive the spectrum of vortex sound. First, the sound pressure was solved from an alternative treatment of the Lighthill s acoustic analogy approach [1]. After the application of Green s function for free space, a tensor analysis was applied to permit the removal of the source term singularity of the wave equation in the far field. Consequently, the sound pressure is expressed in terms of the retarded time that indicates the time history and spacial distribution of the sound source. The Fourier transformation is then applied to the sound pressure to compute its spectrum. As a result, the Fourier transformation greatly simplifies the expression of the vortex sound pressure involving the retarded time, so that the numerical computation is applicable with ease for axisymmetric line vortices during the rolling-up process. The vortex model assumes that the vortex circulation is proportional to the time and the core radius is a constant. In addition, the velocity profile is assumed to be self-similar along the aircraft flight path, so that a benchmark vortex velocity profile can be devised to obtain a closed form solution, which is then used to validate the numerical calculations for other more realistic vortex profiles for which no closed form solutions are available. The study suggests that acoustic sensors operating at low frequency band could be profitably deployed for detecting the vortex sound during the rolling-up process.

Booth, Earl R., Jr.↗

Direct experimental determination of spectral densities of molecular complexes

Determining the spectral density of a molecular system immersed in a proteomic scaffold and in contact to a solvent is a fundamental challenge in the coarse-grained description of, e.g., electron and energy transfer dynamics. Once the spectral density is characterized, all the time scales are captured and no artificial separation between fast and slow processes need to be invoked. Based on the fluorescence Stokes shift function, we utilize a simple and robust strategy to extract the spectral density of a number of molecular complexes from available experimental data. Specifically, we show that experimental data for dye molecules in several solvents, amino acid proteins in water, and some photochemical systems (e.g., rhodopsin and green fluorescence proteins), are well described by a three-parameter family of sub-Ohmic spectral densities that are characterized by a fast initial Gaussian-like decay followed by a slow algebraic-like decay rate at long times.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Coupling dynamic in situ X-ray micro-imaging and indentation: A novel approach to evaluate micromechanics applied to oil shale

Oil and gas shales are a system where understanding the mechanical properties at the microscale is of paramount importance, e.g. to better understand the behavior of proppant-shale contacts and their role in the evolution of propped fractures in unconventional reservoirs. Here we show for the first time an experiment coupling indentation testing with in situ X-ray imaging in a Green River shale sample. A full compliance curve has been measured with the sample in water, allowing to visualize the indentation of the sample in function of axial load, in a purpose-built system for combined in situ indentation and X-ray imaging. A series of 3D datasets were used for a digital volume correlation study to obtain local strain fields. This analysis has been complemented with the analysis of cracks. Finally, geomechanical modeling has been carried out to replicate and generalize the observed behavior in the shale. This study validated this experimental approach, providing a breakthrough in understanding micro-mechanics in shales, and demonstrates how this class of experiments can be important for studies involving the prediction of the evolution of propped fractures in shale reservoirs, with possible applications in a much larger number of application fields (geothermal, materials science, etc.)

04 OIL SHALES AND TAR SANDS↗

Green mechanochemical synthesis of imine-linked covalent organic frameworks for high iodine capture

Covalent organic frameworks (COFs) have emerged as promising adsorbents for radioiodine capture. However, the conventional solvothermal synthesis contradicts the principles of green chemistry due to the use of hazardous solvents, long reaction times (typically 3 days), and high reaction temperatures. Here, to address these issues, we demonstrate for the first time the green, efficient, liquid-assisted mechanochemical synthesis of COF adsorbents for high iodine capture. The ball milling synthesis was performed with various liquid additives at ambient temperature, yielding six imine-linked COFs of diverse pore sizes and functionalities in merely 1 hour. Notably, one representative COF exhibited high crystallinity and a remarkable surface area of 1387 m 2 g –1 in just 1 minute of ball milling. When tested as adsorbents for static iodine vapor capture at 75 °C, four mechanochemically synthesized COFs exhibited outstanding iodine adsorption capacities of 6.4–7.1 g g –1 , comparable to or exceeding those of solvothermally synthesized COF and most reported COF adsorbents. Furthermore, Fourier transform infrared and X-ray photoelectron spectroscopy corroborated the charge transfer between iodine and COF adsorbents. This mechanochemical methodology will pave the path for green, rapid, facile, and scalable synthesis of COFs, revealing great prospects for applications in environmental remediation and beyond.

36 MATERIALS SCIENCE↗

The acoustic response of rooms with open windows to airborne sounds.

The objective of the work described in this and the companion paper was to establish a theory for predicting the sound field generated in a room by a sonic boom incident on an open window. In this paper, some basic theoretical results are presented. First, the case of a normally incident harmonic wave was considered. Expressions for the pressure field were obtained by viewing the room as a terminated duct and by using a Green function method. The concept of mode excitation distribution functions was formulated and used to match the boundary conditions. This concept has been extended for oblique incidence. A modified form of Laplace transform technique was used to obtain expressions in the time domain for transient signals.

Vaidya, P. G.↗

Steady, Oscillatory, and Unsteady Subsonic and Supersonic Aerodynamics, production version (SOUSSA-P 1.1). Volume 1: Theoretical manual

Recent developments of the Green's function method and the computer program SOUSSA (Steady, Oscillatory, and Unsteady Subsonic and Supersonic Aerodynamics) are reviewed and summarized. Applying the Green's function method to the fully unsteady (transient) potential equation yields an integro-differential-delay equation. With spatial discretization by the finite-element method, this equation is approximated by a set of differential-delay equations in time. Time solution by Laplace transform yields a matrix relating the velocity potential to the normal wash. Premultiplying and postmultiplying by the matrices relating generalized forces to the potential and the normal wash to the generalized coordinates one obtains the matrix of the generalized aerodynamic forces. The frequency and mode-shape dependence of this matrix makes the program SOUSSA useful for multiple frequency and repeated mode-shape evaluations.

Morino, L.↗

Experimental flaw detection by scattering of plate waves

The surface displacements of elastic waves scattered from a surface-breaking crack are measured with a capacitive transducer on a 2D plate, and comparisons with theoretical predictions are reported. The noncontacting detector has a wide and flat frequency response which measures the response of a glass plate to the propagation of Rayleigh-Lamb waves. A theoretical simulation of the surface displacements is generated by multiplying experimental traces with a cosine window, and Green's function is used to compute the source function. Power spectra are also recorded from the experiment to compare the results with a finite-element model of the crack, and good agreement is reported for results in both the time and frequency domains. The crack can be detected in the far field when the spacing of the receiver locations is small, and the transducer/probe appears to be a practical flaw-detection instrument.

Spetzler, Hartmut↗

Rationally designed bidirectional promoter improves the evolutionary stability of synthetic genetic circuits

One problem with synthetic genes in genetically engineered organisms is that these foreign DNAs will eventually lose their functions over evolutionary time in absence of selective pressures. This general limitation can restrain the long-term study and industrial application of synthetic genetic circuits. Previous studies have shown that because of their crucial regulatory functions, prokaryotic promoters in synthetic genetic circuits are especially vulnerable to mutations. In this study, we rationally designed robust bidirectional promoters (BDPs), which are self-protected through the complementarity of their overlapping forward and backward promoter sequences on DNA duplex. When the transcription of a target non-essential gene (e.g. green fluorescent protein) was coupled to the transcription of an essential gene (e.g. antibiotic resistance gene) through the BDP, the evolutionary half-time of the gene of interest increases 4–10 times, depending on the strain and experimental conditions used. This design of using BDPs to increase the mutational stability of genetic circuits can be potentially applied to synthetic biology applications in general.

59 BASIC BIOLOGICAL SCIENCES↗

Leaf microscopy applications in photosynthesis research: identifying the gaps

Abstract Leaf imaging via microscopy has provided critical insights into research on photosynthesis at multiple junctures, from the early understanding of the role of stomata, through elucidating C4 photosynthesis via Kranz anatomy and chloroplast arrangement in single cells, to detailed explorations of diffusion pathways and light utilization gradients within leaves. In recent decades, the original two-dimensional (2D) explorations have begun to be visualized in three-dimensional (3D) space, revising our understanding of structure–function relationships between internal leaf anatomy and photosynthesis. In particular, advancing new technologies and analyses are providing fresh insight into the relationship between leaf cellular components and improving the ability to model net carbon fixation, water use efficiency, and metabolite turnover rate in leaves. While ground-breaking developments in imaging tools and techniques have expanded our knowledge of leaf 3D structure via high-resolution 3D and time-series images, there is a growing need for more in vivo imaging as well as metabolite imaging. However, these advances necessitate further improvement in microscopy sciences to overcome the unique challenges a green leaf poses. In this review, we discuss the available tools, techniques, challenges, and gaps for efficient in vivo leaf 3D imaging, as well as innovations to overcome these difficulties.

Plant Sciences↗

Geoid anomalies in a dynamic earth

Potential and surface deformation Love numbers for internal loading have been calculated in order to obtain a dynamically consistent relationship between the geoid and the earth's response to internal buoyancy forces. These quantities depend on the depth and harmonic degree of loading, and can be integrated as Green functions to obtain the dynamic response due to an arbitrary distribution of internal density contrasts. Constructing a series of spherically symmetric, self-gravitating flow models for a variety of radial Newtonian viscosity variations and flow configurations, and calculating relaxation times for spherically symmetric viscous earth models, it is demonstrated that boundary deformation due to internal loading reaches its equilibrium value on the same time scale as postglacial rebound; this is much less time than the time scale for significant change in the convective flow pattern.

Richards, M. A.↗

Wave diffraction in weak cosmic-ray-modified shocks

Weakly multidirectional, long-wavelength cosmic-ray-modified shocks are studied via multiple scale perturbation techniques. The effects of diffraction are discussed in terms of Green's function solutions of the linearized 1 + 3D Burgers and 1 + 3D KdVB equations, and also in terms of solutions with singular Dirac delta initial distributions. The solutions show a monotonic decrease of the wave-front curvature with increasing time owing to the effects of wave diffraction. The shape of the wave surface is discussed in terms of solutions S to the wave eikonal equation corresponding to singular initial conditions. For the fast magnetosonic wave propagating in the positive x-direction, the wave phase surface S = 0 has elliptic cross sections with the planes x = constant and has a convex paraboloidal shape. Plane-wave solutions of the 1 + 3D KdVB equation are discussed.

Webb, G. M.↗

Dynamic conductance in L-shaped graphene nanosystems

Dynamic conductance of nanocircuit, which demonstrates dc and ac transport properties, is regarded as vital indicator for device feature. With the help of nonequilibrium Green's function technology and Buttiker's ac transport theory, we present dynamic conductance in L-shaped graphene nanosystems (LGNSs). It is found that electronic transport is highly sensitive to the geometric feature as well as the size of LGNSs. The armchair edge lead determines whether LGNS shows ac response or not around Dirac point. The increase of width of zigzag edge lead suppresses dc conductance and induces capacitive responses at the anti-resonance states. This is due to large dwell time originated from edge state in zigzag edge lead. In the energy region far away from Dirac point, LGNS responds inductively with the transportation channel opens. Behaviors of dynamic conductance at Dirac point and anti-resonance states are discussed by interesting spacial-resolved local density of states.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Testing thermal conductivity models with equilibrium molecular dynamics simulations of the one-component plasma

Equilibrium molecular dynamics simulations are used to calculate the thermal conductivity of the onecomponent plasma via the Green-Kubo formalism over a broad range of Coulomb coupling strength, 0.1 ≤ Γ ≤180. These simulations address previous discrepancies between computations using equilibrium versus nonequilibrium methods. Analysis of heat flux autocorrelation functions show that very long (6×10 5 $ω^{-1}_{p}$) time series are needed to reduce the noise level to allow ≲2% accuracy. The simulations provide accurate data for Γ ≲ 1. Furthermore, this enables a test of the traditional Landau-Spitzer theory, which is found to agree with the simulations for Γ ≲ 0.3. It also enables tests of theories to address moderate and strong Coulomb coupling. Two are found to provide accurate extensions to the moderate coupling regime of Γ ≲ 10, but none are accurate in the Γ ≳ 10 regime where potential energy transport and coupling between mass flow and stress dominate thermal conduction.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗