Determination Of Plastic Properties By Instrumented Spherical Indentation: Expanding Cavity Model And Similarity Solution Approach

The present paper aims to develop a robust spherical indentation-based method to extract material plastic properties. For this purpose, a new consideration of-piling-up effect is incorporated into the expanding cavity model; an extensive numerical study on the similarity Solution has also been performed. As a consequence, two semi-theoretical relations between the indentation response and material plastic properties are derived, with which plastic properties of materials can be identified from a single instrumented spherical indentation curve, the advantage being that this approach no longer needs estimations of contact radius with given elastic modulus. Moreover, the inconvenience in using multiple indenters with different tip angles can be avoided. Comprehensive sensitivity analyses show that the present algorithm is reliable. Also, by experimental verification performed oil three typical materials, good agreement of the material properties between those obtained from the reverse algorithm and experimental data is obtained.

A study of the length at maturity and hooks/gill net mesh selection in Clarias lazera from Lake Chad

The minimum length at first maturity of Clarias lazera was found to be 24 cm (4.8%) for females and 20 cm (1.8%) for males. Fifty percent maturity was attained at length of 28 cm to 30 cm for both sexes; there being little difference among the sexes at this level of maturity. The modal retention lengths for gill nets were: 13 cm for 25.5 mm mesh; 18 cm for 32 mm mesh; 28 cm for 57 mm mesh; and 38 cm for 76 mm mesh. Modal lengths of Clarias lazera caught by various hooks sizes were No. 10 (28 cm); No. 11 (33 cm); Nos. 15 and 16 (28 cm). It is recommended that to protect the clarias fishery in Lake Chad, the use of gill nets of less than 57 mm mesh size and fishing hook No. 16 (and smaller sizes) which caught 43.94% of immature fishes should be discouraged

Numerical simulation of condensation of bubbles under microgravity conditions by moving mesh method in the double-staggered grid

A numerical 2D method for simulation of two-phase flows including phase change under microgravity conditions is presented in this paper, with a level set method being coupled with the moving mesh method in the double-staggered grid systems. When the grid lines bend very much in a curvilinear grid, great errors may be generated by using the collocated grid or the staggered grid. So the double-staggered grid was adopted in this paper. The level set method is used to track the liquid-vapor interface. The numerical analysis is fulfilled by solving the Navier-Stokes equations using the SIMPLER method, and the surface tension force is modeled by a continuum surface force approximation. A comparison of the numerical results obtained with different numerical strategies shows that the double-staggered grid moving-mesh method presented in this paper is more accurate than that used previously in the collocated grid system. Based on the method presented in this paper, the condensation of a single bubble in the cold water under different level of gravity is simulated. The results show that the condensation process under the normal gravity condition is different from the condensation process under microgravity conditions. The whole condensation time is much longer under the normal gravity than under the microgravity conditions.

Expanding the repertoire of DNA-mediated signaling in DNA repair

DNA damage is extremely detrimental to the cell and must be repaired to protect the genome. DNA is capable of conducting charge through the overlapping π-orbitals of stacked bases; this phenomenon is extremely sensitive to the integrity of the π-stack, as perturbations attenuate DNA charge transport (CT). Based on the E. coli base excision repair (BER) proteins EndoIII and MutY, it has recently been proposed that redox-active proteins containing metal clusters can utilize DNA CT to signal one another to locate sites of DNA damage.

To expand our repertoire of proteins that utilize DNA-mediated signaling, we measured the DNA-bound redox potential of the nucleotide excision repair (NER) helicase XPD from Sulfolobus acidocaldarius. A midpoint potential of 82 mV versus NHE was observed, resembling that of the previously reported BER proteins. The redox signal increases in intensity with ATP hydrolysis in only the WT protein and mutants that maintain ATPase activity and not for ATPase-deficient mutants. The signal increase correlates directly with ATP activity, suggesting that DNA-mediated signaling may play a general role in protein signaling. Several mutations in human XPD that lead to XP-related diseases have been identified; using SaXPD, we explored how these mutations, which are conserved in the thermophile, affect protein electrochemistry.

To further understand the electrochemical signaling of XPD, we studied the yeast S. cerevisiae Rad3 protein. ScRad3 mutants were incubated on a DNA-modified electrode and exhibited a similar redox potential to SaXPD. We developed a haploid strain of S. cerevisiae that allowed for easy manipulation of Rad3. In a survival assay, the ATPase- and helicase-deficient mutants show little survival, while the two disease-related mutants exhibit survival similar to WT. When both a WT and G47R (ATPase/helicase deficient) strain were challenged with different DNA damaging agents, both exhibited comparable survival in the presence of hydroxyurea, while with methyl methanesulfonate and camptothecin, the G47R strain exhibits a significant change in growth, suggesting that Rad3 is involved in repairing damage beyond traditional NER substrates. Together, these data expand our understanding of redox-active proteins at the interface of DNA repair.

Geometric integration applied to moving mesh methods and degenerate Lagrangians

Moving mesh methods (also called r-adaptive methods) are space-adaptive strategies used for the numerical simulation of time-dependent partial differential equations. These methods keep the total number of mesh points fixed during the simulation, but redistribute them over time to follow the areas where a higher mesh point density is required. There are a very limited number of moving mesh methods designed for solving field-theoretic partial differential equations, and the numerical analysis of the resulting schemes is challenging. In this thesis we present two ways to construct r-adaptive variational and multisymplectic integrators for (1+1)-dimensional Lagrangian field theories. The first method uses a variational discretization of the physical equations and the mesh equations are then coupled in a way typical of the existing r-adaptive schemes. The second method treats the mesh points as pseudo-particles and incorporates their dynamics directly into the variational principle. A user-specified adaptation strategy is then enforced through Lagrange multipliers as a constraint on the dynamics of both the physical field and the mesh points. We discuss the advantages and limitations of our methods. The proposed methods are readily applicable to (weakly) non-degenerate field theories---numerical results for the Sine-Gordon equation are presented.

In an attempt to extend our approach to degenerate field theories, in the last part of this thesis we construct higher-order variational integrators for a class of degenerate systems described by Lagrangians that are linear in velocities. We analyze the geometry underlying such systems and develop the appropriate theory for variational integration. Our main observation is that the evolution takes place on the primary constraint and the 'Hamiltonian' equations of motion can be formulated as an index 1 differential-algebraic system. We then proceed to construct variational Runge-Kutta methods and analyze their properties. The general properties of Runge-Kutta methods depend on the 'velocity' part of the Lagrangian. If the 'velocity' part is also linear in the position coordinate, then we show that non-partitioned variational Runge-Kutta methods are equivalent to integration of the corresponding first-order Euler-Lagrange equations, which have the form of a Poisson system with a constant structure matrix, and the classical properties of the Runge-Kutta method are retained. If the 'velocity' part is nonlinear in the position coordinate, we observe a reduction of the order of convergence, which is typical of numerical integration of DAEs. We also apply our methods to several models and present the results of our numerical experiments.

Cluster explosion investigated by linearly chirped spectral scattering of an expanding plasma sphere

Femtosecond explosive processes of argon clusters irradiated by linearly chirped ultraintense laser pulses have been investigated by 90 degrees side spectral scattering. The spectral redshift and blueshift, which correlate with the cluster explosion processes have been measured for negatively and positively chirped driving laser pulses, respectively. The evolution of the heated-cluster polarizability indicates that the core of the cluster is shielded from the laser field in the beginning of the explosion and enhanced scattering occurs after the fast explosion initiates. Evidence of resonant heating is found from the coincidence of enhanced scattering with enhanced absorption measured using the transmitted spectra. Anomalously large-size clusters with very low gas density have been observed in this way and can be used as clean and important cluster targets.

IPCC WGII Fifth Assessment Report (AR5): Expanding the solution space for adaptation

6 p.

Expanding the Toolkit for Synthetic Biology: Frameworks for Native-like Non-natural Gene Circuits

Synthetic biology combines biological parts from different sources in order to engineer non-native, functional systems. While there is a lot of potential for synthetic biology to revolutionize processes, such as the production of pharmaceuticals, engineering synthetic systems has been challenging. It is oftentimes necessary to explore a large design space to balance the levels of interacting components in the circuit. There are also times where it is desirable to incorporate enzymes that have non-biological functions into a synthetic circuit. Tuning the levels of different components, however, is often restricted to a fixed operating point, and this makes synthetic systems sensitive to changes in the environment. Natural systems are able to respond dynamically to a changing environment by obtaining information relevant to the function of the circuit. This work addresses these problems by establishing frameworks and mechanisms that allow synthetic circuits to communicate with the environment, maintain fixed ratios between components, and potentially add new parts that are outside the realm of current biological function. These frameworks provide a way for synthetic circuits to behave more like natural circuits by enabling a dynamic response, and provide a systematic and rational way to search design space to an experimentally tractable size where likely solutions exist. We hope that the contributions described below will aid in allowing synthetic biology to realize its potential.