Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR

Viruses may very well be the most abundant biological entities on the planet. Yet neither metagenomic studies nor classical phage isolation techniques have shed much light on the identity of the hosts of most viruses. We used a microfluidic digital polymerase chain reaction (PCR) approach to physically link single bacterial cells harvested from a natural environment with a viral marker gene. When we implemented this technique on the microbial community residing in the termite hindgut, we found genus-wide infection patterns displaying remarkable intragenus selectivity. Viral marker allelic diversity revealed restricted mixing of alleles between hosts, indicating limited lateral gene transfer of these alleles despite host proximity. Our approach does not require culturing hosts or viruses and provides a method for examining virus-bacterium interactions in many environments

Lagrangian particle paths and ortho-normal quaternion frames

Experimentalists now measure intense rotations of Lagrangian particles in turbulent flows by tracking their trajectories and Lagrangian-average velocity gradients at high Reynolds numbers. This paper formulates the dynamics of an orthonormal frame attached to each Lagrangian fluid particle undergoing three-axis rotations, by using quaternions in combination with Ertel's theorem for frozen-in vorticity. The method is applicable to a wide range of Lagrangian flows including the three-dimensional Euler equations and its variants such as ideal MHD. The applicability of the quaterionic frame description to Lagrangian averaged velocity gradient dynamics is also demonstrated.Comment: 9 pages, one figure, revise

Multi-scale simulation of the nano-metric cutting process

Molecular dynamics (MD) simulation and the finite element (FE) method are two popular numerical techniques for the simulation of machining processes. The two methods have their own strengths and limitations. MD simulation can cover the phenomena occurring at nano-metric scale but is limited by the computational cost and capacity, whilst the FE method is suitable for modelling meso- to macro-scale machining and for simulating macro-parameters, such as the temperature in a cutting zone, the stress/strain distribution and cutting forces, etc. With the successful application of multi-scale simulations in many research fields, the application of simulation to the machining processes is emerging, particularly in relation to machined surface generation and integrity formation, i.e. the machined surface roughness, residual stress, micro-hardness, microstructure and fatigue. Based on the quasi-continuum (QC) method, the multi-scale simulation of nano-metric cutting has been proposed. Cutting simulations are performed on single-crystal aluminium to investigate the chip formation, generation and propagation of the material dislocation during the cutting process. In addition, the effect of the tool rake angle on the cutting force and internal stress under the workpiece surface is investigated: The cutting force and internal stress in the workpiece material decrease with the increase of the rake angle. Finally, to ease multi-scale modelling and its simulation steps and to increase their speed, a computationally efficient MATLAB-based programme has been developed, which facilitates the geometrical modelling of cutting, the simulation conditions, the implementation of simulation and the analysis of results within a unified integrated virtual-simulation environment

Dynamic of a non homogeneously coarse grained system

To study materials phenomena simultaneously at various length scales, descriptions in which matter can be coarse grained to arbitrary levels, are necessary. Attempts to do this in the static regime (i.e. zero temperature) have already been developed. In this letter, we present an approach that leads to a dynamics for such coarse-grained models. This allows us to obtain temperature-dependent and transport properties. Renormalization group theory is used to create new local potentials model between nodes, within the approximation of local thermodynamical equilibrium. Assuming that these potentials give an averaged description of node dynamics, we calculate thermal and mechanical properties. If this method can be sufficiently generalized it may form the basis of a Molecular Dynamics method with time and spatial coarse-graining.Comment: 4 pages, 4 figure

Renormalization group approach to multiscale modelling in materials science

Dendritic growth, and the formation of material microstructure in general, necessarily involves a wide range of length scales from the atomic up to sample dimensions. The phase field approach of Langer, enhanced by optimal asymptotic methods and adaptive mesh refinement, copes with this range of scales, and provides an effective way to move phase boundaries. However, it fails to preserve memory of the underlying crystallographic anisotropy, and thus is ill-suited for problems involving defects or elasticity. The phase field crystal (PFC) equation-- a conserving analogue of the Hohenberg-Swift equation --is a phase field equation with periodic solutions that represent the atomic density. It can natively model elasticity, the formation of solid phases, and accurately reproduces the nonequilibrium dynamics of phase transitions in real materials. However, the PFC models matter at the atomic scale, rendering it unsuitable for coping with the range of length scales in problems of serious interest. Here, we show that a computationally-efficient multiscale approach to the PFC can be developed systematically by using the renormalization group or equivalent techniques to derive appropriate coarse-grained coupled phase and amplitude equations, which are suitable for solution by adaptive mesh refinement algorithms

Lattice Resistance and Peierls Stress in Finite-size Atomistic Dislocation Simulations

Atomistic computations of the Peierls stress in fcc metals are relatively scarce. By way of contrast, there are many more atomistic computations for bcc metals, as well as mixed discrete-continuum computations of the Peierls-Nabarro type for fcc metals. One of the reasons for this is the low Peierls stresses in fcc metals. Because atomistic computations of the Peierls stress take place in finite simulation cells, image forces caused by boundaries must either be relaxed or corrected for if system size independent results are to be obtained. One of the approaches that has been developed for treating such boundary forces is by computing them directly and subsequently subtracting their effects, as developed by V. B. Shenoy and R. Phillips [Phil. Mag. A, 76 (1997) 367]. That work was primarily analytic, and limited to screw dislocations and special symmetric geometries. We extend that work to edge and mixed dislocations, and to arbitrary two-dimensional geometries, through a numerical finite element computation. We also describe a method for estimating the boundary forces directly on the basis of atomistic calculations. We apply these methods to the numerical measurement of the Peierls stress and lattice resistance curves for a model aluminum (fcc) system using an embedded-atom potential.Comment: LaTeX 47 pages including 20 figure

Effects of crack tip geometry on dislocation emission and cleavage: A possible path to enhanced ductility

We present a systematic study of the effect of crack blunting on subsequent crack propagation and dislocation emission. We show that the stress intensity factor required to propagate the crack is increased as the crack is blunted by up to thirteen atomic layers, but only by a relatively modest amount for a crack with a sharp 60$^\circ$ corner. The effect of the blunting is far less than would be expected from a smoothly blunted crack; the sharp corners preserve the stress concentration, reducing the effect of the blunting. However, for some material parameters blunting changes the preferred deformation mode from brittle cleavage to dislocation emission. In such materials, the absorption of preexisting dislocations by the crack tip can cause the crack tip to be locally arrested, causing a significant increase in the microscopic toughness of the crack tip. Continuum plasticity models have shown that even a moderate increase in the microscopic toughness can lead to an increase in the macroscopic fracture toughness of the material by several orders of magnitude. We thus propose an atomic-scale mechanism at the crack tip, that ultimately may lead to a high fracture toughness in some materials where a sharp crack would seem to be able to propagate in a brittle manner. Results for blunt cracks loaded in mode II are also presented.Comment: 12 pages, REVTeX using epsfig.sty. 13 PostScript figures. Final version to appear in Phys. Rev. B. Main changes: Discussion slightly shortened, one figure remove

Hyperviscosity, Galerkin truncation and bottlenecks in turbulence

It is shown that the use of a high power $\alpha$ of the Laplacian in the dissipative term of hydrodynamical equations leads asymptotically to truncated inviscid \textit{conservative} dynamics with a finite range of spatial Fourier modes. Those at large wavenumbers thermalize, whereas modes at small wavenumbers obey ordinary viscous dynamics [C. Cichowlas et al. Phys. Rev. Lett. 95, 264502 (2005)]. The energy bottleneck observed for finite $\alpha$ may be interpreted as incomplete thermalization. Artifacts arising from models with $\alpha > 1$ are discussed.Comment: 4 pages, 2 figures, Phys. Rev. Lett. in pres

Singular Cucker-Smale Dynamics

The existing state of the art for singular models of flocking is overviewed, starting from microscopic model of Cucker and Smale with singular communication weight, through its mesoscopic mean-filed limit, up to the corresponding macroscopic regime. For the microscopic Cucker-Smale (CS) model, the collision-avoidance phenomenon is discussed, also in the presence of bonding forces and the decentralized control. For the kinetic mean-field model, the existence of global-in-time measure-valued solutions, with a special emphasis on a weak atomic uniqueness of solutions is sketched. Ultimately, for the macroscopic singular model, the summary of the existence results for the Euler-type alignment system is provided, including existence of strong solutions on one-dimensional torus, and the extension of this result to higher dimensions upon restriction on the smallness of initial data. Additionally, the pressureless Navier-Stokes-type system corresponding to particular choice of alignment kernel is presented, and compared - analytically and numerically - to the porous medium equation