There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

Considerable confusion surrounds the longstanding question of what constitutes a vortex, especially in a turbulent flow. This question, frequently misunderstood as academic, has recently acquired particular significance since coherent structures (CS) in turbulent flows are now commonly regarded as vortices. An objective definition of a vortex should permit the use of vortex dynamics concepts to educe CS, to explain formation and evolutionary dynamics of CS, to explore the role of CS in turbulence phenomena, and to develop viable turbulence models and control strategies for turbulence phenomena. We propose a definition of a vortex in an incompressible flow in terms of the eigenvalues of the symmetric tensor ${\bm {\cal S}}^2 + {\bm \Omega}^2$ are respectively the symmetric and antisymmetric parts of the velocity gradient tensor ${\bm \Delta}{\bm u}$. This definition captures the pressure minimum in a plane perpendicular to the vortex axis at high Reynolds numbers, and also accurately defines vortex cores at low Reynolds numbers, unlike a pressure-minimum criterion. We compare our definition with prior schemes/definitions using exact and numerical solutions of the Euler and Navier–Stokes equations for a variety of laminar and turbulent flows. In contrast to definitions based on the positive second invariant of ${\bm \Delta}{\bm u}$ or the complex eigenvalues of ${\bm \Delta}{\bm u}$, our definition accurately identifies the vortex core in flows where the vortex geometry is intuitively clear.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0022112095000462

On the identification of a vortex

Biological barriers to drug transport prevent successful accumulation of nanotherapeutics specifically at diseased sites, limiting efficacious responses in disease processes ranging from cancer to inflammation. Although substantial research efforts have aimed to incorporate multiple functionalities and moieties within the overall nanoparticle design, many of these strategies fail to adequately address these barriers. Obstacles, such as nonspecific distribution and inadequate accumulation of therapeutics, remain formidable challenges to drug developers. A reimagining of conventional nanoparticles is needed to successfully negotiate these impediments to drug delivery. Site-specific delivery of therapeutics will remain a distant reality unless nanocarrier design takes into account the majority, if not all, of the biological barriers that a particle encounters upon intravenous administration. By successively addressing each of these barriers, innovative design features can be rationally incorporated that will create a new generation of nanotherapeutics, realizing a paradigmatic shift in nanoparticle-based drug delivery.

/pdf/principles-of-nanoparticle-design-for-overcoming-biological-4c2c5quqtc.pdf

Principles of nanoparticle design for overcoming biological barriers to drug delivery

We present a new mechanism for generation of near-wall streamwise vortices – which dominate turbulence phenomena in boundary layers – using linear perturbation analysis and direct numerical simulations of turbulent channel flow. The base flow, consisting of the mean velocity profile and low-speed streaks (free from any initial vortices), is shown to be linearly unstable to sinuous normal modes only for relatively strong streaks, i.e. for wall inclination angles of streak vortex lines exceeding 50°. Analysis of streaks extracted from fully developed near-wall turbulence indicates that about 20% of streak regions in the buffer layer exceed the strength threshold for instability. More importantly, these unstable streaks exhibit only moderate (twofold) normal-mode amplification, the growth being arrested by self-annihilation of streak-flank normal vorticity due to viscous cross-diffusion. We present here an alternative, streak transient growth (STG) mechanism, capable of producing much larger (tenfold) linear ampliflcation of x-dependent disturbances. Note the distinction of STG – responsible for perturbation growth on a streak velocity distribution U(y, z) – from prior transient growth analyses of the (streakless) mean velocity U(y). We reveal that streamwise vortices are generated from the more numerous normal-mode-stable streaks, via a new STG-based scenario: (i) transient growth of perturbations leading to formation of a sheet of streamwise vorticity ωx (by a ‘shearing’ mechanism of vorticity generation), (ii) growth of sinuous streak waviness and hence ∂u/∂x as STG reaches nonlinear amplitude, and (iii) the ωx sheet’s collapse via stretching by ∂u/∂x (rather than rollup) into streamwise vortices. Significantly, the three-dimensional features of the (instantaneous) streamwise vortices of x-alternating sign generated by STG agree well with the (ensemble-averaged) coherent structures educed from fully turbulent flow. The STG-induced formation of internal shear layers, along with quadrant Reynolds stresses and other turbulence measures, also agree well with fully developed turbulence. Results indicate the prominent – possibly dominant – role of this new, transient-growth-based vortex generation scenario, and suggest interesting possibilities for robust control of drag and heat transfer.

/pdf/coherent-structure-generation-in-near-wall-turbulence-36o0srxpc5.pdf

Coherent structure generation in near-wall turbulence

Coherent structures (CS) near the wall (i.e. y + ≤ 60) in a numerically simulated turbulent channel flow are educed using a conditional sampling scheme which extracts the entire extent of dominant vortical structures. Such structures are detected from the instantaneous flow field using our newly developed vortex definition (Jeong & Hussain 1995) - a region of negative λ 2, the second largest eigenvalue of the tensor SikSkj + ΩikΩkj - which accurately captures the structure details (unlike velocity-, vorticity- or pressure-based eduction). Extensive testing has shown that λ 2 correctly captures vortical structures, even in the presence of the strong shear occurring near the wall of a boundary layer. We have shown that the dominant near-wall educed (i.e. ensemble averaged after proper alignment) CS are highly elongated quasi-streamwise vortices; the CS are inclined 9° in the vertical (x, y)-plane and tilted ±4° in the horizontal (x, z)-plane. The vortices of alternating sign overlap in x as a staggered array; there is no indication near the wall of hairpin vortices, not only in the educed data but also in instantaneous fields. Our model of the CS array reproduces nearly all experimentally observed events reported in the literature, such as VITA, Reynolds stress distribution, wall pressure variation, elongated low-speed streaks, spanwise shear, etc. In particular, a phase difference (in space) between streamwise and normal velocity fluctuations created by CS advection causes Q4 ('sweep’) events to dominate Q2 ('ejection’) and also creates counter-gradient Reynolds stresses (such as Ql and Q3 events) above and below the CS. We also show that these effects are adequately modelled by half of a Batchelor's dipole embedded in (and decoupled from) a background shear U(y). The CS tilting (in the (x, z)-plane) is found to be responsible for sustaining CS through redistribution of streamwise turbulent kinetic energy to normal and spanwise components via coherent pressure-strain effects.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0022112096003965

Coherent structures near the wall in a turbulent channel flow

Experimental studies of incompressible elliptic jets of different aspect ratios and initial conditions are summarized along with the effects of excitations at selected frequencies and amplitudes. The experimental facilities and procedures are described and jet spread and decay are discussed. The instability of elliptic shear layers, the behavior of the jet column under controlled excitation, and the time-average measures of unexcited jets are addressed.

Elliptic jets. I - Characteristics of unexcited and excited jets

A database obtained from direct numerical simulation of a turbulent channel flow is analyzed to extract the streamwise component of the propagation velocity V of velocity, vorticity, and pressure fluctuations from their space-time correlations. A surprising result is that V is approximately the same as the local mean velocity for most of the channel, except for the near-wall region. For y(+) less than 15, V is virtually constant, implying that perturbations of all flow variables propagate like waves near the wall. In this region V is 55 percent of the centerline velocity Uc for velocity and vorticity perturbations and 75 percent of U sub c for pressure perturbations. This is equal to U at y(+) = 15 for velocity and vorticity perturbations, and equal to U at y(+) = 20 for pressure perturbations, indicating that the dynamics of the nearwall turbulence is controlled by turbulence structures present near y(+) about 15-20. Scale dependence of V is also examined by analyzing the bandpass-filtered flow fields. This paper contains comprehensive documentation on the propagation velocities, which should prove useful in the evaluation of Taylor's hypothesis.

Fazle Hussain

Papers

On the identification of a vortex

Coherent structure generation in near-wall turbulence

Coherent structures near the wall in a turbulent channel flow

Elliptic jets. I - Characteristics of unexcited and excited jets

Propagation velocity of perturbations in turbulent channel flow