General Physical Mechanism Research Articles

Dehydrogenation of defects and hot-electron degradation in GaN high-electron-mobility transistors

Degradation mechanisms limiting the electrical reliability of GaN high-electron-mobility transistors (HEMTs) are generally attributed to defect generation by hot-electrons but specific mechanisms for such processes have not been identified. Here we give a model for the generation of active defects by the release of hydrogen atoms that passivate pre-exisiting defects. We report first-principles density-functional calculations of several candidate point defects and their interaction with hydrogen in GaN, under different growth conditions. Candidate precursor point defects in device quality GaN are identified by correlating previously observed trap levels with calculated optical levels. We propose dehydrogenation of point defects as a generic physical mechanism for defect generation in HEMTs under hot-electron stress when the degradation is not spontaneously reversible. Dehydrogenation of point defects explains (1) observed hot electron stress transconductance degradation, (2) increase in yellow luminescence, and opposite threshold voltage shifts in devices where the material was grown under nitrogen- and ammonia-rich conditions.

Binding of DNA to Zwitterionic Lipid Layers Mediated by Divalent Cations

Divalent cations, i.e., calcium, magnesium, and others, are able to enhance the ability of DNA to interact with membranes that are composed of zwitterionic lipids such as phosphatidylcholine. The resulting condensed complexes offer potential applications as nontoxic gene delivery vehicles. The present study suggests a generic theoretical model to describe the energetics and structural features of a zwitterionic lipid-DNA complex in the presence of divalent cations. Specifically, we consider the adsorption of a single molecule of double-stranded DNA onto a planar zwitterionic lipid layer. Our theoretical model is based on the continuum Poisson-Boltzmann formalisms, which we modified so as to account for the two opposite charges and orientational freedom of the zwitterionic lipid headgroups. We find a substantially more favorable adsorption free energy of the DNA if divalent cations are present. In addition, our model predicts the divalent cations to preferentially interact with the phosphate groups of the zwitterionic lipids, given these lipids are located in close vicinity to the DNA. This is accompanied by a small but notable reorientation of the zwitterionic headgroups toward the DNA. We demonstrate that the binding of DNA onto a zwitterionic lipid layer is not driven by the release of counterions. Instead, the binding leads to a partial redistribution of the divalent cations, from the phosphate groups of the DNA (prior to the binding) to the phosphate groups of the zwitterionic lipids (after the binding). Our results thus suggest a general physical mechanism underlying complex formation between DNA and zwitterionic lipids in terms of mean-field electrostatics, i.e., neither involving correlations nor specific interactions of the divalent cations.

Limb pattern, physical mechanisms and morphological evolution - an interview with Stuart A. Newman

Stuart A. Newman grew up in New York City. He received a Bachelor of Arts from Columbia University and obtained a Ph.D. in chemical physics from the University of Chicago in 1970. He did post-doctoral studies in several institutions and disciplines with a focus on theoretical and developmental biology. He had a rich experience interacting with people like Stuart Kauffman, Arthur Winfree, Brian Goodwin, and John W. Saunders, Jr. He was also exposed to many interesting experimental models of development. These early experiences fostered his interest in biological pattern formation. He joined the State University of New York at Albany as a junior faculty member when Saunders was still there. With his physical science background, Newmans approach to limb bud patterning was refreshing. In his major Science paper in 1979, he and H.L. Frisch proposed a model showing how reaction-diffusion can produce chemical standing waves to set up limb skeletal patterns. He then used limb bud micromass cultures for further development and testing of the model. Extending earlier ideas, he developed a comprehensive framework for the role of physical mechanisms (diffusion, differential adhesion, oscillation, dynamical multistability, reaction diffusion, mechano-chemical coupling, etc.) in morphogenesis. He also applied these mechanisms to understand the origin of multicellularity and evolution of novel body plans. Here Newman reflects on his intellectual growth, and shares with us his ideas on how pattern formation works, and how generic physical mechanisms interact with genetic mechanisms to achieve the evolution and development of animal forms.

Subcritical dynamos in shear flows

AbstractIdentifying generic physical mechanisms responsible for the generation of magnetic fields and turbulence in differentially rotating flows is fundamental to understand the dynamics of astrophysical objects such as accretion disks and stars. In this paper, we discuss the concept of subcritical dynamo action and its hydrodynamic analogue exemplified by the process of nonlinear transition to turbulence in non‐rotating wall‐bounded shear flows. To illustrate this idea, we describe some recent results on nonlinear hydrodynamic transition to turbulence and nonlinear dynamo action in rotating shear flows pertaining to the problem of turbulent angular momentum transport in accretion disks. We argue that this concept is very generic and should be applicable to many astrophysical problems involving a shear flow and non‐axisymmetric instabilities of shearinduced axisymmetric toroidal velocity or magnetic fields, such as Kelvin‐Helmholtz, magnetorotational, Tayler or global magnetoshear instabilities. In the light of several recent numerical results, we finally suggest that, similarly to a standard linear instability, subcritical MHD dynamo processes in high‐Reynolds number shear flows could act as a large‐scale driving mechanism of turbulent flows that would in turn generate an independent small‐scale dynamo. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Arbitrary control of multiple-qubit systems in the symmetric Dicke subspace

We discuss a general physical mechanism for arbitrary control of the quantum states of multiple qubits in the symmetric Dicke subspace. The qubit-qubit coupling leads to unequal energy spacing in the symmetric Dicke subspace. This allows one to manipulate a prechosen transition with an external driving source, with other transitions remaining off-resonant. Any entangled state in the symmetric Dicke subspace can be created from the initial ground state by tuning the driving source. We illustrate the idea in cavity QED, but it should be applicable to other related systems.

Magnetic configurations produced by hydromagnetic dynamos

The dynamo mechanism is a generic physical mechanism which excites large-scale magnetic fields in stars (including the Sun), planets and galaxies. The dynamo action is based on two generators, i.e. differential rotation and the so-called α effect associated with mirror asymmetry of rotating convection or turbulence. We discuss why dynamo excitation gives dynamo waves of dipole symmetry in spherical shells and steady quadrupole configurations in galactic discs. The key factor determining the magnetic configuration is the direction, which gives the maximal shear of differential rotation. Dynamos with the shear directed along the shell grow steadily while dynamos based on the shear directed across the shell result in dynamo wave configurations.

Pattern Formation in Draining Thin Film Suspensions

We demonstrate the emergence of complexity from remarkably simple and ubiquitous systems: draining thin-film suspensions exhibiting a striking transition between two classes of self-organizing patterns. Vertical channels form when attractive forces lead to transient gelation, while horizontal bands result from granular mixtures. We propose an explanation whereby the generic physical mechanisms require only the existence of viscous and excluded-volume couplings among the particles, solvent, and substrate. System-specific, small inhomogeneities trigger large-scale pattern formation, through collective dynamics, where jamming plays a crucial role. Our results shed light on emergent complexity in bio- and geophysical processes and have implications for coatings and food industries.

Exploring the Complex Folding Kinetics of RNA Hairpins: II. Effect of Sequence, Length, and Misfolded States

The complexity of RNA hairpin folding arises from the interplay between the loop formation, the disruption of the slow-breaking misfolded states, and the formation of the slow-forming native base stacks. We investigate the general physical mechanism for the dependence of the RNA hairpin folding kinetics on the sequence and the length of the hairpin loop and the helix stem. For example, 1), the folding would slow down when a stable GC basepair moves to the middle of the stem; 2), hairpin with GC basepair near the loop would fold/unfold faster than the one with GC near the tail of the stem; 3), within a certain range of the stem length, a longer stem can cause faster folding; and 4), certain misfolded states can assist folding through the formation of scaffold structures to lower the entropic barrier for the folding. All our findings are directly applicable and quantitatively testable in experiments. In addition, our results can be useful for molecular design to achieve desirable fast/slow-folding hairpins, hairpins with/without specific misfolded intermediates, and hairpins that fold along designed pathways.

On the Structure of Line‐driven Winds Near Black Holes

A general physical mechanism of the formation of line-driven winds at the vicinity of strong gravitational field sources is investigated in the frame of General Relativity. We argue that gravitational redshifting should be taken into account to model such outflows. The generalization of the Sobolev approximation in the frame of General Relativity is presented. We consider all processes in the metric of a nonrotating (Schwarzschild) black hole. The radiation force that is due to absorbtion of the radiation flux in lines is derived. It is demonstrated that if gravitational redshifting is taken into account, the radiation force becomes a function of the local velocity gradient (as in the standard line-driven wind theory) and the gradient of $g_{00}$. We derive a general relativistic equation of motion describing such flow. A solution of the equation of motion is obtained and confronted with that obtained from the Castor, Abbott & Klein (CAK) theory. It is shown that the proposed mechanism could have an important contribution to the formation of line-driven outflows from compact objects.

False-bottom acoustic echo in mid water? A note on how to evaluate and prevent the interference

The 2000 hydroacoustic survey of Lake Matano, Sulawesi is used to illustrate the mechanism of formation of an artificial, but acoustically-observed density layer in the midst of the water column. Such a spurious signal resembling the true acoustic target can be formed under certain combinations of the lake morphology and the echosounder settings by way of recording the residual echo from the previous ping during the subsequent ping-recording interval. The. generic physical mechanism of the phenomenon is described and the necessary conditions for its formation stated. The echosounder settings sufficient to prevent the interference during the field surveys are suggested, and their application illustrated with an example. The phenomenon described is explained by the physics of sound propagation and hence, the algorithms here developed apply to other water bodies and hydroacoustic equipment.

Line-driven winds in the presence of strong gravitational fields

We propose a general physical mechanism which could contribute to the formation of fast line-driven outflows at the vicinity of strong gravitational field sources. We argue that the gradient of the gravitational potential plays the same role as the velocity gradient plays in the Sobolev approximation. Both the Doppler effect and gravitational redshifting are taken into account in the Sobolev approximation. The radiation force becomes a function of the local velocity gradient and the gradient of the gravitational potential. The derived equation of motion has a critical point that is different from that of Castor, Abbott and Klein (CAK). A solution, which is continuous through the singular point, is obtained numerically. A comparison with CAK theory is presented. It is shown that the developed theory predicts terminal velocities which are greater than those obtained from the CAK theory.

Nonlinear localized waves in a periodic medium.

We analyze the existence and stability of nonlinear localized waves in a periodic medium described by the Kronig-Penney model with a nonlinear defect. We demonstrate the existence of a novel type of stable nonlinear band-gap localized state, and also reveal a generic physical mechanism of the oscillatory wave instabilities associated with the band-gap resonances.

NON‐RESPONSE MODELS FOR THE ANALYSIS OF NON‐MONOTONE IGNORABLE MISSING DATA

We discuss a new class of ignorable non-monotone missing data models – the randomized monotone missingness (RMM) models. We argue that the RMM models represent the most general plausible physical mechanism for generating non-monotone ignorable data. We show that there exists ignorable missing data processes that are not RMM. We argue that it may therefore be inappropriate to analyse non-monotone missing data under the assumption that the missingness mechanism is ignorable, if a statistical test has rejected the hypothesis that the missing data process is RMM representable. We use RMM models to analyse data from a case-control study of the effects of radiation on breast cancer. © 1997 by John Wiley & Sons, Ltd.

Non-response models for the analysis of non-monotone ignorable missing data.

We discuss a new class of ignorable non-monotone missing data models-the randomized monotone missingness (RMM) models. We argue that the RMM models represent the most general plausible physical mechanism for generating non-monotone ignorable data. We show that there exists ignorable missing data processes that are not RMM. We argue that it may therefore be inappropriate to analyse non-monotone missing data under the assumption that the missingness mechanism is ignorable, if a statistical test has rejected the hypothesis that the missing data process is RMM representable. We use RMM models to analyse data from a case-control study of the effects of radiation on breast cancer.

Sunspot numbers as a possible indicator of annual rainfall at Addis Ababa, Ethiopia

AbstractThe variability of the Sun's luminosity is thought to have effects on the world climate. This variability is partly measured by the sunspot numbers. In this paper the statistical link between sunspot numbers and Addis Ababa rainfall is established. For this purpose a transfer function plus noise model (TFN) is constructed, with Box‐Cox transformed annual sunspot numbers, Xv as input and annual Addis Ababa monsoon rainfall, Yv as output. This model explains 50·2 per cent of the annual rainfall variability in the period 1900–1990. The time series of the sunspot numbers is simulated by an autoregressive model and then used to provide the input forecasts to the TFN model; it explains 88·9 per cent of the annual sunspot numbers variability.The TFN model is utilized for long‐range annual rainfall forecasts. A check of the forecasting skill of the TFN model is performed by fitting the TFN model to the 1900–1970 data and forecasts are made for 1971–1991. The results show that 14 out of 21 forecasts generally track the observed rainfall. The correlation coefficient C between the forecast and observed rainfall is 0·58, whereas for the sunspot numbers C yields 0·87. The paired t‐test shows that the forecasts and the observed rainfall are statistically similar at the 95 per cent confidence level.A general physical mechanism that may partly explain how the variability of the Sun's luminosity is related to the world climate is suggested. It is proposed that for those regions whose climatic variables exhibit the 11‐year periodicity, the TFN model approach can be used to find a statistical link between the sunspot numbers and the climatic variables. Furthermore if a global pattern in such a link is found, it may be used for exploring the physical mechanisms of Sun‐climate relationships.

Generic physical mechanisms of tissue morphogenesis: A common basis for development and evolution

AbstractMorphological evolution is usually considered to occur by the selection of small heritable variations in the expression of anatomical traits, on the basis of improved adaptation to new environmental conditions. An alternative mode of morphological evolution is proposed here: the production of a spectrum of forms by the action of intrinsic physical properties of cell aggregates, followed by intense selection for biochemical mechanisms that make the generation of a subset of viable morphologies, and pathways of transition between morphologies, more reliable. This view provides an account of the origins of important features of metazoan body plans and organ forms, including gastrulation and other types of tissue multilayering, lumen formation, and segmentation. It also implies that most major morphological innovations would occur early in phylogeny, often more than once, with much subsequent genetic selection being of a stabilizing or canalizing variety. Consistent with recent findings, this view predicts that functional redundancy among developmentally important genes and genetic circuits should be prevalent.

Generic physical mechanisms of morphogenesis and pattern formation as determinants in the evolution of multicellular organization

Early embryos of metazoan species are subject to the same set of physical forces and interactions as any small parcels of semi-solid material, living or nonliving. It is proposed that such “generic” properties of embryonic tissues have played a major role in the evolution of biological form and pattern by providing an array of morphological templates, during the early stages of metazoan phylogeny, upon which natural selection could act. The generic physical mechanisms considered include sedimentation, diffusion, and reaction-diffusion coupling, all of which can give rise to chemical nonuniformities (including periodic patterns) in eggs and small multicellular aggregates, and differential adhesion, which can lead to the formation of boundaries of non-mixing between adjacent cell populations. Generic mechanisms that produce chemical patterns, acting in concern with the capacity of cells to modulate their adhesivity (presumed to be a primitive, defining property of metazoa), could lead to multilayered gastrulae of various types, segmental organization, and many of the other distinguishing characteristics of extant and extinct metazoan body plans. Similar generic mechanisms, acting on small tissue primordia during and subsequent to the establishment of the major body plans, could have given rise to the forms of organs, such as the vertebrate limbs. Generic physical processes acting on a single system of cells and cell products can often produce a widely divergent set of morphological phenotypes, and these are proposed to be the raw material of the evolution of form. The establishment of any ecologically successful form by these mechanisms will be followed, under this hypothesis, by a period of genetic evolution, in which the recruitment of gene products to produce the “generically templated” morphologies by redundant pathways would be favoured by intense selection, leading to extensive genetic change with little impact on the fossil record. In this view, the stabilizing and reinforcing functions of natural selection are more important than its ability to effect incremental change in morphology. Aspects of evolution which are problematic from the standard neo-Darwinian viewpoint, or not considered within that framework, but which follow in a straightforward fashion from the view presented here, include the beginnings of an understanding of why organisms have the structure and appearance they’ do, why homoplasy (the recurrent evolution of certain forms) is so prevalent, why evolution has the tempo and mode it does (“punctuated equilibrium”), and why a “rapid” burst of morphological evolution occurred so soon after the origin of the metazoa.

‘Generic’ physical mechanisms of morphogenesis and pattern formation

The role of 'generic' physical mechanisms in morphogenesis and pattern formation of tissues is considered. Generic mechanisms are defined as those physical processes that are broadly applicable to living and non-living systems, such as adhesion, surface tension and gravitational effects, viscosity, phase separation, convection and reaction-diffusion coupling. They are contrasted with 'genetic' mechanisms, a term reserved for highly evolved, machine-like, biomolecular processes. Generic mechanisms acting upon living tissues are capable of giving rise to morphogenetic rearrangements of cytoplasmic, tissue and extracellular matrix components, sometimes leading to 'microfingers', and to chemical waves or stripes. We suggest that many morphogenetic and patterning effects are the inevitable outcome of recognized physical properties of tissues, and that generic physical mechanisms that act on these properties are complementary to, and interdependent with genetic mechanisms. We also suggest that major morphological reorganizations in phylogenetic lineages may arise by the action of generic physical mechanisms on developing embryos. Subsequent evolution of genetic mechanisms could stabilize and refine developmental outcomes originally guided by generic effects.

Rarefaction Ion Acoustic Solitons in Two-Electron-Temperature Plasma

This paper shows that rarefaction ion acoustic solitons appear in a two-electron-temperature plasma. And also it presents general conditions and physical mechanism for existence of the rarefaction solitons. It is found that finite amplitude rarefaction and compression solitons coexist in a plasma within a certain parameter region.

The mechanism of cellulose biosynthesis by acetobacter acetigenum

AbstractMeasurement of the yield of cellulose in glucose‐containing cultures of Acetobacter acetigenum as a function of inoculum size and growth time has suggested a general physical mechanism of cellulose synthesis. The physical mechanism is that a certain number of chain initiators, or primers, are produced by each bacterium which then add on monomer units to form cellulose. Models for the synthesis, within the proposed physical mechanism, are described and examined in the light of DP measurements made on cellulose grown for different times. The model in which the average growing time of the chains is less than 40 min. is accepted; models invlving nonterminated chains and chains terminated at cell division are rejected. The DP measurements were made by a viscometric technique which permitted the use of never‐dried cellulose samples. Dried samples and their nitrates were found to be insoluble in their usual solvents. The viscosity average DP of the cellulose was found to be 3500; the mean average generation time of A. acetigenum was found to be 270 min.