bluuebunny/crossref_metadata_2025 huggingface dataset:
On the application of the ideal magnetohydrodynamic linear eigenvalue equation to the Z-pinch
Authors: Kanellopoulos S. , Coppins M. , Haines M. G.
Published: March 2009

A study of the ideal magnetohydrodynamic linear eigenvalue spectrum for free-boundary modes in the Z-pinch is presented. The application of a variational method to estimate eigenvalues is described and limitations imposed by the nature of the spectrum are discussed. An analytic expression for the long-wavelengthm= 0 growth rate is derived
Three-dimensional equilibria in DRAKONs with anisotropic pressure
Authors: Zhang-Hui  , Teng-Cai Ma , Ji-Feng Wang
Published: March 2009

The effect of pressure anisotropy on DRAKON equilibrium is investigated. The angle of neutral beam injection effects flux surface distortions. This can explain the increase or decrease in the equilibrium beta limit.
Wake field in electron–positron plasmas
Authors: Avinash K. , Berezhiani V. I.
Published: March 2009

We have studied the possibility of exciting a wake field in an electron–positron plasma by the injection of relativistic electron bunches. We have investigated the change in frequency of electronmagnetic radiation propagating through the resulting inhomogeneity. Our main conclusion is that it is not necessary to invoke a magnetic field in order to excite a wake field in an electron–positron plasma. As shown here, the necessary charge separation could come from the injection of energetic particle bunches. This mechanism of wake-field creation and subsequent particle/photon acceleration could operate in a pulsar magnetosphere, where particle bunches are extracted energetically from the pulsar surface. For example, pulsar radio emissions exhibit ultra-short intensity variations within individual pulses with time scales ranging from 1 μs to 1 ms (Cordes 1979). Several authors have proposed (Chian & Kennel 1983; Mofiz, De Angelis & Forlani 1985; Mikhailovskii, Onishchenko & Tatarinov 1985) that these pulsations can be explained as being due to soliton formation in the pulsar magnetosphere.

We believe that these micropulsations can also be explained by modulation of the radiation caused by the wake field. In order to have a quantitative estimation, we need to take into account the effects of thermal motion of particles as well as plasma inhomogeneity, etc. The present results should also be useful for understanding nonolinear photon motion in cosmic plasmas, such as those found in the early universe and in active galactic nuclei (Tajima & Taniuti 1990).
Expansion of a quantum electron gas
Authors: Mola S. , Manfredi G. , Feix M. R.
Published: March 2009

The expansion of a quantum electron gas (non-relativistic, no spin) is investigated via the one-particle Schrödinger–Poisson model. Classically, the nonlinear term enhances the formation of a very regular asymptotic state. By means of rescaling methods, we conjecture that the quantum asymptotic solution is identical to the classical one. Subsequent numerical simulations confirm the above conjecture and define precisely the way in which the classical limit is approached.
Thermodynamic stability of a tokamak plasma
Authors: Brusati M. , DiVita A.
Published: March 2009

A thermodynamic analysis of tokamak plasmas is developed, starting from a single-fluid model. Some general propertiesof entropy production in the plasma are discussed. An approach is employed that is more general than the one based on Onsager symmetry relationships. This choice appears to be justified by experiments. The concept of ‘thermodynamic stability’ is introduced, and a general criterion for the stability of stationary states far from thermodynamic equilibrium is assessed. An upper limit on the particle density is found to exist as a necessary condition in order to prevent disruptions. Analysis of the entropy balance shows that this limit is modified when neutral-beam heating is applied. Radial temperature profiles are shown to be stable against external heating under specific experimental conditions, inparticular when ion and electron temperatures are comparable. An offset scaling law for the energy confinement time TE = TE(Pinp) (with Pinp total input power) is obtained for stationary states when stability against additional heating is imposed.
Observation of modulational instability in a multi-component plasma with negative ions
Authors: Bailung† H. , Nakamura Y.
Published: March 2009

The nonlinear evolution of ion-acoustic waves in a multi-component plasma with negative ions has been studied experimentally using a double-plasma device. At a critical concentration of negative ions the phase velocity of the ion- acoustic waves increases with the wave amplitude, and the wave has negative dispersion, which show that the wave satisfies Lighthill's condition. The initial small modulation in amplitude is found to grow spatially. The observed phenomena are compared with the relevant theory using the nonlinear Schrödinger equation. The fluid equations are integrated to confirm the validity of the nonlinear Schrödinger equation.
The Bohm criterion in the presence of radio-frequency fields
Authors: Allen J. E. , Skorik M. A.
Published: March 2009

In d.c. discharges the Bohm condition is the condition for sheath formation, the ion velocity at the plasma boundary having to satisfy the condition ½Mv2= ½kBTe, if the spread of velocities is ignored. The model is a good one if the Debye distance is small compared with the relevant scale length. As there is much current interest in radio-frequency (RF) discharges, the question arises as to whether the criterion remains valid in the presence of RF fields. The question has been studied recently by Riemann, following earlier work by Allen who compared the plasma boundary to a sonic surface. Riemann considered a wider range of frequencies and obtained a dispersion relation that was a quartic equation. The present paper examines the complex roots of this equation, using a method developed by Briggs. The results substantiate Riemann's statement that the Bohm criterion is still valid in the presence of RF fields.
Scintillations in a magnetized plasma. Part 1. The mutual coherence function
Authors: Melrose D. B.
Published: March 2009

A standard theory of strong scintillations in an isotropic medium is extended to the case of polarized radiation propagating through a weakly anisotropic, randomly inhomogeneous, magnetized plasma. A hierarchy of moments of the radiationfield is defined, with an nth-order moment being an nth-rank polarization tensor, and the tensor equation for the evolution of an arbitrary moment is derived. Emphasis isplaced on the mutual coherence function (a second moment), which is rewritten in terms of the Stokes parameters. The evolution of the polarized radiation through the randomly inhomogeneous, weakly anisotropic medium is described in terms ofa matrix equation for the Stokes vector. It is shown that the theory implies that a depolarization occurs as a result ofsuch propagation. This corresponds to a decrease in the degree of linear polarization for propagation through a weakly anisotropic plasma. The rate of depolarization is estimated, and an interpretation is suggested. The polarization dependence of the angular size of the apparent image is determined. Two counter-intuitive results are found: that the image canhave a circularly polarized component even for an unpolarized source, and that the angular size of the linearly polarized source can decrease. These are interpreted in terms of random variations in the ray path with opposite signs for the two natural modes, resulting in a separation of the centroids of the images in the two circular polarizations.
Perturbation region near a biased body in a flowing collision-dominated plasma with low ionization density. Current–voltage chracteristics of a langmuir probe
Authors: Benilov M. S.
Published: March 2009

The asymptotic theory of flows of high-pressure plasmas past biased bodies (electrostatic probes) is extended to relatively low charge densities, where the Debye radius h is comparable to or exceeds the thickness ▴ of the viscous near- probe boundary layer. Various orders of magnitude of h with respect to a dimension of the probe and various ranges of the probe potential are considered. The governing physical mechanism of current transfer in the perturbation region is identified in each regime, and simple formulae for the probe current–voltage characteristic are obtained whenever possible. In particular, it is shown that an earlier conclusion, valid for h ≪ Δ, on the existence of a linear segment on the electron branch of current-voltage characteristic with a slope depending on the electron density, is also valid in the present situation. It h ≫ Δ, a similar conclusion holds for the ion branch; at large enough probe potentials the jon branch saturates —although for a different physical reason than in the case h ≪ Δ
Envoi
Authors: Dougherty J. P.
Published: March 2009

I shall shortly be stepping down from the position of Editor of Journal of Plasnia Physics, although continuing for a while more as an Associate Editor.
Self-similar cylindrical expansion of impurity particles in a plasma
Authors: Yu Ming Y. , Bharuthram R.
Published: March 2009

The radial self-similar expansion of negatively charged impurity or dust particles in a cylindrical geometry is investigated using the multi-fluid theory. Three different types of self-similar solutions are considered. Various asymptotic limits of physical interest in the self-similar space are shown to occur.
Self-focusing of surface waves in a cylindrical plasma waveguide
Authors: Georgieva M. , Shivarova A. , Urdev† I.
Published: March 2009

Self-consistent nonlinear changes of plasma parameters and characteristics of electromagnetic guided waves are studied with regard to the effect of self- focusing and waveguided channel formation in a cylindrical plasma waveguide. Besides the nonlinearity due to the ponderomotive force action usually involved, ionization nonlinearity specified for different regimes of particle loss mechanisms is considered. An azimuthally symmetric electromagnetic surface wave is the guided mode that forms and sustains the wave channel.The nonlinear dispersion law and the nonlinear changes in the wave field distribution and power flow are obtained, describing the effect of the self-focusing of the waves under conditions of weak nonlinearity.
Network thermodynamics: dynamic modelling of biophysical systems
Authors: Oster George F. , Perelson Alan S. , Katchalsky Aharon
Published: March 2009

The success of equilibrium thermodynamics in describing static phenomena has inspired many attempts to develop a rigorous thermodynamics of rate processes.
Biological and model membranes studied by nuclear magnetic resonance of spin one half nuclei
Authors: Wennerström Håkan , Lindblom Göran
Published: March 2009

There is an inherent anisotropy in biological and model membrane systems and this anisotropy has a profound influence on the nuclear magnetic resonance spectra of such systems. For nuclei with a quadrupole moment the quadrupole coupling usually dominates the NMR spectrum, while for nuclei with spin quantum numberI= ½ dipolar couplings provides the most important effects. The quadrupole coupling only affects isolated spins and usually gives rise to simple spectra. The dipole interactions on the other hand couple several spins. In a lipid bilayer with a multitude of spin-½ nuclei these couplings can give rise to complicated manybody effects. Thus the interpretation of the NMR spectra of membrane systems poses problems but at the same time there is a lot of information to be gained.
A short history of the foundation of the International Union for Pure and Applied Biophysics
Authors: Solomon A. K.
Published: March 2009

The following history of the formation of the International Union for Pure and Applied Biophysics (IUPAB) has been assembled from several published accounts in Nature and Science, to which has been added material from the minutes of the meetings of some of the bodies concerned. The introductory paragraphs have been taken from articles by Sutherland (1963) and by Bolt & Sutherland (1960).
Preparative particle separation in density gradients
Authors: Anderson Norman G.
Published: March 2009

The purpose of this review is to summarize the present status of preparative zonal centrifugation and to indicate where the remaining problems, in the reviewer's opinion, may lie. The field is sufficiently new for interest in practical separartions to be uppermost. However, a number of theoretical problems relating to gradient capacity, zonal rotor configuration and particle—particle interactions remain to be fully explored.
My image of the retina
Authors: Bouman Maarten A.
Published: March 2009

The initial act for visual perception is the absorption of light in the photo-pigment of the receptor end-organs. Since both light and the nervous message have a quantal structure, any theory of visual information processing should in principle be a digital processing theory. And not only in principle, since we know for certain that in many situations the number of quanta is rather restricted, so that an over-all thermodynamic theory cannot but fail to adequately describe visual facts.
High-Voltage Electron Microscopy
Authors: Cosslett V. E.
Published: March 2009

The main advantage of high voltage in electron microscopy is greater penetration. When using an aperture of optimum size the thickness of specimen that can be imaged increases almost linearly with applied voltage in the case of light elements, both when the criterion is image intensity and when it is resolution. For heavy elements the increase is less rapid. With a small aperture the increase in observable thickness is still less rapid, and ‘saturates’ towards I MV. For a specimen of given thickness, image definition increases nearly linearly with voltage owing to the decrease in chromatic aberration. Although ultimate resolving power improves with voltage, the gain is slight and is offset by a fall in contrast. The optimum voltage for very high resolution is probably between 200 and 300 kV. Radiation damage arising from ionization decreases with rising voltage, making easier the examination of sensitive materials such as polymers. On the other hand, ejection of atoms by head-on collision increases rapidly above a threshold voltage, causing observable defects in metals.

In construction, a high-voltage microscope differs from the normal type only in size and in having an accelerator instead of a simple electron gun. In operation it differs little, apart from precautions to avoid fiashover in the accelerator. A decrease in response of viewing screens and photographic emulsions is more than compensated by higher brightness of the electron gun. The chief applications so far of the high-voltage microscope have been for studying thick films of metals, magnetic materials, ceramics and polymers. Improved preparation techniques should make it possible to study sections of biological tissues up to 5 μ thick. The observation of micro-organisms and other specimens in the wet state can be carried out in double-walled cells, but only at poor resolution. Still higher voltages, up to 3 or MV coupled with the use of an energy analyser or an image intensifier, should improve further the microscopy of such thick specimens.
From frog skin to sheep rumen: a survey of transport of salts and water across multicellular structures
Authors: Keynes R. D.
Published: March 2009

All higher animals, whether they live in water or on dry land, are faced with the necessity of regulating rather closely their intake and excretion of salts and water in order to maintain the constancy of their internal ionic environment. The kidney is in general the most important organ of the body as far as the excretion of sodium, potassium, chloride and water is concerned, but there are other tissues which also play a part in controlling the ionic balance between the internal and external environments, such as the intestinal mucosa, the skin and urinary bladder in amphibia, the gill epithelium in fishes, the salt gland in marine birds, and the epithelium of the rumen in ruminants. In addition to excretory and absorptive organs of this type, there are others which are secretory and whose function involves the production of fluids differing in ionic composition from the blood plasma. Examples include the glands which secrete saliva and sweat, the oxyntic acid-producing cells of the gastric mucosa, and the epithelium of the stria vascularis which generates the potassium-rich endolymph of the mammalian cochlea. The purpose of this article is to consider briefly what is known about the active transport of salts and water across some typical multicellular secretory tissues, and to attempt in the process to discern what properties they have in common and in what respects they are specialized.
Molecular interactions and structure as analysed by fluorescence relaxation spectroscopy
Authors: Rigler Rudolf , Ehrenberg Måns
Published: March 2009

Spectroscopic probes have become powerful tools in analysing the correlation between structure and function of biological macromolecules. Though these spectral methods cannot give as circumstantial information about the anatomy of a biological structure as, for example, X-ray diffraction they can provide information on physical properties at defined loci in a macromolecule which are not accessible by other techniques. Most important, spectroscopic studies have provided means to study the dynamics of structural changes and interactions in time domains spanning from nanoseconds and less up to infinite time.
Insulin secretion: mechanism of the stimulation by glucose
Authors: Cerasi Erol
Published: March 2009

Glucose is one of the substrates that is controlled with the most efficient hormonal mechanisms in higher organisms. The presence of tissues such as the central nervous system which, under normal conditions, depend solely on glucose as substrate, and the sporadic type of food intake with periods of fasting of various lengths in the mammalians necessitate that the distribution of energy-rich substrates among various tissues be continuously adjusted by changes in the secretion of a number of hormones. The efficiency of this system is evidenced by the stability of the blood glucose level in man, in whom after a carbohydrate-rich meal more than 70% of the glucose that has been ingested will be retained in the liver during a single passage of portal blood, resulting in only small changes of the glucose concentration in peripheral blood. Likewise, periods of fasting up to24–36 h are followed by modest to minimal reductions of the blood glucose level, the liver now supplying the circulation with the hexose.
Ionic pores, gates, and gating currents
Authors: Armstrong Clay M.
Published: March 2009

The current phase of axon physiology began with the invention of the voltage clamp by Cole (1949) and its use by Hodgkin & Huxley (1952d) to produce an astonishingly complete analysis of the ionic permeabilities that are responsible for the action potential. Their description did notcontain much in the way of molecular detail, and left open such questions as whether ions cross the membrane by way of pores or carriers, and the nature of the ‘gating‘ processes that increase ordecrease ion permeability in response to changes of the membrane potential. In the last few years our picture of the ionicchannels has grown considerably more tangible, though it still falls far short of a detailed molecular description. This article describes this sharpened picture and reviews the evidence for it. The viewpoint expressed is a very personal one, andno attempt has been made to review the literature of axonology comprehensively.
The possibilities and prospects of obtaining high-resolution information (below 30 Å) on biological material using the electron microscope
Authors: Beer M. , Frank J. , Hanszen K.-J. , Kellenberger E. , Williams R. C.
Published: March 2009

Commercially available electron microscopes routinely provide resolution of some 2–4 Å, as determined on the spacing of crystalline lattices of certain stable, small-molecular substances. On biological material either macromolecules or macromolecular assemblies— ‘biologically significant’ details below some 20 Å have hitherto not been observed.we consider as ‘biologically significant’ those structural details observed or contained in electronmicrographs which are consistent with, or confirmed by, other data obtained from biochemical or functional experiments or by other physical methods (optical, magnetic, electric).
Spectroscopic studies on two-iron ferredoxins
Authors: Sands R. H. , Dunham W. R.
Published: March 2009

The application of magnetic resonance techniques to biological systems has permitted a detailed study of the nature of the active sites of many proteins that had not been possible previously. Among these is the whole class of iron—sulphur proteins which have been implicated as electron transport proteins in a variety of fundamental processes: photosynthesis, hydroxylation and nitrogen fixation to name but a few.

The single-iron proteins in this class, the rubredoxins, have been studied extensively by chemical, spectroscopic and X-ray crystallographic techniques (Lovenberg, 1973), and the active site is composed of a single iron atom bound in a distorted tetrahedron of cysteine sulphur ligands. The iron is high-spin ferric in the oxidized state and high-spin ferrous in the reduced state. This structure is shown in Fig. I (α).
Zone-plate X-ray microscopy
Authors: Schmahl G. , Rudolph D. , Niemann B. , Christ O.
Published: March 2009

The scope of this article is to describe a transmission X-ray microscope, possible biological applications of soft X-ray microscopy and preliminary results.

For soft X-ray microscopy of biological specimens the wavelength range of 1–10 nm is best suited. Microscopy in this wavelength range requires intense X-ray sources as well as high-resolution X-ray lenses. Intense X-radiation is provided by the synchrotron radiation of electron and positron storage rings. Suited X-ray lenses are zone plates.

A theoretical treatment of the contrast mechanism and the radiation damage as well as first experiments yield the following results. Firstly, relatively thick (1–10 μm) biological specimens can be investigated. This means that unsectioned dried and even wet cells and cell organelles in a natural state can be examined. Second, it will be possible to resolve cellular aggregates in live cells with a resolution in the region of ≤10nm.
Relation between structure and function of α/β–protejns
Authors: Brändén Carl-Ivar
Published: March 2009

Protein chains are usually folded into one or several discrete globular units called domains (Schulz & Schirmer, 1979). Levitt & Chothia (1976) have shown that the structures of such domains frequently fall into one of the following three classes; α-proteins which are mainly α-helical, β-proteins which contain antiparallel β-strands and α/β proteins which have a central core consisting of a sheet of strands, most of which are parallel. The connexions between the parallel strands in αβ-proteins frequently contain helices which are packed on both sides of the sheet in a regular way (Chothia, Levitt & Richardson, 1977).
The transfer function of the cochlea
Authors: Barrett T. W.
Published: March 2009

A sinusoidal signal is generally considered the simplest auditory signal. It is, indeed, a simple signal. However, it does not follow that a complex analysing device, like the cochlea, should treat a simple signal in a simple way. Indeed, a simple signal may appear to be complex when viewed from the standpoint of the device considered. Such an observation becomes cogent when one is attempting to discover the analysing capabilities of a device such as the cochlea, which appears designed to handle signals more complex than a sinusoid or multiple sinusoids.
Channel noise in nerve membranes and lipid bilayers
Authors: Conti F , Wanke E.
Published: March 2009

The basic principles underlying fluctuation phenomena in thermodynamics have long been understood (for reviews see Kubo, 1957; Kubo, Matsuo & Kazuhiro 1973 Lax, 1960). Classical examples of how fluctuation analysis can provide an insight into the corpuscular nature of matter are the determination of Avogadro's number according to Einstein's theory of Brownian motion (see, e.g. Uhlenbeck & Ornstein, 1930; Kac, 1947) and the evaluation of the electronic charge from the shot noise in vacuum tubes (see Van der Ziel, 1970).
The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
Authors: Manning Gerald S.
Published: March 2009

Although the importance of the polyelectrolyte character of DNA has been recognized for some time (Felsenfeld & Miles 1967), few of the implications have been explored, primarily because of a lag in translating the breakthroughs in polyelectrolyte theory of the last decade into a form that is well adapted to the analysis of the specialized problems of biophysical chemistry. Perhaps an analogous situation existed in the field of protein chemistry during the period after the formulation and confirmation of the Debye—Hückel theory of ionic solutions but before Scatchard's incorporation of the theory into his analysis of the binding properties of proteins. An achievement for polynucleotide solutions parallel to Scatchard's was recently presented by Record, Lohman, & de Haseth (1976) and further developed and reviewed by Record, Anderson & Lohman (1978).
Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications
Authors: de la Torre José García , Bloomfield Victor A.
Published: March 2009

Among the Various methods for characterizing macromolecules in solution, hydrodynamic techniques play a major role. Since the advent of the ultracentrifuge and the development of viscometric apparatus, sedimentation coefficients and intrinsic viscosities have been extensively used to learn about the size and shape of synthetic and biological polymers. More recently, refined techniques such as quasielastic light scattering, transient electric birefringence and fluorescence anisotropy decay have made it possible to obtain in a simple and rapid way quantitative information of high precision on the translational and rotational brownian dynamics of dissolved macromolecules.
Spin-labelled nucleic acids
Authors: Kamzolova S. G. , Postnikova G. B.
Published: March 2009

The spin label method developed by McConnell 15 years ago is now widely used in studies of the structure and dynamic properties of a variety of the biological systems such as proteins and protein complexes, lipids and membranes, nucleic acids, nucleoproteins, etc.

The ESR spectrum of the nitroxide radcal – the spin label – is very sensitive to its microenvironment and permits easy registration of even subtle alterations in it. If spin labels are attached to different sites of a macromolecule the information can be gained about conformational properties of all these local regions and, as a result, about the dynamic behaviour of the object as a whole.
Mechanisms of tolerance to DNA lesions in mammalian cells
Authors: Meneghini Rogerio , Menck Carlos F. M. , Schumacher R. Ivan
Published: March 2009

In recent years it has become clear that different pathways are involved in the process of removing lesions from DNA. In spite of a continuous surveillance of the genetic integrity by repair enzymes, quite often lesions are not eliminated before the portion of the genome where they have been inserted is used for DNA replication or transcription. Actually, the number of unexcised lesions a cell can tolerate without significantly losing its capacity to reproduce is surprising. As an example, human fibroblasts from certain patients with the genetic disease xeroderma pigmentosum (XP)† are virtually unable to excise pyrimidine dimers, the major DNA lesion produced by short-wavelength UV light.
Photoreversibly photochromic pigments in organisms: properties and role in biological light perception
Authors: Björn L. O.
Published: March 2009

The two best-known photophysiological processes are photosynthesis and vision. In photosynthesis light energy is absorbed and transformed into ‘life energy’, in vision the information content of light is utilized by organsims. In photosynthesis chlorophyll and other pigments involved in light-gathering are not chemically changed (except that some of the chlorophyll or phaeophytin molecules are oxidized and immediately reduced again). In human vision the rhodopsin and other visual pigments undergo a reaction cycle induced by photon absorption. The pigment is brought back to its original state only after a long chain of chemical reactions.
Osmosis
Authors: Hill Adrian
Published: March 2009

It has virtually become a truism that osmosis, and the inseparable array of related processes comprising ultrafiltration, diffusion, anomalous osmosis, etc., has found its final and lasting exposition to which anything can only be added by way of a few finishing touches. This view, as I shall attempt to show, is quite wrong, if for no other reason than that several of the different approaches to the problem are not complementary. We want two things: to gain an insight into the mechanisms operative in porous systems, and to derive equations which predict the flow rates from a minimal set of properties – if we can decide what these are.
Biophysics of flagellar motility
Authors: Blum Jacob J. , Hines Michael
Published: March 2009

One feature characterizing the transition from prokaryote to eukaryote is the ‘sudden’ appearance of centrioles and their highly structured products, the typical eukaryotic flagella and cilia. These mechanochemical systems appear as fully developed machines, containing some 200 diffierent proteins (Lucket al.1978) arranged in a remarkably complex organization which has undergone little modification since the advent of the first eukaryotic cells. It is now well established (see, for example, Satir, 1974) that ciliary and flagellar motility is based on a sliding filament mechanism that superficially resembles the far more extensively studied sliding filament system of striated skeletal muscle.The flagellar system, however, appears to be much more complex than the muscle system, because it does not ‘merely’ shorten and generate force, but develops propagating waves and exerts its effects via hydrodynamic interactions with a viscous medium.
An analysis of packing in the protein folding problem
Authors: Richards Frederic M. , Lim Wendell A.
Published: March 2009

The number of globular proteins for which high resolution structures are available is rapidly increasing. In each case the particular sequence of the polypeptide appears to yield only a single, compact, biologically active structure. However, peptides with no obvious sequence similarity may form remarkably similar structures.
The kinetics of voltage-gated ion channels
Authors: Keynes R. D.
Published: March 2009

When Hodgkin & Huxley (1952) first embarked on the analysis of their voltageclamp data on the ionic currents in the squid giant axon, they hoped to be able to deduce a mechanism from it, but it soon became clear that the electrical data would by themselves yield only very general information about the class of system likely to be involved.
Silicon pixel detectors for X-ray diffraction studies at synchrotron sources
Authors: Hall G.
Published: March 2009

Customized silicon diode detectors are widely used for elementary particle detection for their good spatial resolution. Silicon detectors are also excellent X-ray detectors in the energy range of interest for applications in synchrotron radiation experiments and, with small elements laid out in a two-dimensional array, may provide high performance imaging devices for future diffraction experiments.
Soft X-ray microscopes and their biological applications
Authors: Kirz Janos , Jacobsen Chris , Howells Malcolm
Published: March 2009

In this review we propose to address the question: for the life-science researcher, what does X-ray microscopy have to offer that is not otherwise easily available?

We will see that the answer depends on a combination of resolution, penetrating power, analytical sensitivity, compatibility with wet specimens, and the ease of image interpretation.
Physical aspects of tissue evagination and biological form
Authors: Gierer Alfred
Published: March 2009

The form of multicellular animals and their organs is mainly defined by the curvature of cell layers. They are boundaries for solid tissues; and some organs and organisms consist mainly of distinct cell layers (Fig. Ia). The form of adult organisms results from a complex interplay of tissue evagination, growth patterns, production of and interaction with extra-cellular material, and other effects; but the rudiments and basic features of the forms produced can often be traced back to processes of evagination or invagination of nearly flat cell sheets at defined locations in the course of embryogenesis.
Protein and protein-bound water dynamics studied by Rayleigh scattering of Mössbauer radiation (RSMR)
Authors: Goldanskii Vitalii I. , Krupyanskii Yurii F.
Published: March 2009

In all contemporary models of enzyme catalysis, the functional activity of enzymes is directly associated with the dynamic properties of proteins (see Blumenfeld, 1977; Chernavaskaya & Chernavskii, 1977; Volkenstein, 1975; Austinet al.1975; Shaitan & Rubin, 1985; Ansariet al.1985). This has recently led to a much greater interest in the dynamical properties of proteins.
Analysis of the mechanism of DNA recombination using tangles
Authors: Sumners De Witt , Ernst Claus , Spengler Sylvia J. , Cozzarelli Nicholas R.
Published: March 2009

The DNA of all organisms has a complex and essential topology. The three topological properties of naturally occurring DNA are supercoiling, catenation, and knotting. Although these properties are denned rigorously only for closed circular DNA, even linear DNAin vivocan have topological properties because it is divided into topologically separate subdomains (Drlica 1987; Roberge & Gasser, 1992). The essentiality of topological properties is demonstrated by the lethal consequence of interfering with topoisomerases, the enzymes that regulate the level of DNA supercoiling and that unlink DNA during its replication (reviewed in Wang, 1991; Bjornsti, 1991; Drlica, 1992; Ullspergeret al. 1995).
Physical properties of the fluid lipid-bilayer component of cell membranes: a perspective
Authors: Bloom Myer , Evans Evan , Mouritsen Ole G.
Published: March 2009

The motivation for this review arises from the conviction that, as a result of the mass of experimental data and observations collected in recent years, the study of the physical properties of membranes is now entering a new stage of development. More and more, experiments are being designed to answer specific, detailed questions about membranes which will lead to a quantitative understanding of the way in which the physical properties of membranes are related to and influence their biological function.
Antitumour drug–DNA interactions: NMR studies of echinomycin and chromomycin complexes
Authors: Gao Xiaolian , Patel Dinshaw J.
Published: March 2009

The intelligent design of new families of DNA-binding antitumour agents must await an understanding at the molecular level of the structure, dynamics and energetics of drug-DNA interactions on currently available systems. Recent progress in this area has been significant and reflects the interplay between footprinting methods that identify the sequence specificity of drug binding, structural approaches that define conformational features in the crystalline and solution states, hydrogen exchange techniques that monitor transient base pair opening and calorimetric methods that partition the enthalpic and entropic contributions to the binding isotherm.
Mechanisms of cooperativity and allosteric regulation in proteins
Authors: Perutz M. F.
Published: March 2009

AUosteric proteins control and coordinate chemical events in the living cell. When Monod conceived that idea he said that he had discovered the second secret of life. The first was the structure of DNA. The theory as published by Monodet al.(1963) was concerned chiefly with cooperativity and feedback inhibition of enzymes, such as the inhibition of threonine deaminase, the first enzyme in the pathway of the synthesis of isoleucine, by isoleucine, and its activation by valine. Two years later the theory was formalized by Monodet al.(1965).
Nuclear magnetic resonance – from molecules to man
Authors: Wüthrich Kurt
Published: March 2009

Initial observations of the physical phenomenon of nuclear magnetic resonance (NMR) date back to the late 1940s. In the following two decades high-resolution NMR in solution became an indispensible analytical tool in chemistry, and solid state NMR had an increasingly important role in physics. Some of the potentialities of the method for investigations of complex biological systems had also long been anticipated, and initial experiments with biological specimens were described already 30 years ago. In practice, however, biological applications of NMR have become really attractive only during the last decade, following revolutionary advances in NMR instrumentation and the methodology for their use. NMR projects in biology and medicine now include studies of biomacromolecular structure and function, work on biological membranes, in vivo studies of biochemical processes, and imaging of macroscopic objects. Because of imminent practical applications in medical diagnosis and thanks to extensive coverage by the popular news media, interest in some of the recent developments spreads far beyond the scientific community, making NMR a widely popular field.
Protein structure by solid-state NMR spectroscopy
Authors: Opella S. J. , Stewart P. L. , Valentine K. G.
Published: March 2009

The three-dimensional structures of proteins are among the most valuable contributions of biophysics to the understanding of biological systems (Dickerson & Geis, 1969; Creighton, 1983). Protein structures are utilized in the description and interpretation of a wide variety of biological phenomena, including genetic regulation, enzyme mechanisms, antibody recognition, cellular energetics, and macroscopic mechanical and structural properties of molecular assemblies. Virtually all of the information currently available about the structures of proteins at atomic resolution has been obtained from diffraction studies of single crystals of proteins (Wyckoffet al, 1985). However, recently developed NMR methods are capable of determining the structures of proteins and are now being applied to a variety of systems, including proteins in solution and other non-crystalline environments that are not amenable for X-ray diffraction studies. Solid-state NMR methods are useful for proteins that undergo limited overall reorientation by virtue of their being in the crystalline solid state or integral parts of supramolecular structures that do not reorient rapidly in solution. For reviews of applications of solid-state NMR spectroscopy to biological systems see Torchia and VanderHart (1979), Griffin (1981), Oldfieldet al. (1982), Opella (1982), Torchia (1982), Gauesh (1984), Torchia (1984) and Opella (1986). This review describes how solid-state NMR can be used to obtain structural information about proteins. Methods applicable to samples with macroscopic orientation are emphasized.
NMR studies of ion binding in biological systems
Authors: Forsén Sture , Drakenberg Torbjörn , Wennerström Håkan
Published: March 2009

Biological systems must have evolved in an interplay between a great many organic and inorganic compounds. As a result a considerable number of elements - estimates range between 25 and 30 - are essential for higher life forms such as animals and man (Underwood, 1977; Williams, 1983, 1984).
Nonlinear dynamics of biopolymers: theoretical models, experimental data
Authors: Yakushevich L. V.
Published: March 2009

Nonlinear dynamics of biopolymers is a new and rapidly developing field of biophysical science. It can be considered as a part of the general dynamics which
deals with the internal mobility of biopolymers. Theoreticians define it also as the next (anharmonic or nonlinear) approximation after the first harmonic or linear one.
Energy profiles in the gramicidin A channel
Authors: Pullman A.
Published: March 2009

Gramicidin A (GA) is a linear pentadecapeptide made of alternating D and L residues, in which the N-and C-terminals are blocked by a formyl group (head) and an ethanolamine end (tail), respectively (Sarges & Witkop, 1964):
DNA and RNA: NMR studies of conformations and dynamics in solution
Authors: Patel Dinshaw J. , Shapiro Lawrence , Hare Dennis
Published: March 2009

The early NMR research on nucleic acids was of a qualitative nature and was restricted to partial characterization of short oligonucleotides in aqueous solution. Major advances in magnet design, spectrometer electronics, pulse techniques, data analysis and computational capabilities coupled with the availability of pure and abundant supply of long oligonucleotides have extended these studies towards the determination of the 3-D structure of nucleic acids in solution.
Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals
Authors: Billeter Martin
Published: March 2009

Following the first determinations of protein structures in the late 1950s and the early 1960s (see for example Kendrewet al.1960; Perutz, 1964), the three-dimensional structures of several hundred proteins have been elucidated by X-ray diffraction on single crystals. By the end of 1991, approximately 150 entries of proteins with substantially different sequences and a well resolved structure (Hobohmet al.1992) were deposited in the Protein Data Bank (Bernsteinet al.1977; Abolaet al.1987). In addition, many structures of homologous proteins or of mutants have been described, bringing the total number of entries to about 600. While it was soon accepted that almost all of these structures do indeed give a correct picture of the fold of the active protein in spite of the non-physiological environment of single crystals, it is not clear to what extent structural details are reliably described by these structures. In particular the surface of a protein may be modified due to the dense packing of protein molecules in the crystal lattice. A detailed knowledge of the protein surface is, however, essential for the understanding of the function of the protein.
Mössbauer spectroscopy of haem proteins
Authors: Lang G.
Published: March 2009

A fair beginning has been made in understanding the Mössbauer spectra of many types of haem proteins. The diamagnetic compounds have all the usual difficulties associated with the calculation of any quadrupole spectra, with the added complication of larger molecules and much less crystallographic data. In the ferric paramagnets the large molecules are quite helpful in that they prevent interaction between neighbouring sites and make possible long electron spin-relaxation times. The resulting magnetic Mössbauer spectra contain a large amount of information and, by their complexity, tend to be a guard against ambiguity in interpretation. The theoretical problem of the magnetic hyperfine interaction appears more complex than the quadrupole interaction, but this apparent complexity is only superficial in the sense that it requires more complex mathematical manipulations. The underlying physical problem is much simpler in the magnetic case because it involves interactions only with the relatively few unpaired electrons, and is insensitive to all others and has no lattice contribution. Fortunately the unpaired electrons are those which lie high in energy, and are most likely to be involved in the chemical activity of the enzyme. Most of the results on ferric haems have been fairly satisfactory, and it seems likely that many of the uncertainties will be cleared up by further work. From the physicist's point of view it appears reasonable to expect that the search for better agreement between theory and paramagnetic spectra may be a route to a better understanding of the factors affecting the quadrupole interaction. The integral spin paramagnets are an intermediate case, usually requiring large applied field to reveal their magnetic properties. No high-spin ferrous haems have yet been subjected to detailed magnetic experimental or theoretical investigation, but this should be a fruitful field.
Neural Nets
Authors: Cowan Jack D , Sharp David H
Published: March 2009

The brain is one of the most highly organized structures in the known universe. It is a biological computer which has evolved over a billion years to program, monitor and control all bodily functions. It is also the organ of knowing, feeling and thinking. To understand how the brain works is perhaps the most difficult of all scientific problems. A scientific theory of the brain would provide a comprehensive understanding of a substantial body of facts on the basis of a few fundamental principles. In this sense, there is no theory of the brain.
The universal RNA genetic code
Authors: Caskey C. T.
Published: March 2009

The code of inheritable information which directs the synthesis of protein molecules is now known. This information is contained in the replicative molecules deoxyribonucleic or ribonucleic acid (Avery, Macleod & McCarty, 1944; Loeb & Zinder, 1961). Translation of the nucleic acid ‘information’ into protein molecules involves the initial transcription of the nucleic acid molecules into transient messenger ribonucleic molecules which are single stranded base paired complements of the more stable ‘information’ nucleic acid molecules. The events leading to the translation of the linear order of nucleic acid information in mRNA to a corresponding linear sequence of amino acids in a protein are largely elucidated at this time and will be the subject of this discussion. Since the knowledge of the genetic code is a result of data obtained fromin vitrotranslational studies which employ the equivalent of mRNA, the genetic code is described as the RNA code rather than its DNA complement. Elucidation of the RNA code has been the focus of research activity for a large number of research laboratories over the past 10–15 years. As a result of these investigations we have a detailed description of the genetic code for life on this planet. This code appears universal in its organization and translational mechanism. Since the interactions of macromolecules necessary for genetic translation are understood with greater precision than the factors responsible for the origin of the Genetic Code, this discussion will deal in more detail with the events in the translation of genetic information.
Microcalorimeters
Authors: Wadsö Ingemar
Published: March 2009

In all life sciences there can be noted a marked trend toward an increased use of physical instrumentation. Calorimeters, which are instruments for measurements of heat quantities or heat effects, offer one approach in this respect.
Linkage graphs: a study in the thermodynamics of macromolecules
Authors: Wyman Jeffries
Published: March 2009

In earlier papers (Wyman, 1975a, b, 1981) I have called attention to the existence of a group of linkage potentials derivable from one another by a corresponding group of Legendre transformations. These potentials are applicable to any system in a state of equilibrium but are especially useful in the study of the behaviour, or, as we may say, the functional chemistry, of a macromolecule in the presence of its ligands. In this paper I show how these potentials may be represented by a set of contour graphs which embody the results of observation and are transformable into one another by a group of graphical permutations equivalent to the Legendre group.