Online_DPI: a web server to calculate the diffraction precision index for a protein structure

An online computing server, Online_DPI (where DPI denotes the diffraction precision index), has been created to calculate the `Cruickshank DPI' value for a given three-dimensional protein or macromolecular structure. It also estimates the atomic coordinate error for all the atoms available in the structure. It is an easy-to-use web server that enables users to visualize the computed values dynamically on the client machine. Users can provide the Protein Data Bank (PDB) identification code or upload the three-dimensional atomic coordinates from the client machine. The computed DPI value for the structure and the atomic coordinate errors for all the atoms are included in the revised PDB file. Further, users can graphically view the atomic coordinate error along with `temperature factors' (i.e. atomic displacement parameters). In addition, the computing engine is interfaced with an up-to-date local copy of the Protein Data Bank. New entries are updated every week, and thus users can access all the structures available in the Protein Data Bank. The computing engine is freely accessible online at http://cluster.physics.iisc.ernet.in/dpi/.

Do we see what we should see? Describing non-covalent interactions in protein structures including precision

The power of X-ray crystal structure analysis as a technique is to `see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this `seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and alpha-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.

Intento explicativo de la teoría austriaca del ciclo y de su relación con conceptos ampliamente aceptados en las finanzas de la empresa y en la economía ortodoxa

Introducción: En el párrafo que citamos, de Sir John R. Hicks, el economista británico reconoce la importancia de tener un abordaje del proceso económico y de las situaciones de desajuste que influyen en su marcha, desde una posición que considere la importancia del capital, el tiempo, y el rol preponderante de la tasa de interés. Que tenga, asimismo, en consideración toda la dinámica del fenómeno de formación de capital y de elección entre distintos sistemas de producción. Ya antes había manifestado: “¿Qué determina el equilibrio de corto plazo de un sistema cerrado, cuando se le concibe no solo en términos de gustos y recursos, sino en términos de planes y expectativas, orientado hacia el futuro que queda fuera del período en cuestión?” (2) Pero: ¿Por qué este interés en analizar el proceso de elección de sistemas de producción y de formación de capital desde una visión dinámica y considerando el punto de vista de los comerciantes, o tomadores de decisión en la economía, es decir, si se prefiere, de los empresarios? ¿De donde surge esta idea? El subtitulo del libro citado en el epígrafe nos puede dar una pista

Broughton Archipelago Clam Terrace Survey : final report

During a 1995 aerial video survey of the coastline of Johnstone Strait, an unusual shoreline feature was noted and termed “clam terraces” (inset) because of the terrace-type morphology and the apparent association with high clam productivity on the sandflats. Typical alongshore lengths of the terrace ridges are 20-50m, and across-shore widths are typically 20-40m. An area with an especially high density of clam terraces was noted in the Broughton Archipelago, between Broughton and Gilford Islands of southeastern Queen Charlotte Strait. Clam terraces in this area were inventoried from the aerial video imagery to quantify their distribution. The terraces accounted for over 14 km of shoreline and 365 clam terraces were documented. A three-day field survey by a coastal geomorphologist, archeologist and marine biologist was conducted to document the features and determine their origin. Nine clam terraces were surveyed. The field observations confirmed that: the ridges are comprised of boulder/cobblesized material, ridge crests are typically in the range of 1-1.5m above chart datum, sandflats are comprised almost entirely of shell fragments (barnacles and clams) and sandflats have very high shellfish production. There are an abundance of shell middens in the area (over 175) suggesting that the shellfish associated with the terraces were an important food source of aboriginal peoples. The origin of the ridges is unknown; they appear to be a relict feature in that they are not actively being modified by present-day processes. The ridges may be a relict sea-ice feature, although the mechanics of ridge formation is uncertain. Sand accumulates behind the ridge because the supply rate of the shell fragments exceeds the dispersal rate in these low energy environments. The high density areas of clam terraces correspond to high density areas of shell middens, and it is probable that the clam terraces were subjected to some degree of modification by aboriginal shellfish gatherers over the thousands of years of occupation in the region. (Document contains 39 pages)

Coastal Pelagic Fishes (Report of Working Group 3); Subarctic Gyre (Report of Working Group 6)

This is a report of PICES Working Group 3 (Coastal Pelagic Fishes) for 1993 and the first Annual Report of the Subarctic Gyre Working Group (WG-6). (PDF contains 131 pages)

Generating monoenergetic heavy-ion bunches with laser-induced electrostatic shocks

A method for efficient laser acceleration of heavy ions by electrostatic shock is investigated using particle-in-cell (PIC) simulation and analytical modeling. When a small number of heavy ions are mixed with light ions, the heavy ions can be accelerated to the same velocity as the light ions so that they gain much higher energy because of their large mass. Accordingly, a sandwich target design with a thin compound ion layer between two light-ion layers and a micro-structured target design are proposed for obtaining monoenergetic heavy-ion beams.

Laser-driven coherent betatron oscillation in a laser-wakefield cavity

The origin of beam disparity in emittance and betatron oscillation orbits, in and out of the polarization plane of the drive laser of laser-plasma accelerators, is explained in terms of betatron oscillations driven by the laser field. As trapped electrons accelerate, they move forward and interact with the laser pulse. For the bubble regime, a simple model is presented to describe this interaction in terms of a harmonic oscillator with a driving force from the laser and a restoring force from the plasma wake field. The resulting beam oscillations in the polarization plane, with period approximately the wavelength of the driving laser, increase emittance in that plane and cause microbunching of the beam. These effects are observed directly in 3D particle-in-cell simulations.

Ion acceleration with mixed solid targets interacting with circularly polarized lasers

The interaction of a circularly polarized laser pulse with a mixed solid target containing two species of ions is studied by particle in cell simulations and analytical model. After the interaction tends to be stable, it is demonstrated that the acceleration is more efficient for the heavier ions than that in plasmas containing a single kind of heavy ion and the acceleration efficiency is higher when its proportion is lower. To obtain monoenergetic heavy-ion beams, a sandwich target with a thin mixed ion layer between two light ion layers and a microstructured target are proposed. The influences of parameters of the laser pulse and target on ion acceleration are discussed in detail. It is found that, when the target is thick enough, a cold target is more appropriate for heavy-ion acceleration than a warm target, and the velocity of the reflected heavy ions is proportional to the laser amplitude.