139 research outputs found
An improved DMAP capability
A set of improvements designed and implemented into a test version of the NASTRAN DMAP (Direct Matrix Abstraction Program) compiler is presented. These modifications simplify the use of the DMAP control language while enhancing its power and versatility. The implemented changes are described and examples are presented to illustrate their use
Implementation on a nonlinear concrete cracking algorithm in NASTRAN
A computer code for the analysis of reinforced concrete structures was developed using NASTRAN as a basis. Nonlinear iteration procedures were developed for obtaining solutions with a wide variety of loading sequences. A direct access file system was used to save results at each load step to restart within the solution module for further analysis. A multi-nested looping capability was implemented to control the iterations and change the loads. The basis for the analysis is a set of mutli-layer plate elements which allow local definition of materials and cracking properties
The automated multi-stage substructuring system for NASTRAN
The substructuring capability developed for eventual installation in Level 16 is now operational in a test version of NASTRAN. Its features are summarized. These include the user-oriented, Case Control type control language, the automated multi-stage matrix processing, the independent direct access data storage facilities, and the static and normal modes solution capabilities. A complete problem analysis sequence is presented with card-by-card description of the user input
Thermodynamics of Heat Shock Response
Production of heat shock proteins are induced when a living cell is exposed
to a rise in temperature. The heat shock response of protein DnaK synthesis in
E.coli for temperature shifts from temperature T to T plus 7 degrees,
respectively to T minus 7 degrees is measured as function of the initial
temperature T. We observe a reversed heat shock at low T. The magnitude of the
shock increases when one increase the distance to the temperature , thereby mimicking the non monotous stability of proteins at low
temperature. Further we found that the variation of the heat shock with T
quantitatively follows the thermodynamic stability of proteins with
temperature. This suggest that stability related to hot as well as cold
unfolding of proteins is directly implemented in the biological control of
protein folding. We demonstrate that such an implementation is possible in a
minimalistic chemical network.Comment: To be published in Physical Review Letter
Applying consumer responsibility principle in evaluating environmental load of carbon emissions
There is a need for a proper indicator in order to assess the environmental impact of international
trade, therefore using the carbon footprint as an indicator can be relevant and useful. The aim of this
study is to show from a methodological perspective how the carbon footprint, combined with input-
output models can be used for analysing the impacts of international trade on the sustainable use
of national resources in a country. The use of the input-output approach has the essential advantage
of being able to track the transformation of goods through the economy. The study examines the environmental
impact of consumption related to international trade, using the consumer responsibility
principle. In this study the use of the carbon footprint and input-output methodology is shown on the
example of the Hungarian consumption and the impact of international trade. Moving from a production-
based approach in climate policy to a consumption-perspective principle and allocation,
would also help to increase the efficiency of emission reduction targets and the evaluation of the
ecological impacts of international trade
Mobility of Taxol in Microtubule Bundles
Mobility of taxol inside microtubules was investigated using fluorescence
recovery after photobleaching (FRAP) on flow-aligned bundles. Bundles were made
of microtubules with either GMPCPP or GTP at the exchangeable site on the
tubulin dimer. Recovery times were sensitive to bundle thickness and packing,
indicating that taxol molecules are able to move laterally through the bundle.
The density of open binding sites along a microtubule was varied by controlling
the concentration of taxol in solution for GMPCPP samples. With > 63% sites
occupied, recovery times were independent of taxol concentration and,
therefore, inversely proportional to the microscopic dissociation rate,
k_{off}. It was found that 10*k_{off} (GMPCPP) ~ k_{off} (GTP), consistent
with, but not fully accounting for, the difference in equilibrium constants for
taxol on GMPCPP and GTP microtubules. With < 63% sites occupied, recovery times
decreased as ~ [Tax]^{-1/5} for both types of microtubules. We conclude that
the diffusion of taxol along the microtubule interior is hindered by rebinding
events when open sites are within ~7 nm of each other.Comment: pre print forma
Recent advances in understanding the roles of whole genome duplications in evolution
Ancient whole-genome duplications (WGDs)—paleopolyploidy events—are key to solving Darwin’s ‘abominable mystery’ of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life
Viral nanomotors for packaging of dsDNA and dsRNA
While capsid proteins are assembled around single-stranded genomic DNA or RNA in rod-shaped viruses, the lengthy double-stranded genome of other viruses is packaged forcefully within a preformed protein shell. This entropically unfavourable DNA or RNA packaging is accomplished by an ATP-driven viral nanomotor, which is mainly composed of two components, the oligomerized channel and the packaging enzymes. This intriguing DNA or RNA packaging process has provoked interest among virologists, bacteriologists, biochemists, biophysicists, chemists, structural biologists and computational scientists alike, especially those interested in nanotechnology, nanomedicine, AAA+ family proteins, energy conversion, cell membrane transport, DNA or RNA replication and antiviral therapy. This review mainly focuses on the motors of double-stranded DNA viruses, but double-stranded RNA viral motors are also discussed due to interesting similarities. The novel and ingenious configuration of these nanomotors has inspired the development of biomimetics for nanodevices. Advances in structural and functional studies have increased our understanding of the molecular basis of biological movement to the point where we can begin thinking about possible applications of the viral DNA packaging motor in nanotechnology and medical applications
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