Search results for " function"
showing 10 items of 9395 documents
RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing
2021
The alignment of reads to a transcriptome is an important initial step in a variety of bioinformatics RNA-seq pipelines. As traditional alignment-based tools suffer from high runtimes, alternative, alignment-free methods have recently gained increasing importance. We present a novel approach to the detection of local similarities between transcriptomes and RNA-seq reads based on context-aware minhashing. We introduce RNACache, a three-step processing pipeline consisting of minhashing of k-mers, match-based (online) filtering, and coverage-based filtering in order to identify truly expressed transcript isoforms. Our performance evaluation shows that RNACache produces transcriptomic mappings …
Freenet-like GUIDs for implementing xanalogical hypertext
2002
We discuss the use of Freenet-like content hash GUIDs as a primitive for implementing the Xanadu model in a peer-to-peer framework. Our current prototype is able to display the implicit connection (transclusion) between two different references to the same permanent ID. We discuss the next layers required in the implementation of the Xanadu model on a world-wide peer-to-peer network.
Circular dichroism in X-ray photoemission from Pd(111) and CO/Pd(111)
1995
It is shown experimentally that in the soft X-ray region a large circular dichroism in the photoelectron angular distribution (CDAD) exists for both valence orbitals and core levels of CO molecules adsorbed on Pd(111). From theoretical consideration it follows that in the case of a spherically symmetric ground state wave function, like the 1σ and 2σ orbitals of CO, CDAD appears due to the lack of spherical symmetry in the final state. For carbonK-shell experimental results are compared to model calculations. Investigations at the Pd core levels proved that CDAD does also arise in X-ray photo-emission from non-magnetic crystals.
A high-temperature x-ray absorption spectroscopy study of
1996
We present for the first time a high-temperature x-ray absorption spectroscopy study of at the edge. The analysis both of the XANES and of the EXAFS regions shows that, in , a progressive localization of the 5d states following the temperature rise is accompanied at T > 350 K by a distortion of the octahedra, which increases up to the decomposition temperature . The distortion leads to the lowering of the rhenium site symmetry from and is due to the electron - phonon coupling of the 5d electrons with the and phonons and to the Jahn - Teller effect caused by the rhenium electron which becomes localized at high temperature.
cis-[(η5-C5H5)Fe(η1-CO)(μ-CO)]2, the poor relative between cis and trans tautomers. A theoretical study of the gas-phase Fe L3-edge and C and O K-edg…
2021
The relative stability of trans-[(η5-C5H5)Fe(η1-CO)(μ-CO)]2 (trans-I) and cis-I tautomers in a vacuum and in solvents with different dielectric constants (e) has been investigated by exploiting density functional theory (DFT). Theoretical results indicate that, in agreement with experimental evidence, trans-I is more stable than cis-I in a vacuum (∼1.5 kcal mol−1; e = 1), while the opposite is true in media with e > 7. Differently from solution, DFT outcomes pertaining to the vapor-phase cis-I ⇆ trans-I equilibrium at T = 368 K, the temperature at which the Fe L2,3-edges and the C and O K-edge X-ray absorption spectroscopy (XAS) data of I have been recorded, ultimately indicate the trans-I …
X-ray Spectroscopy of (Ba,Sr,La)(Fe,Zn,Y)O3-δIdentifies Structural and Electronic Features Favoring Proton Uptake
2020
Mixed protonic–electronic conducting oxides are key functional materials for protonic ceramic fuel cells. Here, (Ba,Sr,La)(Fe,Zn,Y)O3−δ perovskites are comprehensively investigated by X-ray spectroscopy (in oxidized and reduced states). Extended X-ray absorption fine structure shows that Zn,Y doping strongly increases the tendency for Fe–O–Fe buckling. X-ray absorption near-edge spectroscopy at the Fe K-edge and X-ray Raman scattering at the O K edge demonstrate that both iron and oxygen states are involved when the samples are oxidized, and for the Zn,Y doped materials, the hole transfer from iron to oxygen is less pronounced. This can be correlated with the observation that these material…
Comparative Experimental and Theoretical Study of the Fe L-2,L-3-Edges X-ray Absorption Spectroscopy in Three Highly Popular, Low-Spin Organoiron Com…
2019
The occupied and unoccupied electronic structures of three highly popular, closed shell organoiron complexes ([Fe(CO)(5)], [(eta(5)-C5H5 )Fe(CO)(mu-CO)](2), and [(eta(5)-C5H5)(2)Fe]) have been theoretically investigated by taking advantage of density functional theory (DFT) calculations coupled to the isolobal analogy (Elian et al. Inorg. Chem. 1976, 15, 1148). The adopted approach allowed us to look into the relative role played by the ligand -> Fe donation and the Fe -> ligand back-donation in title molecules, as well as to investigate how CO- (terminal or bridging) and [(eta(5)-C5H5)](-)-based pi* orbitals compete when these two ligands are simultaneously present as in [(eta(5)-C5H…
Oб определении внутримолекулярной потенциальной функции многоатомной молекулы H2S
2008
In modern molecular physics, there are two basic methods of determining the intramolecular potential function of polyatomic molecules. The first method is ab initio calculations and the second is the so-called semi-empirical method in which the Hamiltonian parameters are varied by direct construction of the Hamiltonian matrix. In the present work, the second approach is discussed on the example of the XY2 three-atomic molecule of the C2v symmetry. On the one hand, it is extremely simple for implementation, and on the other hand, it considerably extends the capability of application of the traditional semi-empirical methods. The approach suggested involves two aspects that make it advantageo…
Assessing the root of bilaterian animals with scalable phylogenomic methods.
2009
A clear picture of animal relationships is a prerequisite to understand how the morphological and ecological diversity of animals evolved over time. Among others, the placement of the acoelomorph flatworms, Acoela and Nemertodermatida, has fundamental implications for the origin and evolution of various animal organ systems. Their position, however, has been inconsistent in phylogenetic studies using one or several genes. Furthermore, Acoela has been among the least stable taxa in recent animal phylogenomic analyses, which simultaneously examine many genes from many species, while Nemertodermatida has not been sampled in any phylogenomic study. New sequence data are presented here from org…
Bounds to internal forces for elastic-plastic solids subjected to variable loads
1979
Considering an elastic-plastic workhardening solid with piecewise linear yield surfaces and a piecewise linear workhardening law, we give a method for constructing bounds to the internal forces and to the (hardened) yield stresses produced by the action of variable loads at any point of the body and at any time. The loading history is supposed to be unknown, but the loads range within a given domain.