43 research outputs found
Variational determination of the second-order density matrix for the isoelectronic series of beryllium, neon and silicon
The isoelectronic series of Be, Ne and Si are investigated using a
variational determination of the second-order density matrix. A semidefinite
program was developed that exploits all rotational and spin symmetries in the
atomic system. We find that the method is capable of describing the strong
static electron correlations due to the incipient degeneracy in the hydrogenic
spectrum for increasing central charge. Apart from the ground-state energy
various other properties are extracted from the variationally determined
second-order density matrix. The ionization energy is constructed using the
extended Koopmans' theorem. The natural occupations are also studied, as well
as the correlated Hartree-Fock-like single particle energies. The exploitation
of symmetry allows to study the basis set dependence and results are presented
for correlation-consistent polarized valence double, triple and quadruple zeta
basis sets.Comment: 19 pages, 7 figures, 3 tables v2: corrected typo in Eq. (52
The tensor hypercontracted parametric reduced density matrix algorithm: coupled-cluster accuracy with O(r^4) scaling
Tensor hypercontraction is a method that allows the representation of a
high-rank tensor as a product of lower-rank tensors. In this paper, we show how
tensor hypercontraction can be applied to both the electron repulsion integral
(ERI) tensor and the two-particle excitation amplitudes used in the parametric
reduced density matrix (pRDM) algorithm. Because only O(r) auxiliary functions
are needed in both of these approximations, our overall algorithm can be shown
to scale as O(r4), where r is the number of single-particle basis functions. We
apply our algorithm to several small molecules, hydrogen chains, and alkanes to
demonstrate its low formal scaling and practical utility. Provided we use
enough auxiliary functions, we obtain accuracy similar to that of the
traditional pRDM algorithm, somewhere between that of CCSD and CCSD(T).Comment: 11 pages, 1 figur
Equivalence of particle-particle random phase approximation correlation energy and ladder-coupled-cluster doubles
We present an analytical proof and numerical demonstrations of the
equivalence of the correlation energy from particle-particle random phase
approximation (pp-RPA) and ladder-couple-cluster-doubles (ladder-CCD). These
two theories reduce to the identical algebraic matrix equation and correlation
energy expressions, under the assumption that the pp-RPA equation is stable.
The numerical examples illustrate that the correlation energy missed by pp-RPA
in comparison with couple-cluster single and double is largely canceled out
when considering reaction energies. This theoretical connection will be
beneficial to future pp-RPA studies based on the well established couple
cluster theory
Variational two-particle density matrix calculation for the Hubbard model below half filling using spin-adapted lifting conditions
The variational determination of the two-particle density matrix is an
interesting, but not yet fully explored technique that allows to obtain
ground-state properties of a quantum many-body system without reference to an
-particle wave function. The one-dimensional fermionic Hubbard model has
been studied before with this method, using standard two- and three-index
conditions on the density matrix [J. R. Hammond {\it et al.}, Phys. Rev. A 73,
062505 (2006)], while a more recent study explored so-called subsystem
constraints [N. Shenvi {\it et al.}, Phys. Rev. Lett. 105, 213003 (2010)].
These studies reported good results even with only standard two-index
conditions, but have always been limited to the half-filled lattice. In this
Letter we establish the fact that the two-index approach fails for other
fillings. In this case, a subset of three-index conditions is absolutely needed
to describe the correct physics in the strong-repulsion limit. We show that
applying lifting conditions [J.R. Hammond {\it et al.}, Phys. Rev. A 71, 062503
(2005)] is the most economical way to achieve this, while still avoiding the
computationally much heavier three-index conditions. A further extension to
spin-adapted lifting conditions leads to increased accuracy in the intermediate
repulsion regime. At the same time we establish the feasibility of such studies
to the more complicated phase diagram in two-dimensional Hubbard models.Comment: 10 pages, 2 figure
Molecular responses of European flounder (Platichthys flesus) chronically exposed to contaminated estuarine sediments
Molecular responses to acute toxicant exposure can be effective biomarkers, however responses to chronic exposure are less well characterised. The aim of this study was to determine chronic molecular responses to environmental mixtures in a controlled laboratory setting, free from the additional variability encountered with environmental sampling of wild organisms. Flounder fish were exposed in mesocosms for seven months to a contaminated estuarine sediment made by mixing material from the Forth (high organics) and Tyne (high metals and tributyltin) estuaries (FT) or a reference sediment from the Ythan estuary (Y). Chemical analyses demonstrated that FT sediment contained significantly higher concentrations of key environmental pollutants (including polycyclic aromatic hydrocarbons (PAHs), chlorinated biphenyls and heavy metals) than Y sediment, but that chronically exposed flounder showed a lack of differential accumulation of contaminants, including heavy metals. Biliary 1-hydroxypyrene concentration and erythrocyte DNA damage increased in FT-exposed fish. Transcriptomic and 1H NMR metabolomic analyses of liver tissues detected small but statistically significant alterations between fish exposed to different sediments. These highlighted perturbance of immune response and apoptotic pathways, but there was a lack of response from traditional biomarker genes. Gene-chemical association annotation enrichment analyses suggested that polycyclic aromatic hydrocarbons were a major class of toxicants affecting the molecular responses of the exposed fish. This demonstrated that molecular responses of sentinel organisms can be detected after chronic mixed toxicant exposure and that these can be informative of key components of the mixture
Integrating Omic Technologies into Aquatic Ecological Risk Assessment and Environmental Monitoring: Hurdles, Achievements, and Future Outlook
Background: In this commentary we present the findings from an international consortium on fish toxicogenomics sponsored by the U.K. Natural Environment Research Council (Fish Toxicogenomics—Moving into Regulation and Monitoring, held 21–23 April 2008 at the Pacific Environmental Science Centre, Vancouver, BC, Canada).
Objectives: The consortium from government agencies, academia, and industry addressed three topics: progress in ecotoxicogenomics, regulatory perspectives on roadblocks for practical implementation of toxicogenomics into risk assessment, and dealing with variability in data sets.
Discussion: Participants noted that examples of successful application of omic technologies have been identified, but critical studies are needed to relate molecular changes to ecological adverse outcome. Participants made recommendations for the management of technical and biological variation. They also stressed the need for enhanced interdisciplinary training and communication as well as considerable investment into the generation and curation of appropriate reference omic data.
Conclusions: The participants concluded that, although there are hurdles to pass on the road to regulatory acceptance, omics technologies are already useful for elucidating modes of action of toxicants and can contribute to the risk assessment process as part of a weight-of-evidence approach
Transcriptional Response of Zebrafish Embryos Exposed to Neurotoxic Compounds Reveals a Muscle Activity Dependent hspb11 Expression
Acetylcholinesterase (AChE) inhibitors are widely used as pesticides and drugs. Their primary effect is the overstimulation of cholinergic receptors which results in an improper muscular function. During vertebrate embryonic development nerve activity and intracellular downstream events are critical for the regulation of muscle fiber formation. Whether AChE inhibitors and related neurotoxic compounds also provoke specific changes in gene transcription patterns during vertebrate development that allow them to establish a mechanistic link useful for identification of developmental toxicity pathways has, however, yet not been investigated. Therefore we examined the transcriptomic response of a known AChE inhibitor, the organophosphate azinphos-methyl (APM), in zebrafish embryos and compared the response with two non-AChE inhibiting unspecific control compounds, 1,4-dimethoxybenzene (DMB) and 2,4-dinitrophenol (DNP). A highly specific cluster of APM induced gene transcripts was identified and a subset of strongly regulated genes was analyzed in more detail. The small heat shock protein hspb11 was found to be the most sensitive induced gene in response to AChE inhibitors. Comparison of expression in wildtype, ache and sopfixe mutant embryos revealed that hspb11 expression was dependent on the nicotinic acetylcholine receptor (nAChR) activity. Furthermore, modulators of intracellular calcium levels within the whole embryo led to a transcriptional up-regulation of hspb11 which suggests that elevated intracellular calcium levels may regulate the expression of this gene. During early zebrafish development, hspb11 was specifically expressed in muscle pioneer cells and Hspb11 morpholino-knockdown resulted in effects on slow muscle myosin organization. Our findings imply that a comparative toxicogenomic approach and functional analysis can lead to the identification of molecular mechanisms and specific marker genes for potential neurotoxic compounds
Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach
The acquisition and analysis of datasets including multi-level omics and physiology from non-model species, sampled from field populations, is a formidable challenge, which so far has prevented the application of systems biology approaches. If successful, these could contribute enormously to improving our understanding of how populations of living organisms adapt to environmental stressors relating to, for example, pollution and climate. Here we describe the first application of a network inference approach integrating transcriptional, metabolic and phenotypic information representative of wild populations of the European flounder fish, sampled at seven estuarine locations in northern Europe with different degrees and profiles of chemical contaminants. We identified network modules, whose activity was predictive of environmental exposure and represented a link between molecular and morphometric indices. These sub-networks represented both known and candidate novel adverse outcome pathways representative of several aspects of human liver pathophysiology such as liver hyperplasia, fibrosis, and hepatocellular carcinoma. At the molecular level these pathways were linked to TNF alpha, TGF beta, PDGF, AGT and VEGF signalling. More generally, this pioneering study has important implications as it can be applied to model molecular mechanisms of compensatory adaptation to a wide range of scenarios in wild populations
Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring
Abstract Background The Manila clam, Ruditapes philippinarum, is one of the major aquaculture species in the world and a potential sentinel organism for monitoring the status of marine ecosystems. However, genomic resources for R. philippinarum are still extremely limited. Global analysis of gene expression profiles is increasingly used to evaluate the biological effects of various environmental stressors on aquatic animals under either artificial conditions or in the wild. Here, we report on the development of a transcriptomic platform for global gene expression profiling in the Manila clam. Results A normalized cDNA library representing a mixture of adult tissues was sequenced using a ultra high-throughput sequencing technology (Roche 454). A database consisting of 32,606 unique transcripts was constructed, 9,747 (30%) of which could be annotated by similarity. An oligo-DNA microarray platform was designed and applied to profile gene expression of digestive gland and gills. Functional annotation of differentially expressed genes between different tissues was performed by enrichment analysis. Expression of Natural Antisense Transcripts (NAT) analysis was also performed and bi-directional transcription appears a common phenomenon in the R. philippinarum transcriptome. A preliminary study on clam samples collected in a highly polluted area of the Venice Lagoon demonstrated the applicability of genomic tools to environmental monitoring. Conclusions The transcriptomic platform developed for the Manila clam confirmed the high level of reproducibility of current microarray technology. Next-generation sequencing provided a good representation of the clam transcriptome. Despite the known limitations in transcript annotation and sequence coverage for non model species, sufficient information was obtained to identify a large set of genes potentially involved in cellular response to environmental stress.This work was partially supported by a grant from European Union-funded Network of Excellence "Marine Genomics Europe". CS wishes to acknowledge additional funding from the Ministry of Education and Science (Spain) through grant AGL2007-60049. MM had a PhD scholarship from the University of Florence, Italy. RL was recipient of PhD fellowship SFRH/BD/30112/2006, from the Portuguese Science and Technology Foundation (FCT) and LC and RL acknowledge a grant from FCT project ISOPERK (PTDC/CVT/72083/2006).Peer Reviewe