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1.
BMC Genom Data ; 22(1): 33, 2021 09 14.
Artigo em Inglês | MEDLINE | ID: mdl-34521352

RESUMO

BACKGROUND: The lymphatic and the blood vasculature are closely related systems that collaborate to ensure the organism's physiological function. Despite their common developmental origin, they present distinct functional fates in adulthood that rely on robust lineage-specific regulatory programs. The recent technological boost in sequencing approaches unveiled long noncoding RNAs (lncRNAs) as prominent regulatory players of various gene expression levels in a cell-type-specific manner. RESULTS: To investigate the potential roles of lncRNAs in vascular biology, we performed antisense oligonucleotide (ASO) knockdowns of lncRNA candidates specifically expressed either in human lymphatic or blood vascular endothelial cells (LECs or BECs) followed by Cap Analysis of Gene Expression (CAGE-Seq). Here, we describe the quality control steps adopted in our analysis pipeline before determining the knockdown effects of three ASOs per lncRNA target on the LEC or BEC transcriptomes. In this regard, we especially observed that the choice of negative control ASOs can dramatically impact the conclusions drawn from the analysis depending on the cellular background. CONCLUSION: In conclusion, the comparison of negative control ASO effects on the targeted cell type transcriptomes highlights the essential need to select a proper control set of multiple negative control ASO based on the investigated cell types.

2.
Methods Mol Biol ; 2351: 67-90, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34382184

RESUMO

The Cap Analysis of Gene Expression (CAGE) is a powerful method to identify Transcription Start Sites (TSSs) of capped RNAs while simultaneously measuring transcripts expression level. CAGE allows mapping at single nucleotide resolution at all active promoters and enhancers. Large CAGE datasets have been produced over the years from individual laboratories and consortia, including the Encyclopedia of DNA Elements (ENCODE) and Functional Annotation of the Mammalian Genome (FANTOM) consortia. These datasets constitute open resource for TSS annotations and gene expression analysis. Here, we provide an experimental protocol for the most recent CAGE method called Low Quantity (LQ) single strand (ss) CAGE "LQ-ssCAGE", which enables cost-effective profiling of low quantity RNA samples. LQ-ssCAGE is especially useful for samples derived from cells cultured in small volumes, cellular compartments such as nuclear RNAs or for samples from developmental stages. We demonstrate the reproducibility and effectiveness of the method by constructing 240 LQ-ssCAGE libraries from 50 ng of THP-1 cell extracted RNAs and discover lowly expressed novel enhancer and promoter-derived lncRNAs.


Assuntos
Biologia Computacional/métodos , Elementos Facilitadores Genéticos , Regiões Promotoras Genéticas , Capuzes de RNA , Sítio de Iniciação de Transcrição , Bases de Dados Genéticas , Regulação da Expressão Gênica , Biblioteca Gênica , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Anotação de Sequência Molecular , Sequências Reguladoras de Ácido Nucleico , Reprodutibilidade dos Testes , Fluxo de Trabalho
3.
Nat Commun ; 12(1): 3297, 2021 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-34078885

RESUMO

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.


Assuntos
Repetições de Microssatélites , Redes Neurais de Computação , Doenças Neurodegenerativas/genética , Sítio de Iniciação de Transcrição , Iniciação da Transcrição Genética , Células A549 , Animais , Sequência de Bases , Biologia Computacional/métodos , Aprendizado Profundo , Elementos Facilitadores Genéticos , Genoma Humano , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Camundongos , Doenças Neurodegenerativas/diagnóstico , Doenças Neurodegenerativas/metabolismo , Polimorfismo Genético , Regiões Promotoras Genéticas
4.
Nucleic Acids Res ; 49(D1): D892-D898, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33211864

RESUMO

The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the FANTOM web-interfaces and databases are being regularly updated, enhanced and expanded with new data types. In recent years, the FANTOM Consortium's efforts have been mainly focused on creating new non-coding RNA datasets and resources. The existing FANTOM5 human and mouse miRNA atlas was supplemented with rat, dog, and chicken datasets. The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs). From its creation until 2020, FANTOM6 has contributed to the research community a large dataset generated from the knock-down of 285 lncRNAs in human dermal fibroblasts; this is followed with extensive expression profiling and cellular phenotyping. Other updates to the FANTOM resource includes the reprocessing of the miRNA and promoter atlases of human, mouse and chicken with the latest reference genome assemblies. To facilitate the use and accessibility of all above resources we further enhanced FANTOM data viewers and web interfaces. The updated FANTOM web resource is publicly available at https://fantom.gsc.riken.jp/.


Assuntos
Anotação de Sequência Molecular , RNA Longo não Codificante/genética , Transcriptoma/genética , Animais , Sítios de Ligação , Cromatina/metabolismo , Drosophila/genética , Fibroblastos/citologia , Fibroblastos/metabolismo , Genoma , Humanos , Metadados , Camundongos , MicroRNAs/genética , MicroRNAs/metabolismo , Regiões Promotoras Genéticas , RNA Longo não Codificante/metabolismo , Fatores de Transcrição/metabolismo , Interface Usuário-Computador
5.
Nat Commun ; 11(1): 5011, 2020 10 06.
Artigo em Inglês | MEDLINE | ID: mdl-33024107

RESUMO

Development of high throughput single-cell sequencing technologies has made it cost-effective to profile thousands of cells from diverse samples containing multiple cell types. To study how these different cell types work together, here we develop NATMI (Network Analysis Toolkit for Multicellular Interactions). NATMI uses connectomeDB2020 (a database of 2293 manually curated ligand-receptor pairs with literature support) to predict and visualise cell-to-cell communication networks from single-cell (or bulk) expression data. Using multiple published single-cell datasets we demonstrate how NATMI can be used to identify (i) the cell-type pairs that are communicating the most (or most specifically) within a network, (ii) the most active (or specific) ligand-receptor pairs active within a network, (iii) putative highly-communicating cellular communities and (iv) differences in intercellular communication when profiling given cell types under different conditions. Furthermore, analysis of the Tabula Muris (organism-wide) atlas confirms our previous prediction that autocrine signalling is a major feature of cell-to-cell communication networks, while also revealing that hundreds of ligands and their cognate receptors are co-expressed in individual cells suggesting a substantial potential for self-signalling.


Assuntos
Comunicação Celular , Biologia Computacional/métodos , Software , Fatores Etários , Animais , Comunicação Autócrina , Visualização de Dados , Bases de Dados Factuais , Feminino , Ligantes , Glândulas Mamárias Animais , Camundongos , Proteínas/metabolismo , Análise de Célula Única , Interface Usuário-Computador
6.
Genome Res ; 30(7): 951-961, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32718981

RESUMO

Gene expression profiles in homologous tissues have been observed to be different between species, which may be due to differences between species in the gene expression program in each cell type, but may also reflect differences in cell type composition of each tissue in different species. Here, we compare expression profiles in matching primary cells in human, mouse, rat, dog, and chicken using Cap Analysis Gene Expression (CAGE) and short RNA (sRNA) sequencing data from FANTOM5. While we find that expression profiles of orthologous genes in different species are highly correlated across cell types, in each cell type many genes were differentially expressed between species. Expression of genes with products involved in transcription, RNA processing, and transcriptional regulation was more likely to be conserved, while expression of genes encoding proteins involved in intercellular communication was more likely to have diverged during evolution. Conservation of expression correlated positively with the evolutionary age of genes, suggesting that divergence in expression levels of genes critical for cell function was restricted during evolution. Motif activity analysis showed that both promoters and enhancers are activated by the same transcription factors in different species. An analysis of expression levels of mature miRNAs and of primary miRNAs identified by CAGE revealed that evolutionary old miRNAs are more likely to have conserved expression patterns than young miRNAs. We conclude that key aspects of the regulatory network are conserved, while differential expression of genes involved in cell-to-cell communication may contribute greatly to phenotypic differences between species.

7.
Genome Res ; 30(7): 1060-1072, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32718982

RESUMO

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.

8.
Genome Res ; 29(3): 506-519, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30760547

RESUMO

Organogenesis involves dynamic regulation of gene transcription and complex multipathway interactions. Despite our knowledge of key factors regulating various steps of heart morphogenesis, considerable challenges in understanding its mechanism still exist because little is known about their downstream targets and interactive regulatory network. To better understand transcriptional regulatory mechanism driving heart development and the consequences of its disruption in vivo, we performed time-series analyses of the transcriptome and genome-wide chromatin accessibility in isolated cardiomyocytes (CMs) from wild-type zebrafish embryos at developmental stages corresponding to heart tube morphogenesis, looping, and maturation. We identified genetic regulatory modules driving crucial events of heart development that contained key cardiac TFs and are associated with open chromatin regions enriched for DNA sequence motifs belonging to the family of the corresponding TFs. Loss of function of cardiac TFs Gata5, Tbx5a, and Hand2 affected the cardiac regulatory networks and caused global changes in chromatin accessibility profile, indicating their role in heart development. Among regions with differential chromatin accessibility in mutants were highly conserved noncoding elements that represent putative enhancers driving heart development. The most prominent gene expression changes, which correlated with chromatin accessibility modifications within their proximal promoter regions, occurred between heart tube morphogenesis and looping, and were associated with metabolic shift and hematopoietic/cardiac fate switch during CM maturation. Our results revealed the dynamic regulatory landscape throughout heart development and identified interactive molecular networks driving key events of heart morphogenesis.


Assuntos
Montagem e Desmontagem da Cromatina , Regulação da Expressão Gênica no Desenvolvimento , Coração/crescimento & desenvolvimento , Miócitos Cardíacos/metabolismo , Transcriptoma , Animais , Células Cultivadas , Cromatina/genética , Redes Reguladoras de Genes , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Peixe-Zebra , Proteínas de Peixe-Zebra/genética , Proteínas de Peixe-Zebra/metabolismo
9.
Nature ; 543(7644): 199-204, 2017 03 09.
Artigo em Inglês | MEDLINE | ID: mdl-28241135

RESUMO

Long non-coding RNAs (lncRNAs) are largely heterogeneous and functionally uncharacterized. Here, using FANTOM5 cap analysis of gene expression (CAGE) data, we integrate multiple transcript collections to generate a comprehensive atlas of 27,919 human lncRNA genes with high-confidence 5' ends and expression profiles across 1,829 samples from the major human primary cell types and tissues. Genomic and epigenomic classification of these lncRNAs reveals that most intergenic lncRNAs originate from enhancers rather than from promoters. Incorporating genetic and expression data, we show that lncRNAs overlapping trait-associated single nucleotide polymorphisms are specifically expressed in cell types relevant to the traits, implicating these lncRNAs in multiple diseases. We further demonstrate that lncRNAs overlapping expression quantitative trait loci (eQTL)-associated single nucleotide polymorphisms of messenger RNAs are co-expressed with the corresponding messenger RNAs, suggesting their potential roles in transcriptional regulation. Combining these findings with conservation data, we identify 19,175 potentially functional lncRNAs in the human genome.


Assuntos
Bases de Dados Genéticas , RNA Longo não Codificante/química , RNA Longo não Codificante/genética , Transcriptoma/genética , Células Cultivadas , Sequência Conservada/genética , Conjuntos de Dados como Assunto , Elementos Facilitadores Genéticos/genética , Epigênese Genética , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Genoma Humano/genética , Estudo de Associação Genômica Ampla , Genômica , Humanos , Internet , Anotação de Sequência Molecular , Especificidade de Órgãos/genética , Polimorfismo de Nucleotídeo Único , Regiões Promotoras Genéticas/genética , Locos de Características Quantitativas/genética , Estabilidade de RNA , RNA Mensageiro/genética
10.
Nucleic Acids Res ; 45(D1): D737-D743, 2017 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-27794045

RESUMO

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives.


Assuntos
Bases de Dados Genéticas , Perfilação da Expressão Gênica/métodos , Genômica/métodos , Mamíferos/genética , Software , Navegador , Animais , Biologia Computacional , Humanos , Ferramenta de Busca
12.
Nat Commun ; 6: 7866, 2015 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-26198319

RESUMO

Cell-to-cell communication across multiple cell types and tissues strictly governs proper functioning of metazoans and extensively relies on interactions between secreted ligands and cell-surface receptors. Herein, we present the first large-scale map of cell-to-cell communication between 144 human primary cell types. We reveal that most cells express tens to hundreds of ligands and receptors to create a highly connected signalling network through multiple ligand-receptor paths. We also observe extensive autocrine signalling with approximately two-thirds of partners possibly interacting on the same cell type. We find that plasma membrane and secreted proteins have the highest cell-type specificity, they are evolutionarily younger than intracellular proteins, and that most receptors had evolved before their ligands. We provide an online tool to interactively query and visualize our networks and demonstrate how this tool can reveal novel cell-to-cell interactions with the prediction that mast cells signal to monoblastic lineages via the CSF1-CSF1R interacting pair.


Assuntos
Comunicação Celular , Receptores de Superfície Celular/metabolismo , Animais , Evolução Molecular , Humanos , Ligantes , Software
13.
J Allergy Clin Immunol ; 136(3): 638-48, 2015 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25863981

RESUMO

BACKGROUND: Children with problematic severe asthma have poor disease control despite high doses of inhaled corticosteroids and additional therapy, leading to personal suffering, early deterioration of lung function, and significant consumption of health care resources. If no exacerbating factors, such as smoking or allergies, are found after extensive investigation, these children are given a diagnosis of therapy-resistant (or therapy-refractory) asthma (SA). OBJECTIVE: We sought to deepen our understanding of childhood SA by analyzing gene expression and modeling the underlying regulatory transcription factor networks in peripheral blood leukocytes. METHODS: Gene expression was analyzed by using Cap Analysis of Gene Expression in children with SA (n = 13), children with controlled persistent asthma (n = 15), and age-matched healthy control subjects (n = 9). Cap Analysis of Gene Expression sequencing detects the transcription start sites of known and novel mRNAs and noncoding RNAs. RESULTS: Sample groups could be separated by hierarchical clustering on 1305 differentially expressed transcription start sites, including 816 known genes and several novel transcripts. Ten of 13 tested novel transcripts were validated by means of RT-PCR and Sanger sequencing. Expression of RAR-related orphan receptor A (RORA), which has been linked to asthma in genome-wide association studies, was significantly upregulated in patients with SA. Gene network modeling revealed decreased glucocorticoid receptor signaling and increased activity of the mitogen-activated protein kinase and Jun kinase cascades in patients with SA. CONCLUSION: Circulating leukocytes from children with controlled asthma and those with SA have distinct gene expression profiles, demonstrating the possible development of specific molecular biomarkers and supporting the need for novel therapeutic approaches.


Assuntos
Asma/tratamento farmacológico , Asma/genética , Resistência a Medicamentos/genética , Glucocorticoides/uso terapêutico , RNA Mensageiro/genética , Transcriptoma , Adolescente , Asma/patologia , Estudos de Casos e Controles , Criança , Pré-Escolar , Feminino , Perfilação da Expressão Gênica , Estudo de Associação Genômica Ampla , Humanos , Proteínas Quinases JNK Ativadas por Mitógeno/genética , Masculino , Membro 1 do Grupo F da Subfamília 1 de Receptores Nucleares/genética , Receptores de Glucocorticoides/genética , Índice de Gravidade de Doença
14.
Plant Cell Physiol ; 54(5): 697-710, 2013 May.
Artigo em Inglês | MEDLINE | ID: mdl-23589666

RESUMO

Medicinal and industrial properties of phytochemicals (e.g. glycyrrhizin) from the root of Glycyrrhiza uralensis (licorice plant) made it an attractive, multimillion-dollar trade item. Bioengineering is one of the solutions to overcome such high market demand and to protect plants from extinction. Unfortunately, limited genomic information on medicinal plants restricts their research and thus biosynthetic mechanisms of many important phytochemicals are still poorly understood. In this work we utilized the de novo (no reference genome sequence available) assembly of Illumina RNA-Seq data to study the transcriptome of the licorice plant. Our analysis is based on sequencing results of libraries constructed from samples belonging to different tissues (root and leaf) and collected in different seasons and from two distinct strains (low and high glycyrrhizin producers). We provide functional annotations and the expression profile of 43,882 assembled unigenes, which are suitable for various further studies. Here, we searched for G. uralensis-specific enzymes involved in isoflavonoid biosynthesis as well as elucidated putative cytochrome P450 enzymes and putative vacuolar saponin transporters involved in glycyrrhizin production in the licorice root. To disseminate the data and the analysis results, we constructed a publicly available G. uralensis database. This work will contribute to a better understanding of the biosynthetic pathways of secondary metabolites in licorice plants, and possibly in other medicinal plants, and will provide an important resource to further advance transcriptomic studies in legumes.


Assuntos
Glycyrrhiza uralensis/genética , Compostos Fitoquímicos/metabolismo , Transcriptoma/genética , Sequência de Aminoácidos , Bases de Dados como Assunto , Perfilação da Expressão Gênica , Biblioteca Gênica , Ontologia Genética , Glycyrrhiza uralensis/enzimologia , Ácido Glicirrízico/química , Ácido Glicirrízico/metabolismo , Proteínas de Membrana Transportadoras/metabolismo , Redes e Vias Metabólicas/genética , Anotação de Sequência Molecular , Dados de Sequência Molecular , Fases de Leitura Aberta/genética , Compostos Fitoquímicos/química , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Transporte Proteico , RNA de Plantas/isolamento & purificação , Análise de Sequência de DNA , Frações Subcelulares/metabolismo , Vacúolos/metabolismo
15.
Phys Chem Chem Phys ; 14(22): 8123-36, 2012 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-22538980

RESUMO

The diffusion Monte Carlo (DMC) method is a widely used algorithm for computing both ground and excited states of many-particle systems; for states without nodes the algorithm is numerically exact. In the presence of nodes approximations must be introduced, for example, the fixed-node approximation. Recently we have developed a genetic algorithm (GA) based approach which allows the computation of nodal surfaces on-the-fly [Ramilowski and Farrelly, Phys. Chem. Chem. Phys., 2010, 12, 12450]. Here GA-DMC is applied to the computation of rovibrational states of CO-(4)He(N) complexes with N≤ 10. These complexes have been the subject of recent high resolution microwave and millimeter-wave studies which traced the onset of microscopic superfluidity in a doped (4)He droplet, one atom at a time, up to N = 10 [Surin et al., Phys. Rev. Lett., 2008, 101, 233401; Raston et al., Phys. Chem. Chem. Phys., 2010, 12, 8260]. The frequencies of the a-type (microwave) series, which correlate with end-over-end rotation in the CO-(4)He dimer, decrease from N = 1 to 3 and then smoothly increase. This signifies the transition from a molecular complex to a quantum solvated system. The frequencies of the b-type (millimeter-wave) series, which evolves from free rotation of the rigid CO molecule, initially increase from N = 0 to N∼ 6 before starting to decrease with increasing N. An interesting feature of the b-type series, originally observed in the high resolution infra-red (IR) experiments of Tang and McKellar [J. Chem. Phys., 2003, 119, 754] is that, for N = 7, two lines are observed. The GA-DMC algorithm is found to be in good agreement with experimental results and possibly detects the small (∼0.7 cm(-1)) splitting in the b-series line at N = 7. Advantages and disadvantages of GA-DMC are discussed.

16.
J Am Chem Soc ; 132(40): 14104-12, 2010 Oct 13.
Artigo em Inglês | MEDLINE | ID: mdl-20857982

RESUMO

Bulk carbon and boron form very different materials, which are also reflected in their clusters. Small carbon clusters form linear structures, whereas boron clusters are planar. For example, it is known that the B(5)(-) cluster possesses a C(2v) planar structure and C(5)(-) is a linear chain. Here we study B/C mixed clusters containing five atoms, C(x)B(5-x)(-) (x = 1-5), which are expected to exhibit a planar to linear structural transition as a function of the C content. The C(x)B(5-x)(-) (x = 1-5) clusters were produced and studied by photoelectron spectroscopy; their geometric and electronic structures were investigated using a variety of theoretical methods. We found that the planar-to-linear transition occurs between x = 2 and 3: the global minimum structures of the B-rich clusters, CB(4)(-) and C(2)B(3)(-), are planar, similar to B(5)(-), and those of the C-rich clusters, C(3)B(2)(-) and C(4)B(-), are linear, similar to C(5)(-).

17.
Phys Chem Chem Phys ; 12(39): 12450-6, 2010 Oct 21.
Artigo em Inglês | MEDLINE | ID: mdl-20717596

RESUMO

The fixed-node diffusion Monte Carlo (DMC) algorithm is a powerful way of computing excited state energies in a remarkably diverse number of contexts in quantum chemistry and physics. The main difficulty in implementing the procedure lies in obtaining a good estimate of the nodal surface of the excited state in question. Although the nodal surface can sometimes be obtained from symmetry or by making approximations this is not always the case. In any event, nodal surfaces are usually obtained in an ad hoc way. In fact, the search for nodal surfaces can be formulated as an optimization problem within the DMC procedure itself. Here we investigate the use of a genetic algorithm to systematically and automatically compute nodal surfaces. Application is made to the computation of excited states of the HCN-(4)He complex and to the computation of tunneling splittings in the hydrogen bonded HCl-HCl complex.

18.
Phys Chem Chem Phys ; 11(37): 8203-13, 2009 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-19756276

RESUMO

The classical dynamics of weakly bound floppy van der Waals complexes have been extensively studied in the past except for the weakest of all, i.e., those involving He atoms. These complexes are of considerable current interest in light of recent experimental work focussed on the study of molecules trapped in small droplets of the quantum solvent (4)He. Despite a number of quantum investigations, details on the dynamics of how quantum solvation occurs remain unclear. In this paper, the classical rotational dynamics of a series of van der Waals complexes, HX-(4)He with X = F, Cl, Br, CN, are studied. In all cases, the ground state dynamics are found to be almost entirely chaotic, in sharp contrast to other floppy complexes, such as HCl-Ar, for which chaos sets in only at relatively high energies. The consequences of this result for quantum solvation are discussed. We also investigate rotationally excited states with J = 1 which, except for HCN-(4)He, are actually resonances that decay by rotational pre-dissociation.

19.
Phys Rev E Stat Nonlin Soft Matter Phys ; 80(5 Pt 2): 055201, 2009 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-20365032

RESUMO

We numerically show fractal Weyl law behavior in an open Hamiltonian system that is described by a smooth potential and which supports numerous above-barrier resonances. This behavior holds even relatively far away from the classical limit. The complex resonance wave functions are found to be localized on the fractal classical repeller.

20.
J Phys Chem A ; 111(49): 12275-88, 2007 Dec 13.
Artigo em Inglês | MEDLINE | ID: mdl-17929781

RESUMO

Diffusion Monte Carlo calculations are performed for ground and excited rotational states of HX(4He)N, complexes with N

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