| 1. |
- Carninci, P, et al.
(författare)
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The transcriptional landscape of the mammalian genome
- 2005
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 309:5740, s. 1559-1563
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Tidskriftsartikel (refereegranskat)abstract
- This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5′ and 3′ boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
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| 2. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 3. |
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| 4. |
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| 5. |
- Gao, Bin, et al.
(författare)
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An efficient first-principle approach for electronic structures calculations of nanomaterials
- 2008
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 29:3, s. 434-444
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Tidskriftsartikel (refereegranskat)abstract
- An efficient parallel implementation has been realized for a recently proposed central insertion scheme (Jiang, Liu, Lu, Luo. J Chem Phys 2006,124,214711; J Chem Phys 2006,125, 149902) that allows to calculate electronic structures of nanomaterials at various density functional theory levels. It has adopted the sparse-matrix format for Fock/Kohn-Sham and overlap matrices, as well as a combination of implicitly restarted Arnoldi methods (IRAM) and spectral transformation for computing selected eigenvalues/eigenvectors. A systematic error analysis and control for the proposed method has been provided based on a strict mathematical basis. The efficiency and applicability of the new implementation have been demonstrated by calculations of electronic structures of two different nanomaterials consisting of one hundred thousand electrons.
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| 6. |
- Heck, J., et al.
(författare)
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Structure-property relationship in organometallic compounds regarding SHG
- 2007
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Ingår i: Linear and Nonlinear Optics of Organic Materials VII. - : SPIE - International Society for Optical Engineering. - 9780819468017 ; , s. R6530-R6530
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Konferensbidrag (refereegranskat)abstract
- Structure-property relationships based on experimental as well as theoretical results will be elucidated. For this purpose different dipolar organometallic compounds were synthesized and characterized. The alteration of the donor and acceptor termini in mono- and dinuclear sesquifulvalene complexes results in spectroscopic and even structural modifications. The structural and 1H NMR spectroscopic changes correlate with the experimentally obtained first hyperpolarizability. The potent electron-donating (D) group [(CpFeCO)2(μ-CO)(μ-C=CH-)] is combined with different electron-accepting units (A), yielding the push-pull complexes [(CpFeCO) 2(μ-CO)(μ-C=CH-CH=A)]. The extent of electron derealization within the π-bridge connecting the donor D and the acceptor A can be monitored by means of 1H NMR spectroscopy. A correlation between the 3J(Hβ-Hγ) coupling constants and the first hyperpolarizability is found, which very much resembles the dependence of the first hyperpolarizability on the bond length alternation. In order to elucidate the dependence of the NLO response on the conformation of triply branched NLOphores, a new series of dendritic D-π-A structures has been synthesized. A combined approach of experiments and computational predictions was applied both on the dendrimers and on the corresponding single-strand chromophores. These results demonstrate that theoretical calculations are able to reproduce experimental results and show the tendency of the effects due to structural changes.
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| 7. |
- Holtmann, J., et al.
(författare)
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Three-branched dendritic dipolar nonlinear optical chromophores, more than three times a single-strand chromophore?
- 2008
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 112:47, s. 14751-14761
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Tidskriftsartikel (refereegranskat)abstract
- To elucidate the dependence of the nonlinear optical (NLO) response on the conformation of triply branched derivatives, a new series of D-pi-A dendrimers has been synthesized. A combined approach of experiments (UV-vis and EOA measurements) and computational predictions (semiempirical and ab initio) was applied both on the dendrimers and on the corresponding single-strand chromophores. It has been shown that depending on the surrounding media the NLO activity of a flexible dendrimer can be very different. Two limiting cases are proposed: (i) the dendrimer resembles a solution of the corresponding single-strand chromophores with about 3-fold concentration, where the hyperpolarizability is the sum of the effect of three noninteracting single-strand subunits ("independent chromophores" limit); (ii) the dendrimers show nearly parallel or helical alignments of the single-strand subunits. Because of this change of conformation the NLO activity can be enhanced up to nine times the value of the "independent chromophores" limit and, thus, are more than a single strand chromophore. Conformers of dendrimers with interacting single-strand chromophores have been identified experimentally in nonpolar solutions by the EOA spectroscopy and possible structures have been revealed by numerical calculations, which could moreover show the tendency of the effects on the hyperpolarizability due to structural changes of the flexible dendritic architecture. Implications for future research developments are given to implement the "more than three times" concept.
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| 8. |
- Jiang, Jun, et al.
(författare)
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An elongation method for first principle simulations of electronic structures and electron transport properties of finite nanostructures
- 2006
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 124:21, s. 214711-
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Tidskriftsartikel (refereegranskat)abstract
- An effective elongation method has been developed to study electronic structures and electron transport properties of nanoelectronic and bioelectronic devices at a hybrid density functional theory level. It enables to treat finite nanostructures consisting of as many as 28 000 electrons and has been successfully applied to sub-120-nm-long conjugated polymers, sub-60-nm-long single-walled carbon nanotubes, and 30 base-pair DNA molecules. The calculated current-voltage characteristics of different systems are found to be in good agreement with the experiments. Some unexpected behaviors of these nanosized devices have been discovered.
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| 10. |
- Liu, Kai, 1981, et al.
(författare)
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Adsorbate vibration and resonance lifetime broadening of a cobalt adatom on a Cu(111) surface
- 2006
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Ingår i: PHYSICAL REVIEW B. ; 74:(19), s. 195433-
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Tidskriftsartikel (refereegranskat)abstract
- We present a theoretical calculation of the vibrational spectrum and resonance lifetime of Co/Cu(111) surface based on a well-tested empirical potential model. The phonon dispersions and local vibrational densities are obtained as a function of adsorbate coverage. The frequencies of the adsorbate-induced vibrational modes are in close agreement with those given by first-principles calculations and comparable with available experimental data. Analysis of the polarization distributions shows that both the frustrated translation (FT) and vertical vibration of the adsorbate are strongly coupled with atomic vibrations in the substrate. We also determined the lifetime of the FT mode caused by resonance broadening in the single-adsorbate limit. These results provide the basis for detailed study of nonadiabatic dynamics of vibrational excitation and damping of adatoms at metal surfaces.
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