| 1. |
- Sodergren, Erica, et al.
(författare)
-
The genome of the sea urchin Strongylocentrotus purpuratus.
- 2006
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
-
Tidskriftsartikel (refereegranskat)abstract
- We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
|
|
| 2. |
- Dong, Jin Song, et al.
(författare)
-
Timed Automata Patterns
- 2008
-
Ingår i: IEEE Transactions on Software Engineering. - 0098-5589 .- 1939-3520. ; 34:6, s. 844-859
-
Tidskriftsartikel (refereegranskat)
|
|
| 3. |
- Gao, Bin, et al.
(författare)
-
Studies of bromine modified single-walled carbon nanotubes using photoelectron spectroscopy and density-functional theory
- 2006
-
Ingår i: Radiation Physics and Chemistry. - : Elsevier BV. - 0969-806X .- 1879-0895. ; 75:11, s. 1939-1942
-
Tidskriftsartikel (refereegranskat)abstract
- Many applications based on single-walled carbon nanotubes (SWNTs) require chemical modification of carbon nanotube to optimize the functionalities of the device. In this contribution we discuss the properties of SWNTs immersed in a hydrobromic acid (HBr) solution. Changes of atomic and electronic structures of bromine modified SWNTs were investigated using photoelectron spectroscopy (PES). Spectra of SWNTs before and after immersion in the HBr solution exhibit different features. To understand the mechanism of interaction between SWNTs and bromine, we performed density-functional theory calculations to reveal the structural changes, adsorption energy and chemical bonding information of SWNTs interacting with bromine. In addition, based on the Gelius model, from the molecular orbitals (MOs), we calculated ultraviolet photoelectron spectra (UPS) of SWNTs with and without functionalizing and compared them with the experiment. The present study is a first step in the understanding of the functionalization mechanism of carbon nanotubes.
|
|
| 4. |
- Hong, Junmei, et al.
(författare)
-
Focusing on RISC assembly in mammalian cells.
- 2008
-
Ingår i: Biochem Biophys Res Commun. - : Elsevier BV. - 1090-2104 .- 0006-291X. ; 368:3, s. 703-8
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- RISC (RNA-induced silencing complex) is a central protein complex in RNAi, into which a siRNA strand is assembled to become effective in gene silencing. By using an in vitro RNAi reaction based on Drosophila embryo extract, an asymmetric model was recently proposed for RISC assembly of siRNA strands, suggesting that the strand that is more loosely paired at its 5' end is selectively assembled into RISC and results in target gene silencing. However, in the present study, we were unable to establish such a correlation in cell-based RNAi assays, as well as in large-scale RNAi data analyses. This suggests that the thermodynamic stability of siRNA is not a major determinant of gene silencing in mammalian cells. Further studies on fork siRNAs showed that mismatch at the 5' end of the siRNA sense strand decreased RISC assembly of the antisense strand, but surprisingly did not increase RISC assembly of the sense strand. More interestingly, measurements of melting temperature showed that the terminal stability of fork siRNAs correlated with the positions of the mismatches, but not gene silencing efficacy. In summary, our data demonstrate that there is no definite correlation between siRNA stability and gene silencing in mammalian cells, which suggests that instead of thermodynamic stability, other features of the siRNA duplex contribute to RISC assembly in RNAi.
|
|
| 5. |
- Jaskorzynska, Bozena, et al.
(författare)
-
Dielectric and Plasmon Slot Waveguides for Photonic Integration
- 2009
-
Ingår i: ICTON 2009: 11th International Conference on Transparent Optical Networks. - NEW YORK : IEEE. ; , s. 653-656
-
Konferensbidrag (refereegranskat)abstract
- Slot waveguides formed either in high-index dielectrics or in metals attract great interest because they provide sub-wavelength confinement in the slot region. While this feature is very attractive for devices relying on stimulated emission or nonlinear effects, it does not necessarily improve the integration density. The spacing between dielectric slot waveguides is still limited by diffraction. Although for metal (plasmon) waveguides the total field can be shrunk far beyond the diffraction limit, the associated increase in propagation loss will set practical limits on both the minimum waveguide width and edge-to-edge separation. Here we compare the packing densities for 3D slot waveguides in silicon and plasmon waveguides in gold with a silicon slot. As a reference we also consider silicon photonic wire. We calculate center-to-center waveguide separations (pitch) versus cross-talk level. We show that at ca 24 dB/mu m cross-talk and requiring the attenuation length of at least 5 mu m, plasmon slot waveguides can be packed ca 3.5 times denser than silicon slot waveguides, and ca 2.5 times denser than photonic wires. We also show examples of the fabricated devices.
|
|
| 6. |
- Jaskorzynska, Bozena, et al.
(författare)
-
Tradeoff between mode confinement, loss, and cross-talk, for dielectric and metal slot waveguides
- 2009
-
Ingår i: Photonics Letters of Poland. - : Photonics Society of Poland. - 2080-2242. ; 1, s. 172-174
-
Tidskriftsartikel (refereegranskat)abstract
- Slot waveguides formed in high-index dielectrics or metals provide strong field enhancement in the slot region. When filled with nonlinear or lasing materials, they have the potential for highly efficient components for intensity dependent signal processing in integrated photonic circuits. In view of the increasing demand for high integration, metal slot waveguides have the great advantage of sub-diffraction mode confinement but they suffer from serious transmission loss. The total lateral field extent in their low-loss dielectric counterparts is, in turn, diffraction limited. Considering those tradeoffs, we show that at 24dB/ÎŒm cross-talk and the attenuation length of at least 5ÎŒm, gold slot waveguides can be spaced only ca 3.5 times denser than slot waveguides in silicon.
|
|
| 7. |
- Lin, Li-Li, et al.
(författare)
-
Effect of Aromatic Coupling on Electronic Transport in Bimolecular Junctions
- 2009
-
Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 113:32, s. 14474-14477
-
Tidskriftsartikel (refereegranskat)abstract
- We have performed a systematic first-principles study on conductance-voltage characteristics of bioligo(phenylene ethynylene)-monothiol molecular junctions as recently reported by Wu et al.[Nalure Nanotech. 2008, 3, 569]. It is found that the molecular conductance is very sensitive to the vertical distance between two molecules as well as the titled angle between two molecular planes. By comparing with experimental results, key structure parameters for bimolecular junction are determined, indicating that in the experimental devices, the vertical distance between two molecules is around 0.30 mn, the two planar molecules have a cofacial arrangement, and the length of the molecular bridge is about 2.88 nm. The underlying mechanism for electron transport in these aromatically coupled bimolecular junctions has also been discussed.
|
|
| 8. |
- Zhong, Jun, et al.
(författare)
-
Bio-nano interaction of proteins adsorbed on single-walled carbon nanotubes
- 2009
-
Ingår i: Carbon. - : Elsevier BV. - 0008-6223 .- 1873-3891. ; 47:4, s. 967-973
-
Tidskriftsartikel (refereegranskat)abstract
- We applied X-ray absorption near edge structure (XANES) spectroscopy to investigate the adsorption of proteins onto single-walled carbon nanotubes (SWCNTs). Specific XANES spectral features such as peptide C=O bonds in proteins were recognized and found to be affected by the corresponding aromatic structure of SWCNTs. Experimental data combined with first-principle calculation of the investigated nano-complex allow the understanding of adsorption mechanism and reveal that an interface interaction occurs leading to precise structural distortions of proteins. The study also demonstrates that XANES is a powerful tool to characterize structural details of proteins at the interface of complex systems.
|
|
| 9. |
- Zou, Bin, et al.
(författare)
-
Effects of field-induced geometry relaxation on the electron transport properties of 4,4'-biphenyldithiol molecular junction
- 2007
-
Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614 .- 1873-4448. ; 447:03-jan, s. 69-73
-
Tidskriftsartikel (refereegranskat)abstract
- The non-linear charge transport properties of 4,4 '-biphenyldithiol molecular junction have been studied using the generalized Green's function theory. It is shown that the torsion angle between two phenyls is slightly decreased as increase of the external voltage while the whole molecule moves slightly along the reversed direction of the electric field. Calculations indicate that the inclusion of molecular geometry relaxation can avoid a false prediction of negative differential resistance behavior. The charge redistribution under the external bias results in resistive dipoles inside the molecule. The calculated I-V curves of 4,4 '-biphenyldithiol molecular junction is consistent with experimental observations in some ways.
|
|
