Brownian dynamics simulation of DNA condensation.

DNA condensation observed in vitro with the addition of polyvalent counterions is due to intermolecular attractive forces. We introduce a quantitative model of these forces in a Brownian dynamics simulation in addition to a standard mean-field Poisson-Boltzmann repulsion. The comparison of a theoretical value of the effective diameter calculated from the second virial coefficient in cylindrical geometry with some experimental results allows a quantitative evaluation of the one-parameter attractive potential. We show afterward that with a sufficient concentration of divalent salt (typically approximately 20 mM MgCl(2)), supercoiled DNA adopts a collapsed form where opposing segments of interwound regions present zones of lateral contact. However, under the same conditions the same plasmid without torsional stress does not collapse. The condensed molecules present coexisting open and collapsed plectonemic regions. Furthermore, simulations show that circular DNA in 50% methanol solutions with 20 mM MgCl(2) aggregates without the requirement of torsional energy. This confirms known experimental results. Finally, a simulated DNA molecule confined in a box of variable size also presents some local collapsed zones in 20 mM MgCl(2) above a critical concentration of the DNA. Conformational entropy reduction obtained either by supercoiling or by confinement seems thus to play a crucial role in all forms of condensation of DNA.

Empirical studies of cloud effects on UV radiation: A review

The interest in solar ultraviolet (UV) radiation from the scientific community and the general population has risen significantly in recent years because of the link between increased UV levels at the Earth's surface and depletion of ozone in the stratosphere. As a consequence of recent research, UV radiation climatologies have been developed, and effects of some atmospheric constituents (such as ozone or aerosols) have been studied broadly. Correspondingly, there are well-established relationships between, for example, total ozone column and UV radiation levels at the Earth's surface. Effects of clouds, however, are not so well described, given the intrinsic difficulties in properly describing cloud characteristics. Nevertheless, the effect of clouds cannot be neglected, and the variability that clouds induce on UV radiation is particularly significant when short timescales are involved. In this review we show, summarize, and compare several works that deal with the effect of clouds on UV radiation. Specifically, works reviewed here approach the issue from the empirical point of view: Some relationship between measured UV radiation in cloudy conditions and cloud-related information is given in each work. Basically, there are two groups of methods: techniques that are based on observations of cloudiness (either from human observers or by using devices such as sky cameras) and techniques that use measurements of broadband solar radiation as a surrogate for cloud observations. Some techniques combine both types of information. Comparison of results from different works is addressed through using the cloud modification factor (CMF) defined as the ratio between measured UV radiation in a cloudy sky and calculated radiation for a cloudless sky. Typical CMF values for overcast skies range from 0.3 to 0.7, depending both on cloud type and characteristics. Despite this large dispersion of values corresponding to the same cloud cover, it is clear that the cloud effect on UV radiation is 15–45% lower than the cloud effect on total solar radiation. The cloud effect is usually a reducing effect, but a significant number of works report an enhancement effect (that is increased UV radiation levels at the surface) due to the presence of clouds. The review concludes with some recommendations for future studies aimed to further analyze the cloud effects on UV radiation

Feature Extraction from Whole-Sky Ground-Based Images for Cloud-Type Recognition

Several features that can be extracted from digital images of the sky and that can be useful for cloud-type classification of such images are presented. Some features are statistical measurements of image texture, some are based on the Fourier transform of the image and, finally, others are computed from the image where cloudy pixels are distinguished from clear-sky pixels. The use of the most suitable features in an automatic classification algorithm is also shown and discussed. Both the features and the classifier are developed over images taken by two different camera devices, namely, a total sky imager (TSI) and a whole sky imager (WSC), which are placed in two different areas of the world (Toowoomba, Australia; and Girona, Spain, respectively). The performance of the classifier is assessed by comparing its image classification with an a priori classification carried out by visual inspection of more than 200 images from each camera. The index of agreement is 76% when five different sky conditions are considered: clear, low cumuliform clouds, stratiform clouds (overcast), cirriform clouds, and mottled clouds (altocumulus, cirrocumulus). Discussion on the future directions of this research is also presented, regarding both the use of other features and the use of other classification techniques

Optical nebulosities associated with IRAS sources in dense cloud cores

I, H¿ and [SII] CCD images of the regions around 4 young IRAS sources embedded in the dense molecular cloud cores CB 6, CB 39, AFGL 5142, and L 1251 are presented. Reflection nebulosities are found in all 4 regions. Herbig-Haro objects are detected in AFGL 5142 and L 1251. In both cases, the HH objects are new discoveries.

Activation of c-Jun in the nuclei of neurons of the CA-1 in thrombin preconditioning occurs via PAR-1.

Recently it has been shown that the c-Jun N-terminal kinase (JNK) plays a role in thrombin preconditioning (TPC) in vivo and in vitro. To investigate further the pathways involved in TPC, we performed an immunohistochemical study in hippocampal slice cultures. Here we show that the major target of JNK, the AP-1 transcription factor c-Jun, is activated by phosphorylation in the nuclei of neurons of the CA1 region by using phospho-specific antibodies against the two JNK phosphorylation sites. The activation is early and transient, peaking at 90 min and not present by 3 hr after low-dose thrombin administration. Treatment of cultures with a synthetic thrombin receptor agonist results in the same c-Jun activation profile and protection against subsequent OGD, both of which are prevented by specific JNK inhibitors, showing that thrombin signals through PAR-1 to JNK. By using an antibody against the Ser 73 phosphorylation site of c-Jun, we identify possible additional TPC substrates.

Condensation of helium in nanoscopic alkali wedges at zero temperature

We present a complete calculation of the structure of liquid 4He confined to a concave nanoscopic wedge, as a function of the opening angle of the walls. This is achieved within a finite-range density functional formalism. The results here presented, restricted to alkali metal substrates, illustrate the change in meniscus shape from rather broad to narrow wedges on weak and strong alkali adsorbers, and we relate this change to the wetting behavior of helium on the corresponding planar substrate. As the wedge angle is varied, we find a sequence of stable states that, in the case of cesium, undergo one filling and one emptying transition at large and small openings, respectively. A computationally unambiguous criterion to determine the contact angle of 4He on cesium is also proposed.

Momentum distribution in nuclear matter and finite nuclei

A simple method is presented to evaluate the effects of short-range correlations on the momentum distribution of nucleons in nuclear matter within the framework of the Greens function approach. The method provides a very efficient representation of the single-particle Greens function for a correlated system. The reliability of this method is established by comparing its results to those obtained in more elaborate calculations. The sensitivity of the momentum distribution on the nucleon-nucleon interaction and the nuclear density is studied. The momentum distributions of nucleons in finite nuclei are derived from those in nuclear matter using a local-density approximation. These results are compared to those obtained directly for light nuclei like 16O.

Nuclei beyond the drip line

In the Thomas-Fermi model, calculations are presented for nuclei beyond the nuclear drip line at zero temperature. These nuclei are in equilibrium by the presence of an external gas, as may be envisaged in the astrophysical scenario. We find that there is a limiting asymmetry beyond which these nuclei can no longer be made stable.

Delta(1232) isobar excitations and the ground state of nuclei

The influence of Delta isobar components on the ground-state properties of nuclear systems is investigated for nuclear matter as well as finite nuclei. Many-body wave functions, including isobar configurations and binding energies, are evaluated employing the framework of the coupled-cluster theory. It is demonstrated that the effect of isobar configurations depends in a rather sensitive way on the model used for the baryon-baryon interaction. As examples for realistic baryon-baryon interactions with explicit inclusion of isobar channels we use the local (V28) and nonlocal meson-exchange potentials (Bonn2000) but also a model recently developed by the Salamanca group, which is based on a quark picture. The differences obtained for the nuclear observables are related to the treatment of the interaction, the pi-exchange contributions in particular, at high momentum transfers.

Isospin-rich nuclei in neutron star matter

Stability of nuclei beyond the drip lines in the presence of an enveloping gas of nucleons and electrons, as prevailing in the inner crust of a neutron star, is studied in the temperature-dependent Thomas-Fermi framework. A limiting asymmetry in the isospin space beyond which nuclei cannot exist emerges from the calculations. The ambient conditions such as temperature, baryon density, and neutrino concentration under which these exotic nuclear systems can be formed are studied in some detail.

Superheavy nuclei in relativistic effective Lagrangian model

Isotopic and isotonic chains of superheavy nuclei are analyzed to search for spherical double shell closures beyond Z=82 and N=126 within the new effective field theory model of Furnstahl, Serot, and Tang for the relativistic nuclear many-body problem. We take into account several indicators to identify the occurrence of possible shell closures, such as two-nucleon separation energies, two-nucleon shell gaps, average pairing gaps, and the shell correction energy. The effective Lagrangian model predicts N=172 and Z=120 and N=258 and Z=120 as spherical doubly magic superheavy nuclei, whereas N=184 and Z=114 show some magic character depending on the parameter set. The magicity of a particular neutron (proton) number in the analyzed mass region is found to depend on the number of protons (neutrons) present in the nucleus.

Atomic parity nonconservation, neutron radii, and effective field theories of nuclei

Accurately calibrated effective field theories are used to compute atomic parity nonconserving (APNC) observables. Although accurately calibrated, these effective field theories predict a large spread in the neutron skin of heavy nuclei. Whereas the neutron skin is strongly correlated to numerous physical observables, in this contribution we focus on its impact on new physics through APNC observables. The addition of an isoscalar-isovector coupling constant to the effective Lagrangian generates a wide range of values for the neutron skin of heavy nuclei without compromising the success of the model in reproducing well-constrained nuclear observables. Earlier studies have suggested that the use of isotopic ratios of APNC observables may eliminate their sensitivity to atomic structure. This leaves nuclear structure uncertainties as the main impediment for identifying physics beyond the standard model. We establish that uncertainties in the neutron skin of heavy nuclei are at present too large to measure isotopic ratios to better than the 0.1% accuracy required to test the standard model. However, we argue that such uncertainties will be significantly reduced by the upcoming measurement of the neutron radius in 208^Pb at the Jefferson Laboratory.