Molecular Dynamics Study of Charged Dendrimers in Salt-Free Solution: Effect of Counterions

Polyamidoamine (PAMAM) dendrimers, being protonated under physiological conditions, represent a promising class of nonviral, nano-sized vectors for drug and gene delivery. We performed extensive molecular dynamics simulations of a generic model dendrimer in a salt-free solution with dendrimer's terminal beads positively charged. Solvent molecules as well as counterions were explicitly included as interacting beads. We find that the size of the charged dendrimer depends non-monotonically on the strength of electrostatic interactions demonstrating a maximum when the Bjerrum length equals the diameter of a bead. Many other structural and dynamic characteristics of charged dendrimers are also found to follow this pattern. We address such a behavior to the interplay between repulsive interactions of the charged terminal beads and their attractive interactions with oppositely charged counterions. The former favors swelling at small Bjerrum lengths and the latter promotes counterion condensation. Thus, counterions can have a dramatic effect on the structure and dynamics of charged dendrimers and, under certain conditions, cannot be treated implicitly

Quiet Sun magnetic fields from simultaneous inversions of visible and infrared spectropolarimetric observations

We study the quiet Sun magnetic fields using spectropolarimetric observations of the infrared and visible Fe I lines at 6301.5, 6302.5, 15648 and 15653 A. Magnetic field strengths and filling factors are inferred by the simultaneous fit of the observed Stokes profiles under the MISMA hypothesis. The observations cover an intra-network region at the solar disk center. We analyze 2280 Stokes profiles whose polarization signals are above noise in the two spectral ranges, which correspond to 40% of the field of view. Most of these profiles can be reproduced only with a model atmosphere including 3 magnetic components with very different field strengths, which indicates the co-existence of kG and sub-kG fields in our 1.5" resolution elements. We measure an unsigned magnetic flux density of 9.6 G considering the full field of view. Half of the pixels present magnetic fields with mixed polarities in the resolution element. The fraction of mixed polarities increases as the polarization weakens. We compute the probability density function of finding each magnetic field strength. It has a significant contribution of kG field strengths, which concentrates most of the observed magnetic flux and energy. This kG contribution has a preferred magnetic polarity, while the polarity of the weak fields is balanced.Comment: 16 pages and 14 figure

Charge-induced conformational changes of dendrimers

We study the effect of chargeable monomers on the conformation of dendrimers of low generation by computer simulations, employing bare Coulomb interactions. The presence of the latter leads to an increase in size of the dendrimer due to a combined effect of electrostatic repulsion and the presence of counterions within the dendrimer, and also enhances a shell-like structure for the monomers of different generations. In the resulting structures the bond-length between monomers, especially near the center, will increase to facilitate a more effective usage of space in the outer-regions of the dendrimer.Comment: 7 pages, 12 figure

Stellar Iron Abundances: non-LTE Effects

We report new statistical equilibrium calculations for Fe I and Fe II in the atmosphere of Late-Type stars. We used atomic models for Fe I and Fe II having respectively 256 and 190 levels, as well as 2117 and 3443 radiative transitions. Photoionization cross-sections are from the Iron Project. These atomic models were used to investigate non-LTE effects in iron abundances of Late-Type stars with different atmospheric parameters. We found that most Fe I lines in metal-poor stars are formed in conditions far from LTE. We derived metallicity corrections of about 0.3 dex with respect to LTE values, for the case of stars with [Fe/H] ~ -3.0. Fe II is found not to be affected by significant non-LTE effects. The main non-LTE effect invoked in the case of Fe I is overionization by ultraviolet radiation, thus classical ionization equilibrium is far to be satisfied. An important consequence is that surface gravities derived by LTE analysis are in error and should be corrected before final abundances corrections. This apparently solves the observed discrepancy between spectroscopic surface gravities derived by LTE analyses and those derived from Hipparcos parallaxes. A table of non-LTE [Fe/H] and log g values for a sample of metal-poor late-type stars is given.Comment: 22 pages, 9 figures, 1 table, ApJ style, accepte

Signatures of small-world and scale-free properties in large computer programs

A large computer program is typically divided into many hundreds or even thousands of smaller units, whose logical connections define a network in a natural way. This network reflects the internal structure of the program, and defines the ``information flow'' within the program. We show that, (1) due to its growth in time this network displays a scale-free feature in that the probability of the number of links at a node obeys a power-law distribution, and (2) as a result of performance optimization of the program the network has a small-world structure. We believe that these features are generic for large computer programs. Our work extends the previous studies on growing networks, which have mostly been for physical networks, to the domain of computer software.Comment: 4 pages, 1 figure, to appear in Phys. Rev.

Purification and Activity Testing of the Full-Length YycFGHI Proteins of Staphylococcus aureus

Background: The YycFG two-component regulatory system (TCS) of Staphylococcus aureus represents the only essential TCS that is almost ubiquitously distributed in Gram-positive bacteria with a low G+C-content. YycG (WalK/VicK) is a sensor histidine-kinase and YycF (WalR/VicR) is the cognate response regulator. Both proteins play an important role in the biosynthesis of the cell envelope and mutations in these proteins have been involved in development of vancomycin and daptomycin resistance. Methodology/Principal Findings: Here we present high yield expression and purification of the full-length YycG and YycF proteins as well as of the auxiliary proteins YycH and YycI of Staphylococcus aureus. Activity tests of the YycG kinase and a mutated version, that harbours an Y306N exchange in its cytoplasmic PAS domain, in a detergent-micelle-model and a phosholipid-liposome-model showed kinase activity (autophosphorylation and phosphoryl group transfer to YycF) only in the presence of elevated concentrations of alkali salts. A direct comparison of the activity of the kinases in the liposomemodel indicated a higher activity of the mutated YycG kinase. Further experiments indicated that YycG responds to fluidity changes in its microenvironment. Conclusions/Significance: The combination of high yield expression, purification and activity testing of membrane and membrane-associated proteins provides an excellent experimental basis for further protein-protein interaction studies an

Determining Peptide Partitioning Properties via Computer Simulation

The transfer of polypeptide segments into lipid bilayers to form transmembrane helices represents the crucial first step in cellular membrane protein folding and assembly. This process is driven by complex and poorly understood atomic interactions of peptides with the lipid bilayer environment. The lack of suitable experimental techniques that can resolve these processes both at atomic resolution and nanosecond timescales has spurred the development of computational techniques. In this review, we summarize the significant progress achieved in the last few years in elucidating the partitioning of peptides into lipid bilayer membranes using atomic detail molecular dynamics simulations. Indeed, partitioning simulations can now provide a wealth of structural and dynamic information. Furthermore, we show that peptide-induced bilayer distortions, insertion pathways, transfer free energies, and kinetic insertion barriers are now accurate enough to complement experiments. Further advances in simulation methods and force field parameter accuracy promise to turn molecular dynamics simulations into a powerful tool for investigating a wide range of membrane active peptide phenomena