Energetic preference and topological constraint effects on the formation of DNA twisted toroidal bundles.

DNA toroids are compact torus-shaped bundles formed by one or multiple DNA molecules being condensed from the solution due to various condensing agents. It has been shown that the DNA toroidal bundles are twisted. However, the global conformations of DNA inside these bundles are still not well understood. In this study, we investigate this issue by solving different models for the toroidal bundles and performing replica-exchange molecular dynamics (REMD) simulations for self-attractive stiff polymers of various chain lengths. We find that a moderate degree of twisting is energetically favorable for toroidal bundles, yielding optimal configurations of lower energies than for other bundles corresponding to spool-like and constant radius of curvature arrangements. The REMD simulations show that the ground states of the stiff polymers are twisted toroidal bundles with the average twist degrees close to those predicted by the theoretical model. Constant-temperature simulations show that twisted toroidal bundles can be formed through successive processes of nucleation, growth, quick tightening, and slow tightening of the toroid, with the two last processes facilitating the polymer threading through the toroid's hole. A relatively long chain of 512 beads has an increased dynamical difficulty to access the twisted bundle states due to the polymer's topological constraint. Interestingly, we also observed significantly twisted toroidal bundles with a sharp U-shaped region in the polymer conformation. It is suggested that this U-shaped region makes the formation of twisted bundles easier by effectively reducing the polymer length. This effect can be equivalent to having multiple chains in the toroid.

Childhood hospitalisation and related deaths in Hanoi, Vietnam: a tertiary hospital database analysis from 2007 to 2014.

OBJECTIVE: To describe hospital admission and emergency visit rates and potential risk factors of prolonged hospitalisation and death among children in Hanoi. STUDY DESIGN: A retrospective study reviewed 212 216 hospitalisation records of children (aged 0-17) who attended the Vietnam National Children's Hospital in Hanoi between 2007 and 2014. Four indicators were analysed and reported: (1) rate of emergency hospital visits, (2) rate of hospitalisation, (3) length of hospital stay and (4) number of deaths. The risk of prolonged hospitalisation was investigated using Cox proportion hazard, and the risk of death was investigated through logistic regressions. RESULTS: During 2007-2014, the average annual rate of emergency visits was 2.2 per 1000 children and the rate of hospital admissions was 13.8 per 1000 children. The annual rates for infants increased significantly by 3.9 per 1000 children during 2012-2014 for emergency visits and 25.1 per 1000 children during 2009-2014 for hospital admissions. Digestive diseases (32.0%) and injuries (30.2%) were common causes of emergency visits, whereas respiratory diseases (37.7%) and bacterial and parasitic infections (19.8%) accounted for most hospital admissions. Patients with mental and behavioural disorders remained in the hospital the longest (median=12 days). Morbidities related to the perinatal period dominated mortality causes (32.5% of deaths among those admitted to the hospital. Among the respiratory diseases, pneumonia was the leading cause of both prolonged hospitalisation and death. CONCLUSIONS: Preventable health problems, such as common bacterial infections and respiratory diseases, were the primary causes of hospital admissions in Vietnam.

On the density of states of circular graphene quantum dots.

We suggest a simple approach to calculate the local density of states that effectively applies to any structure created by an axially symmetric potential on a continuous graphene sheet such as circular graphene quantum dots or rings. Calculations performed for the graphene quantum dot studied in a recent scanning tunneling microscopy measurement (Gutierrez et al 2016 Nat. Phys. 12 1069-75) show an excellent experimental-theoretical agreement.

Mixed-Metal Zeolitic Imidazolate Frameworks and their Selective Capture of Wet Carbon Dioxide over Methane.

A presynthesized, square planar copper imidazole complex, [Cu(imidazole)4](NO3)2, was utilized as a precursor in the synthesis of a new series of zeolitic imidazolate frameworks, termed ZIF-202, -203, and -204. The structures of all three members were solved by single-crystal X-ray diffraction analysis, which revealed ZIF-203 and -204 having successfully integrated square planar units within the backbones of their respective frameworks. As a result of this unit, the structures of both ZIF-203 and -204 were found to adopt unprecedented three-dimensional nets, namely, ntn and thl, respectively. One member of this series, ZIF-204, was demonstrated to be highly porous, exhibit exceptional stability in water, and selectively capture CO2 over CH4 under both dry and wet conditions without any loss in performance over three cycles. Remarkably, the regeneration of ZIF-204 was performed under the mild conditions of flowing a pure N2 gas through the material at ambient temperature.

The transfer matrix approach to circular graphene quantum dots.

We adapt the transfer matrix (T-matrix) method originally designed for one-dimensional quantum mechanical problems to solve the circularly symmetric two-dimensional problem of graphene quantum dots. Similar to one-dimensional problems, we show that the generalized T-matrix contains rich information about the physical properties of these quantum dots. In particular, it is shown that the spectral equations for bound states as well as quasi-bound states of a circular graphene quantum dot and related quantities such as the local density of states and the scattering coefficients are all expressed exactly in terms of the T-matrix for the radial confinement potential. As an example, we use the developed formalism to analyse physical aspects of a graphene quantum dot induced by a trapezoidal radial potential. Among the obtained results, it is in particular suggested that the thermal fluctuations and electrostatic disorders may appear as an obstacle to controlling the valley polarization of Dirac electrons.

Three-Dimensional Metal-Catecholate Frameworks and Their Ultrahigh Proton Conductivity.

A series of three-dimensional (3D) extended metal catecholates (M-CATs) was synthesized by combining the appropriate metal salt and the hexatopic catecholate linker, H6THO (THO(6-) = triphenylene-2,3,6,7,10,11-hexakis(olate)) to give Fe(THO)·Fe(SO4) (DMA)3, Fe-CAT-5, Ti(THO)·(DMA)2, Ti-CAT-5, and V(THO)·(DMA)2, V-CAT-5 (where DMA = dimethylammonium). Their structures are based on the srs topology and are either a 2-fold interpenetrated (Fe-CAT-5 and Ti-CAT-5) or noninterpenetrated (V-CAT-5) porous anionic framework. These examples are among the first catecholate-based 3D frameworks. The single crystal X-ray diffraction structure of the Fe-CAT-5 shows bound sulfate ligands with DMA guests residing in the pores as counterions, and thus ideally suited for proton conductivity. Accordingly, Fe-CAT-5 exhibits ultrahigh proton conductivity (5.0 × 10(-2) S cm(-1)) at 98% relative humidity (RH) and 25 °C. The coexistence of sulfate and DMA ions within the pores play an important role in proton conductivity as also evidenced by the lower conductivity values found for Ti-CAT-5 (8.2 × 10(-4) S cm(-1) at 98% RH and 25 °C), whose structure only contained DMA guests.

Selective capture of carbon dioxide under humid conditions by hydrophobic chabazite-type zeolitic imidazolate frameworks.

Hydrophobic zeolitic imidazolate frameworks (ZIFs) with the chabazite (CHA) topology are synthesized by incorporating two distinct imidazolate links. Zn(2-mIm)0.86 (bbIm)1.14 (ZIF-300), Zn(2-mIm)0.94 (cbIm)1.06 (ZIF-301), and Zn(2-mIm)0.67 (mbIm)1.33 (ZIF-302), where 2-mIm = 2-methylimidazolate, bbIm = 5(6)-bromobenzimidazolate, cbIm = 5(6)-chlorobenzimidazolate, and mbIm = 5(6)-methylbenzimidazolate, were prepared by reacting zinc nitrate tetrahydrate and 2-mIm with the respective bIm link in a mixture of N,N-dimethylformamide (DMF) and water. Their structures were determined by single-crystal X-ray diffraction and their permanent porosity shown. All of these structures are hydrophobic as confirmed by water adsorption isotherms. All three ZIFs are equally effective at the dynamic separation of CO2 from N2 under both dry and humid conditions without any loss of performance over three cycles and can be regenerated simply by using a N2 flow at ambient temperature.

From toroidal to rod-like condensates of semiflexible polymers.

The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA, and the form of the long-range interactions between neighboring molecules, using analytical theory supported by Monte Carlo simulations. Both conformations considered are characterized by a local nematic order with hexagonal packing symmetry of neighboring DNA molecules, but differ in global configuration of the chain and the distribution of its curvature as it wraps around to form a condensate. The long-range interactions driving the DNA condensation are assumed to be of the form pertaining to the attractive depletion potential as well as the attractive counterion induced soft potential. In the stiffness-length plane we find a transition between rod-like to toroid condensate for increasing stiffness at a fixed chain length L. Strikingly, the transition line is found to have a L(1/3) dependence irrespective of the details of the long-range interactions between neighboring molecules. When realistic DNA parameters are used, our description reproduces rather well some of the experimental features observed in DNA condensates.

A model for ballistic transport across locally gated graphene bipolar junctions.

An alternative model of Gaussian-type potential is suggested, which allows us to describe the transport properties of the locally gated graphene bipolar junctions in all possible charge density regimes, including a smooth transition between the regimes. Using this model we systematically study the transmission probability, the resistances, the current-voltage characteristics, and the shot noise for ballistic graphene bipolar junctions of different top gate lengths under largely varying gate voltages. Obtained results on the one hand show multifarious manifestations of the Klein tunneling and the interference effects, and on the other hand describe well typical experimental data on the junction resistances.