Two-level system with a thermally fluctuating transfer matrix element: Application to the problem of DNA charge transfer

Charge transfer along the base-pair stack in DNA is modeled in terms of thermally-assisted tunneling between adjacent base pairs. Central to our approach is the notion that tunneling between fluctuating pairs is rate-limited by the requirement of their optimal alignment. We focus on this aspect of the process by modeling two adjacent base pairs in terms of a classical damped oscillator subject to thermal fluctuations as described by a Fokker-Planck equation. We find that the process is characterized by two time scales, a result that is in accord with experimental findings.Comment: original file is revtex4, 10 pages, three eps figure

A non-variational approach to nonlinear stability in stellar dynamics applied to the King model

In previous work by Y. Guo and G. Rein, nonlinear stability of equilibria in stellar dynamics, i.e., of steady states of the Vlasov-Poisson system, was accessed by variational techniques. Here we propose a different, non-variational technique and use it to prove nonlinear stability of the King model against a class of spherically symmetric, dynamically accessible perturbations. This model is very important in astrophysics and was out of reach of the previous techniques

Leaf shape influences the scaling of leaf dry mass vs. area: a test case using bamboos

Key message A highly significant and positive scaling relationship between bamboo leaf dry mass and leaf surface area was observed; leaf shape (here, represented by the quotient of leaf width and length) had a significant influence on the scaling exponent of leaf dry mass vs. area. Context The scaling of leaf dry mass vs. leaf area is important for understanding how plants effectively intercept sunlight and invest carbon to do so. However, comparatively few, if any, studies have focused on whether leaf shape influences this scaling relationship. Aims In order to explore the effects of leaf shape on the scaling relationship between leaf dry mass and area, we examined 101 species, varieties, forms, and cultivars of bamboo growing in China and identified the relationship between the scaling exponent of leaf dry mass vs. area and leaf shape. This taxon was used because its leaf shape is conserved across species and, therefore, easily quantified. Methods Ten thousand and forty-five leaves from 101 bamboo species, varieties, forms, and cultivars growing in China were collected, and leaf dry mass, the quotient of leaf width and length, leaf area, and leaf dry mass per unit area were measured. The effect of leaf shape that can be easily quantified using the quotient of leaf width and length on the relevant and ecologically important scaling exponents was explored using this data base. Results Leaf dry mass and area differed significantly across bamboo genera, and even within the same genus. However, a statistically robust log-log linear and positive scaling relationship was observed for mass and area with a 1.115 scaling exponent (95% CI = 1.107, 1.122; r(2) = 0.907). Leaf shape had a significant influence on the numerical values of the scaling exponent of leaf dry mass vs. area. When the median of the quotient of leaf width and length was below 0.125, the numerical value of the scaling exponent increased with increasing quotient of leaf width and length. When the median of the quotient of leaf width and length was above 0.125, the scaling exponent numerically decreased toward 1.0. Conclusion We show, for the first time, that a significant relationship exists between leaf shape and the numerical values of scaling exponents governing the scaling of leaf dry mass with respect to leaf area. In addition, we show that with the quotient of leaf width and length increasing mean LMA increases, which implies a negative correlation between mean LMA and the estimated exponent of leaf dry mass vs. area for the grouped data based on the sorted quotients of leaf width and length

An Integrated Imaging Approach to the Study of Oxidative Stress Generation by Mitochondrial Dysfunction in Living Cells

BACKGROUND: The mechanisms of action of many environmental agents commonly involve oxidative stress resulting from mitochondrial dysfunction. Zinc is a common environmental metallic contaminant that has been implicated in a variety of oxidant-dependent toxicological responses. Unlike ions of other transition metals such as iron, copper, and vanadium, Zn(2+) does not generate reactive oxygen species (ROS) through redox cycling. OBJECTIVE: To characterize the role of oxidative stress in zinc-induced toxicity. METHODS: We used an integrated imaging approach that employs the hydrogen peroxide (H2O2)-specific fluorophore Peroxy Green 1 (PG1), the mitochondrial potential sensor 5,5 ,6,6 -tetrachloro-1,1 ,3,3 -tetraethylbenzimidazolylcarbocyanine iodide (JC-1), and the mitochondria-targeted form of the redox-sensitive genetically encoded fluorophore MTroGFP1 in living cells. RESULTS: Zinc treatment in the presence of the Zn(2+) ionophore pyrithione of A431 skin carcinoma cells preloaded with the H(2)O(2)-specific indicator PG1 resulted in a significant increase in H(2)O(2) production that could be significantly inhibited with the mitochondrial inhibitor carbonyl cyanide 3-chlorophenylhydrazone. Mitochondria were further implicated as the source of zinc-induced H(2)O(2) formation by the observation that exposure to zinc caused a loss of mitochondrial membrane potential. Using MTroGFP1, we showed that zinc exposure of A431 cells induces a rapid loss of reducing redox potential in mitochondria. We also demonstrated that zinc exposure results in rapid swelling of mitochondria isolated from mouse hearts. CONCLUSION: Taken together, these findings show a disruption of mitochondrial integrity, H(2)O(2) formation, and a shift toward positive redox potential in cells exposed to zinc. These data demonstrate the utility of real-time, live-cell imaging to study the role of oxidative stress in toxicological responses

A Single Laser System for Ground-State Cooling of 25-Mg+

We present a single solid-state laser system to cool, coherently manipulate and detect $^{25}$Mg$^+$ ions. Coherent manipulation is accomplished by coupling two hyperfine ground state levels using a pair of far-detuned Raman laser beams. Resonant light for Doppler cooling and detection is derived from the same laser source by means of an electro-optic modulator, generating a sideband which is resonant with the atomic transition. We demonstrate ground-state cooling of one of the vibrational modes of the ion in the trap using resolved-sideband cooling. The cooling performance is studied and discussed by observing the temporal evolution of Raman-stimulated sideband transitions. The setup is a major simplification over existing state-of-the-art systems, typically involving up to three separate laser sources

Rate-equation calculations of the current flow through two-site molecular device and DNA-based junction

Here we present the calculations of incoherent current flowing through the two-site molecular device as well as the DNA-based junction within the rate-equation approach. Few interesting phenomena are discussed in detail. Structural asymmetry of two-site molecule results in rectification effect, which can be neutralized by asymmetric voltage drop at the molecule-metal contacts due to coupling asymmetry. The results received for poly(dG)-poly(dC) DNA molecule reveal the coupling- and temperature-independent saturation effect of the current at high voltages, where for short chains we establish the inverse square distance dependence. Besides, we document the shift of the conductance peak in the direction to higher voltages due to the temperature decrease.Comment: 12 pages, 6 figure

Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations

We present a method to automatically identify and track nuclei in time-lapse microscopy recordings of entire developing embryos. The method combines deep learning and global optimization. On a mouse dataset, it reconstructs 75.8% of cell lineages spanning 1 h, as compared to 31.8% for the competing method. Our approach improves understanding of where and when cell fate decisions are made in developing embryos, tissues, and organs

A first-principles approach to electrical transport in atomic-scale nanostructures

We present a first-principles numerical implementation of Landauer formalism for electrical transport in nanostructures characterized down to the atomic level. The novelty and interest of our method lies essentially on two facts. First of all, it makes use of the versatile Gaussian98 code, which is widely used within the quantum chemistry community. Secondly, it incorporates the semi-infinite electrodes in a very generic and efficient way by means of Bethe lattices. We name this method the Gaussian Embedded Cluster Method (GECM). In order to make contact with other proposed implementations, we illustrate our technique by calculating the conductance in some well-studied systems such as metallic (Al and Au) nanocontacts and C-atom chains connected to metallic (Al and Au) electrodes. In the case of Al nanocontacts the conductance turns out to be quite dependent on the detailed atomic arrangement. On the contrary, the conductance in Au nanocontacts presents quite universal features. In the case of C chains, where the self-consistency guarantees the local charge transfer and the correct alignment of the molecular and electrode levels, we find that the conductance oscillates with the number of atoms in the chain regardless of the type of electrode. However, for short chains and Al electrodes the even-odd periodicity is reversed at equilibrium bond distances.Comment: 14 pages, two-column format, submitted to PR