Effect of shear force on the separation of double stranded DNA

Using the Langevin Dynamics simulation, we have studied the effects of the shear force on the rupture of short double stranded DNA at different temperatures. We show that the rupture force increases linearly with the chain length and approaches to the asymptotic value in accordance with the experiment. The qualitative nature of these curves almost remains same for different temperatures but with a shift in the force. We observe three different regimes in the extension of covalent bonds (back bone) under the shear force.Comment: 4 pages, 4 figure

Self-energy limited ion transport in sub-nanometer channels

The current-voltage characteristics of the alpha-Hemolysin protein pore during the passage of single-stranded DNA under varying ionic strength, C, are studied experimentally. We observe strong blockage of the current, weak super-linear growth of the current as a function of voltage, and a minimum of the current as a function of C. These observations are interpreted as the result of the ion electrostatic self-energy barrier originating from the large difference in the dielectric constants of water and the lipid bilayer. The dependence of DNA capture rate on C also agrees with our model.Comment: more experimental material is added. 4 pages, 7 figure

Diamond based detectors for high temperature, high radiation environments

Single crystal CVD diamond has many desirable properties as a radiation detector; exceptional radiation hardness and physical hardness, chemical inertness, low Z (close to human tissue, good for dosimetry and transmission mode applications), wide bandgap (high temperature operation with low noise and solar blind), an intrinsic pathway to fast neutron detection through the 12C(n,α)9Be reaction. This combination of radiation hardness, temperature tolerance and ability to detect mixed radiation types with a single sensor makes diamond particularly attractive as a detector material for harsh environments such as nuclear power station monitoring (fission and fusion) and oil well logging. Effective exploitation of these properties requires the development of a metallisation scheme to give contacts that remain stable over extended periods at elevated temperatures (up to 250°C in this instance). Due to the cost of the primary detector material, computational modelling is essential to best utilise the available processing methods for optimising sensor response through geometry and conversion media configurations and to fully interpret experimental data. Monte Carlo simulations of our diamond based sensor have been developed, using MCNP6 and FLUKA2011, assessing the sensor performance in terms of spectral response and overall efficiency as a function of the detector and converter geometry. Sensors with varying metallisation schemes for high temperature operation have been fabricated at Brunel University London and by Micron Semiconductor Limited. These sensors have been tested under a varied set of conditions including irradiation with fast neutrons and alpha particles at high temperatures. The presented study indicates that viable metallisation schemes for high temperature contacts have been successfully developed and the modelling results, supported by preliminary experimental data from partners, indicate that the simulations provide a reasonable representation of detector response.For funding the academic and industrial efforts (respectively) on this project the aauthors acknowledge the EPSRC (Engineering and Physical Sciences Research Council) (Grant no: EP/L504671/1) and InnovateUK (Grant no: HTRaD 101427).EPSRC (Engineering and Physical Sciences Research Council) (Grant no: EP/L504671/1); InnovateUK (Grant no: HTRaD 101427)

Variations in water use by a mature mangrove of Avicennia germinans, French Guiana

In the tropical intertidal zones, little is known on water uptake by mangroves. Transpiration rates are generally measured at leaf level, but few studies exist on water use at tree or stand levels. The objective of this study was to measure sap flow in trees of different sizes to appreciate the range of variation in water use that may exist in a site dominated by 80% mature Avicennia germinans. The results showed that from the dry to the wet season the mean water use increased from 3.2 to 5.3 dm3 d−1 in small trees (DBH ∼ 13 cm), from 11.5 to 30.8 dm3 d−1 in medium trees (∼24 cm) and from 40.8 to 64.1 dm3 d−1 in large ones (∼45 cm). Sapwood remained active up to a depth of 8 cm with radial variations within the stem. Weak correlations were obtained with VPD and net radiation. This study confirmed that transpiration was larger under low levels of salinity. Water use at stand level (∼1900 living stems ha−1) was estimated to be in the range of 5.8 to 11.8 m3 ha−1 d−1 according to the season

Numerical Calculations of the B1g Raman Spectrum of the Two-Dimensional Heisenberg Model

The B1g Raman spectrum of the two-dimensional S=1/2 Heisenberg model is discussed within Loudon-Fleury theory at both zero and finite temperature. The exact T=0 spectrum for lattices with up to 6*6 sites is computed using Lanczos exact diagonalization. A quantum Monte Carlo (QMC) method is used to calculate the corresponding imaginary-time correlation function and its first two derivatives for lattices with up to 16*16 spins. The imaginary-time data is continued to real frequency using the maximum-entropy method, as well as a fit based on spinwave theory. The numerical results are compared with spinwave calculations for finite lattices. There is a surprisingly large change in the exact spectrum going from 4*4 to 6*6 sites. In the former case there is a single dominant two-magnon peak at frequency w/J appr. 3.0, whereas in the latter case there are two approximately equal-sized peaks at w/J appr. 2.7 and 3.9. This is in good qualitative agreement with the spinwave calculations including two-magnon processes on the same lattices. Both the Lanczos and the QMC results indicate that the actual infinite-size two-magnon profile is broader than the narrow peak obtained in spinwave theory, but the positions of the maxima agree to within a few percent. The higher-order contributions present in the numerical results are merged with the two-magnon profile and extend up to frequencies w/J appr. 7. The first three frequency cumulants of the spectrum are in excellent agreement with results previously obtained from a series expansion around the Ising limit. Typical experimental B1g$ spectra for La2CuO4 are only slightly broader than what we obtain here. The exchange constant extracted from the peak position is J appr. 1400K, in good agreement with values obtained from neutron scattering and NMR experiments.Comment: 15 pages, Revtex, 13 PostScript figure

Attraction between DNA molecules mediated by multivalent ions

The effective force between two parallel DNA molecules is calculated as a function of their mutual separation for different valencies of counter- and salt ions and different salt concentrations. Computer simulations of the primitive model are used and the shape of the DNA molecules is accurately modelled using different geometrical shapes. We find that multivalent ions induce a significant attraction between the DNA molecules whose strength can be tuned by the averaged valency of the ions. The physical origin of the attraction is traced back either to electrostatics or to entropic contributions. For multivalent counter- and monovalent salt ions, we find a salt-induced stabilization effect: the force is first attractive but gets repulsive for increasing salt concentration. Furthermore, we show that the multivalent-ion-induced attraction does not necessarily correlate with DNA overcharging.Comment: 51 pages and 13 figure

Uncovering the underlying mechanisms and whole-brain dynamics of deep brain stimulation for Parkinson's disease

Deep brain stimulation (DBS) for Parkinson's disease is a highly effective treatment in controlling otherwise debilitating symptoms. Yet the underlying brain mechanisms are currently not well understood. Whole-brain computational modeling was used to disclose the effects of DBS during resting-state functional Magnetic Resonance Imaging in ten patients with Parkinson's disease. Specifically, we explored the local and global impact that DBS has in creating asynchronous, stable or critical oscillatory conditions using a supercritical bifurcation model. We found that DBS shifts global brain dynamics of patients towards a Healthy regime. This effect was more pronounced in very specific brain areas such as the thalamus, globus pallidus and orbitofrontal regions of the right hemisphere (with the left hemisphere not analyzed given artifacts arising from the electrode lead). Global aspects of integration and synchronization were also rebalanced. Empirically, we found higher communicability and coherence brain measures during DBS-ON compared to DBS-OFF. Finally, using our model as a framework, artificial in silico DBS was applied to find potential alternative target areas for stimulation and whole-brain rebalancing. These results offer important insights into the underlying large-scale effects of DBS as well as in finding novel stimulation targets, which may offer a route to more efficacious treatmentsIn this work, Gustavo Deco is supported by the ERC Advanced Grant: DYSTRUCTURE (n. 295129), by the Spanish Research Project PSI2016-75688-P and by the the European Union's Horizon 2020 research and innovation programme under grant agreement n. 720270 (HBP SGA1). Morten Kringelbach is supported by the ERC Consolidator Grant CAREGIVING (n. 615539) and the Center for Music in the Brain, funded by the Danish National Research Foundation (DNRF117). Victor M Saenger is supported by the Research Personnel Training program PSI2013-42091-P funded by the Spanish Ministry of Economy and Competitiveness.info:eu-repo/semantics/publishedVersio

Chromatin: a tunable spring at work inside chromosomes

This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give for the first time the complete set of elastic constants (twist and bend persistence lengths, stretch modulus and twist-stretch coupling constant) of the so-called 30-nm chromatin fiber, in terms of DNA elastic properties and geometric properties of the fiber assembly. The computation naturally embeds the fiber within a current analytical model known as the ``extensible worm-like rope'', allowing a straightforward prediction of the force-extension curves. We show that these elastic constants are strongly sensitive to the linker length, up to 1 bp, or equivalently to its twist, and might locally reach very low values, yielding a highly flexible and extensible domain in the fiber. In particular, the twist-stretch coupling constant, reflecting the chirality of the chromatin fiber, exhibits steep variations and sign changes when the linker length is varied. We argue that this tunable elasticity might be a key feature for chromatin function, for instance in the initiation and regulation of transcription.Comment: 38 pages 15 figure