Multi-site H-bridge breathers in a DNA--shaped double strand

We investigate the formation process of nonlinear vibrational modes representing broad H-bridge multi--site breathers in a DNA--shaped double strand. Within a network model of the double helix we take individual motions of the bases within the base pair plane into account. The resulting H-bridge deformations may be asymmetric with respect to the helix axis. Furthermore the covalent bonds may be deformed distinctly in the two backbone strands. Unlike other authors that add different extra terms we limit the interaction to the hydrogen bonds within each base pair and the covalent bonds along each strand. In this way we intend to make apparent the effect of the characteristic helicoidal structure of DNA. We study the energy exchange processes related with the relaxation dynamics from a non-equilibrium conformation. It is demonstrated that the twist-opening relaxation dynamics of a radially distorted double helix attains an equilibrium regime characterized by a multi-site H-bridge breather.Comment: 27 pages and 10 figure

Combined proton NMR wideline and NMR relaxometry to study SOM-water interactions of cation-treated soils

Focusing on the idea that multivalent cations affect SOM matrix and surface, we treated peat and soil samples by solutions of NaCl, CaCl2 or AlCl3. Water binding was characterized with low field 1H-NMR-relaxometry (20 MHz) and 1H wideline NMR spectroscopy (400 MHz) and compared to contact angles. From 1H wideline, we distinguished mobile water and water involved in water molecule bridges (WaMB). Large part of cation bridges (CaB) between SOM functional groups are associated with WaMB. Unexpectedly, 1H NMRrelaxometry relaxation rates suggest that cross-linking in the Al-containing peat is not stronger than that by Ca. The relation between percentage of mobile water and WaMB water in the context of wettability and 1H NMR relaxation times confirms that wettability controls the water film surrounding soil particles. Wettability is controlled by WaMB-CaB associations fixing hydrophilic functional groups in the SOM interior. This can lead to severe water repellency. Wettability decreases with increasing involvement of functional groups in CaB-WaMB associations. The results demonstrate the relevance of CaB and WaMB for the dynamics of biogeochemical and hydrological processes under field conditions, as only a few percent of organic matter can affect the physical, chemical, and biological functioning of the entire 3-phase ecosystem

Unzipping Kinetics of Double-Stranded DNA in a Nanopore

We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip each molecule was inferred from the ionic current signature of DNA traversal. The distribution of times to unzip under various experimental conditions fit a simple kinetic model. Using this model, we estimated the enthalpy barriers to unzipping and the effective charge of a nucleotide in the pore, which was considerably smaller than previously assumed.Comment: 10 pages, 5 figures, Accepted: Physics Review Letter

Stretching and relaxation dynamics in double stranded DNA

We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special attention to the opening-closing dynamics of double-stranded DNA molecules which are forced into non-equilibrium conformations. Mechanical stress imposed at one terminal end of the DNA molecule brings it into a partially opened configuration. We examine the subsequent relaxation dynamics connected with energy exchange processes between the various degrees of freedom and structural rearrangements leading to complete recombination to the double-stranded conformation. The similarities and differences between the relaxation dynamics for a planar ladder-like DNA molecule and a twisted one are discussed in detail. In this way we show that the attainment of a quasi-equilibrium regime proceeds faster in the case of the twisted DNA form than for its thus less flexible ladder counterpart. Furthermore we find that the velocity of the complete recombination of the DNA molecule is lower than the velocity imposed by the forcing unit which is in compliance with the experimental observations for the opening-closing cycle of DNA molecules.Comment: 21 pages, 9 figure

Global Optimization by Energy Landscape Paving

We introduce a novel heuristic global optimization method, energy landscape paving (ELP), which combines core ideas from energy surface deformation and tabu search. In appropriate limits, ELP reduces to existing techniques. The approach is very general and flexible and is illustrated here on two protein folding problems. For these examples, the technique gives faster convergence to the global minimum than previous approaches.Comment: to appear in Phys. Rev. Lett. (2002

In-situ formation of solidified hydrogen thin-membrane targets using a pulse tube cryocooler

An account is given of the Central Laser Facility's work to produce a cryogenic hydrogen targetry system using a pulse tube cryocooler. Due to the increasing demand for low Z thin laser targets, CLF (in collaboration with TUD) have been developing a system which allows the production of solid hydrogen membranes by engineering a design which can achieve this remotely; enabling the gas injection, condensation and solidification of hydrogen without compromising the vacuum of the target chamber. A dynamic sealing mechanism was integrated which allows targets to be grown and then remotely exposed to open vacuum for laser interaction. Further research was conducted on the survivability of the cryogenic targets which concluded that a warm gas effect causes temperature spiking when exposing the solidified hydrogen to the outer vacuum. This effect was shown to be mitigated by improving the pumping capacity of the environment and reducing the minimum temperature obtainable on the target mount. This was achieved by developing a two-stage radiation shield encased with superinsulating blanketing; reducing the base temperature from 14 0.5 K to 7.2 0.2 K about the coldhead as well as improving temperature control stability following the installation of a high-performance temperature controller and sensor apparatus. The system was delivered experimentally and in July 2014 the first laser shots were taken upon hydrogen targets in the Vulcan TAP facility.</p

Epidemiology and antifungal resistance in invasive candidiasis

The epidemiology of Candida infections has changed over the last two decades: The number of patients suffering from such infections has increased dramatically and the Candida species involved have become more numerous as Candida albicans is replaced as an infecting agent by various non-C. albicans species (NAC). At the same time, additional antifungal agents have become available. The different Candida species may vary in their susceptibility for these various antifungals. This draws more attention to in vitro susceptibility testing. Unfortunately, several different test methods exist that may deliver different results. Moreover, clinical breakpoints (CBP) that classify test results into susceptible, intermediate and resistant are controver- sial between CLSI and EUCAST. Therefore, clinicians should be aware that interpretations may vary with the test system being followed by the microbiological laboratory. Thus, knowledge of actual MIC values and pharmacokinetic properties of individual antifungal agents is important in delivering appropriate therapy to patient

Wettability of natural root mucilage studied by atomic force microscopy and contact angle: Links between nanoscale and macroscale surface properties

Organic coatings are considered as main cause of soil water repellency (SWR). This phenomenon plays a crucial role in the rhizosphere, at the interface of plant water uptake and soil hydraulics. Still, there is little knowledge about the nanoscale properties of natural soil compounds such as root-mucilage and its mechanistic effect on wettability. In this study, dried films of pure and diluted natural root-mucilage from Sorghum (Sorghum sp., moench) on glass substrates were studied in order to explore experimental and evaluation methods that allow to link between macroscopic wettability and nano-/microscopic surface properties in this model soil system. SWR was assessed by optical contact angle (CA) measurements. The nanostructure of topography and adhesion forces of the mucilage surfaces was characterized by atomic force microscopy (AFM) measurements in ambient air, using PeakForce Quantitative Nanomechanical Mapping (PFQNM). Undiluted mucilage formed hydrophobic films on the substrate with CA &gt; 90° and rather homogeneous nanostructure whereas the contact angles of diluted samples were &lt; 90°. AFM height and adhesion images displayed incomplete mucilage surface coverage for diluted samples. Hole-like structures in the film frequently exhibited increased adhesion forces. The spatial analysis of the AFM data via variograms enabled a numerical description of such ‘adhesion holes’. The use of geostatistical approaches in AFM studies of the complex surface structure of soil compounds was considered meaningful in view of the need of comprehensive analysis of large AFM image data sets that exceed the capability of comparative visual inspection. Furthermore, force curves measured with the AFM showed increased break-free distances and pull-off forces inside the observed ‘adhesion holes’, indicating enhanced capillary forces due to adsorbed water films at hydrophilic domains for ambient RH (40 ± 2 %). This offers the possibility of mapping the nanostructure of water layers on soil surfaces and assessing the consequences for wettability. The collected information on macroscopic wetting properties, nanoscale roughness and adhesion structure of the investigated surfaces in this study are discussed in view of the applicability of the mechanistic wetting models given by Wenzel and Cassie-Baxter

Single Molecule Statistics and the Polynucleotide Unzipping Transition

We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force value of order 10 pN, with different critical behavior for homopolymers and for random heteropolymers. We extend results on the disorder-averaged behavior of DNA's with random sequences to the more experimentally accessible problem of unzipping a single DNA molecule. As the applied force approaches the critical value, the double-stranded DNA unravels in a series of discrete, sequence-dependent steps that allow it to reach successively deeper energy minima. Plots of extension versus force thus take the striking form of a series of plateaus separated by sharp jumps. Similar qualitative features should reappear in micromanipulation experiments on proteins and on folded RNA molecules. Despite their unusual form, the extension versus force curves for single molecules still reveal remnants of the disorder-averaged critical behavior. Above the transition, the dynamics of the unzipping fork is related to that of a particle diffusing in a random force field; anomalous, disorder-dominated behavior is expected until the applied force exceeds the critical value for unzipping by roughly 5 pN.Comment: 40 pages, 18 figure