Structural basis for tetrodotoxin-resistant sodium channel binding by μ-conotoxin SmIIIA

Journal ArticleSmIIIA is a new μ-conotoxin isolated recently from Conus stercusmuscarum. Although it shares several biochemical characteristics with other μ-conotoxins (the arrangement of cysteine residues and a conserved arginine believed to interact with residues near the channel pore), it has several distinctive features, including the absence of hydroxyproline, and is the first specific antagonist of tetrodotoxin-resistant voltage-gated sodium channels to be characterized

Trajectory Deflection of Spinning Magnetic Microparticles, the Magnus Effect at the Microscale

The deflection due to the Magnus force of magnetic particles with a diameter of 80 micrometer dropping through fluids and rotating in a magnetic field was measured. With Reynolds number for this experiment around 1, we found trajectory deflections of the order of 1 degree, in agreement within measurement error with theory. This method holds promise for the sorting and analysis of the distribution in magnetic moment and particle diameter of suspensions of microparticles, such as applied in catalysis, or objects loaded with magnetic particles.Comment: 12 pages, 3 figures. Appendix with 6 figure

Efficient Reactive Brownian Dynamics

We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and disassociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion, and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently process reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as Reaction-Diffusion Master Equation (RDME) algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction- and diffusion-limited irreversible association in three dimensions. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. We find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.Comment: To appear in J. Chem. Phy

Possible experiment to check the reality of a nonequilibrium temperature

An experiment is proposed to check the physical reality of a nonequilibrium absolute temperature previously proposed from theoretical grounds in the framework of extended irreversible thermodynamics

Extending the linear-noise approximation to biochemical systems influenced by intrinsic noise and slow lognormally distributed extrinsic noise

It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from the interaction of unknown molecular components with the network and from the cell's changing environment. While there are many methods to study the effect of intrinsic noise on the system dynamics, few exist to study the influence of both types of noise. Here we show how one can extend the conventional linear-noise approximation to allow for the rapid evaluation of the molecule numbers statistics of a biochemical network influenced by intrinsic noise and by slow lognormally distributed extrinsic noise. The theory is applied to simple models of gene regulatory networks and its validity confirmed by comparison with exact stochastic simulations. In particular we show how extrinsic noise modifies the dependence of the variance of the molecule number fluctuations on the rate constants, the mutual information between input and output signalling molecules and the robustness of feed-forward loop motifs.Comment: 43 pages, 4 figure

Applying infrared thermography to soil surface temperature monitoring: Case study of a high-resolution 48 h survey in a vineyard (Anadia, Portugal)

The soil surface albedo decreases with an increasing biochar application rate as a power decay function, but the net impact of biochar application on soil temperature dynamics remains to be clarified. The objective of this study was to assess the potential of infrared thermography (IRT) sensing by monitoring soil surface temperature (SST) with a high spatiotemporal and thermal resolution in a scalable agricultural application. We monitored soil surface temperature (SST) variations over a 48 h period for three treatments in a vineyard: bare soil (plot S), 100% biochar cover (plot B), and biochar-amended topsoil (plot SB). The SST of all plots was monitored at 30 min intervals with a tripod-mounted IR thermal camera. The soil temperature at 10 cm depth in the S and SB plots was monitored continuously with a 5 min resolution probe. Plot B had greater daily SST variations, reached a higher daily temperature peak relative to the other plots, and showed a faster rate of T increase during the day. However, on both days, the SST of plot B dipped below that of the control treatment (plot S) and biochar-amended soil (plot SB) from about 18:00 onward and throughout the night. The diurnal patterns/variations in the IRT-measured SSTs were closely related to those in the soil temperature at a 10 cm depth, confirming that biochar-amended soils showed lower thermal inertia than the unamended soil. The experiment provided interesting insights into SST variations at a local scale. The case study may be further developed using fully automated SST monitoring protocols at a larger scale for a range of environmental and agricultural applications

Proximity-driven source of highly spin-polarized ac current on the basis of superconductor/weak ferromagnet/superconductor voltage-biased Josephson junction

We theoretically investigate an opportunity to implement a source of highly spin-polarized ac current on the basis of superconductor/weak ferromagnet/superconductor (SFS) voltage-biased junction in the regime of essential proximity effect and calculate the current flowing through the probe electrode tunnel coupled to the ferromagnetic interlayer region. It is shown that while the polarization of the dc current component is generally small in case of weak exchange field of the ferromagnet, there is an ac component of the current in the system. This ac current is highly spin-polarized and entirely originated from the non-equilibrium proximity effect in the interlayer. The frequency of the current is controlled by the voltage applied to SFS junction. We discuss a possibility to obtain a source of coherent ac currents with a certain phase shift between them by tunnel coupling two probe electrodes at different locations of the interlayer region.Comment: 8 pages, 5 figure