Uncoupled Phosphorylation and Activation in Bacterial Chemotaxis - The 2.3 Å structure of an aspartate to lysine mutant at position 13 of CheY

An aspartate to lysine mutation at position 13 of the chemotaxis regulatory protein CheY causes a constitutive tumbly phenotype when expressed at high copy number in vivo even though the mutant protein is not phosphorylatable. These properties suggest that the D13K mutant adopts the active, signaling conformation of CheY independent of phosphorylation, so knowledge of its structure could explain the activation mechanism of CheY. The x-ray crystallographic structure of the CheY D13K mutant has been solved and refined at 2.3 Å resolution to an R-factor of 14.3%. The mutant molecule shows no significant differences in backbone conformation when compared with the wild-type, Mg2+-free structure, but there are localized changes within the active site. The side chain of lysine 13 blocks access to the active site, whereas its epsilon -amino group has no bonding interactions with other groups in the region. Also in the active site, the bond between lysine 109 and aspartate 57 is weakened, and the solvent structure is perturbed. Although the D13K mutant has the inactive conformation in the crystalline form, rearrangements in the active site appear to weaken the overall structure of that region, potentially creating a metastable state of the molecule. If a conformational change is required for signaling by CheY D13K, then it most likely proceeds dynamically, in solution

Non-Fourier heat transport in metal-dielectric core-shell nanoparticles under ultrafast laser pulse excitation

Relaxation dynamics of embedded metal nanoparticles after ultrafast laser pulse excitation is driven by thermal phenomena of different origins the accurate description of which is crucial for interpreting experimental results: hot electron gas generation, electron-phonon coupling, heat transfer to the particle environment and heat propagation in the latter. Regardingthis last mechanism, it is well known that heat transport in nanoscale structures and/or at ultrashort timescales may deviate from the predictions of the Fourier law. In these cases heat transport may rather be described by the Boltzmann transport equation. We present a numerical model allowing us to determine the electron and lattice temperature dynamics in a spherical gold nanoparticle core under subpicosecond pulsed excitation, as well as that of the surrounding shell dielectric medium. For this, we have used the electron-phonon coupling equation in the particle with a source term linked with the laser pulse absorption, and the ballistic-diffusive equations for heat conduction in the host medium. Either thermalizing or adiabatic boundary conditions have been considered at the shell external surface. Our results show that the heat transfer rate from the particle to the matrix can be significantly smaller than the prediction of Fourier's law. Consequently, the particle temperature rise is larger and its cooling dynamics might be slower than that obtained by using Fourier's law. This difference is attributed to the nonlocal and nonequilibrium heat conduction in the vicinity of the core nanoparticle. These results are expected to be of great importance for analyzing pump-probe experiments performed on single nanoparticles or nanocomposite media

Optical diode based on the chirality of guided photons

Photons are nonchiral particles: their handedness can be both left and right. However, when light is transversely confined, it can locally exhibit a transverse spin whose orientation is fixed by the propagation direction of the photons. Confined photons thus have chiral character. Here, we employ this to demonstrate nonreciprocal transmission of light at the single-photon level through a silica nanofibre in two experimental schemes. We either use an ensemble of spin-polarised atoms that is weakly coupled to the nanofibre-guided mode or a single spin-polarised atom strongly coupled to the nanofibre via a whispering-gallery-mode resonator. We simultaneously achieve high optical isolation and high forward transmission. Both are controlled by the internal atomic state. The resulting optical diode is the first example of a new class of nonreciprocal nanophotonic devices which exploit the chirality of confined photons and which are, in principle, suitable for quantum information processing and future quantum optical networks

On Calculation of Thermal Conductivity from Einstein Relation in Equilibrium MD

In equilibrium molecular dynamics, Einstein relation can be used to calculate the thermal conductivity. This method is equivalent to Green-Kubo relation and it does not require a derivation of an analytical form for the heat current. However, it is not commonly used as Green-Kubo relationship. Its wide use is hindered by the lack of a proper definition for integrated heat current (energy moment) under periodic boundary conditions. In this paper, we developed an appropriate definition for integrated heat current to calculate thermal conductivity of solids under periodic conditions. We applied this method to solid argon and silicon based systems; compared and contrasted with the Green-Kubo approach.Comment: We updated this manuscript from second version by changing the title and abstract. This paper is submitted to J. Chem. Phy

Data report: solid-phase major and minor elements and iron and sulfur species in sediments of the Anholt Basin, Baltic Sea, collected during IODP Expedition 347

In this report, we present bulk solid-phase major and minor element contents and Fe and S species in sediments from Site M0060 in the Anholt Basin recovered during Integrated Ocean Drilling Program Expedition 347 to the Baltic Sea. Site M0060 is characterized by alternating sand- and clay-/silt-dominated sediment sequences that indicate deposition under brackish-marine and limnic conditions, respectively. We use Al-normalized elemental ratios and transition metal data to characterize the different sediment sequences and to study the impact of early diagenetic processes on the abundance and reactivity of Fe oxide and Fe sulfide mineral phases across lithologic boundaries. Ratios of Fe/Al and Mn/Al exceed the continental crustal average in the clay-/silt-dominated sequences, whereas low ratios are associated with the sandy units. About 10%–20% of the total bulk Fe content is associated with Fe oxides and Fe sulfides, whereas the major Fe fraction is bound in clay minerals. The transition metals (V, Ni, Cr, and Co) correlate with the depth profile of Fe/Al, which indicates that they are adsorbed onto Fe oxides and concomitantly deposited. Sequential leaching reveals that magnetite is the most abundant Fe oxide phase. Leached contents approach 1 wt% followed by crystalline and easily reducible Fe oxides. Pyrite is the dominant Fe sulfide phase and is enriched at several lithologic boundaries that can likely be associated with the formation of pyrite. Pyrite is formed through the reaction of Fe monosulfides with (1) polysulfides and/or S0 in zones dominated by organoclastic sulfate and Fe oxide reduction and (2) sulfide released during the anaerobic oxidation of methane

Impact of deep-sea mining on redox environment, biogeochemical processes and element fluxes within and from sediments of the Clarion-Clipperton Zone, Pacific Ocean

The economic interest in deep-sea mineral resources has grown in recent years. Minerals of interest include polymetallic nodules, which occur in extensive deposits at more than 4000 m water depth in the Clarion-Clipperton Zone (CCZ), NE Pacific Ocean. In light of recent technological advances in mining equipment, the CCZ represents a prospective area for commercial deep-sea mining. In the framework of this PhD thesis, sediments from four European contract areas for the exploration of polymetallic nodules in the CCZ and one of the protected Areas of Particular Environmental Interest (APEI) were investigated. Comprehensive pore-water and solid phase data were produced for undisturbed sediments and sediments from disturbance tracks of small-scale deep sea mining experiments. The presented studies provide new insights into the spatial and temporal variation of redox zonation, biogeochemical processes and element fluxes in the sediments and the impact of potential mining activities in the CCZ

Thermodiffusion in model nanofluids by molecular dynamics simulations

In this work, a new algorithm is proposed to compute single particle (infinite dilution) thermodiffusion using Non-Equilibrium Molecular Dynamics simulations through the estimation of the thermophoretic force that applies on a solute particle. This scheme is shown to provide consistent results for simple Lennard-Jones fluids and for model nanofluids (spherical non-metallic nanoparticles + Lennard-Jones fluid) where it appears that thermodiffusion amplitude, as well as thermal conductivity, decrease with nanoparticles concentration. Then, in nanofluids in the liquid state, by changing the nature of the nanoparticle (size, mass and internal stiffness) and of the solvent (quality and viscosity) various trends are exhibited. In all cases the single particle thermodiffusion is positive, i.e. the nanoparticle tends to migrate toward the cold area. The single particle thermal diffusion 2 coefficient is shown to be independent of the size of the nanoparticle (diameter of 0.8 to 4 nm), whereas it increases with the quality of the solvent and is inversely proportional to the viscosity of the fluid. In addition, this coefficient is shown to be independent of the mass of the nanoparticle and to increase with the stiffness of the nanoparticle internal bonds. Besides, for these configurations, the mass diffusion coefficient behavior appears to be consistent with a Stokes-Einstein like law

Beyond clustering: mean-field dynamics on networks with arbitrary subgraph composition

Clustering is the propensity of nodes that share a common neighbour to be connected. It is ubiquitous in many networks but poses many modelling challenges. Clustering typically manifests itself by a higher than expected frequency of triangles, and this has led to the principle of constructing networks from such building blocks. This approach has been generalised to networks being constructed from a set of more exotic subgraphs. As long as these are fully connected, it is then possible to derive mean-field models that approximate epidemic dynamics well. However, there are virtually no results for non-fully connected subgraphs. In this paper, we provide a general and automated approach to deriving a set of ordinary differential equations, or mean-field model, that describes, to a high degree of accuracy, the expected values of system-level quantities, such as the prevalence of infection. Our approach offers a previously unattainable degree of control over the arrangement of subgraphs and network characteristics such as classical node degree, variance and clustering. The combination of these features makes it possible to generate families of networks with different subgraph compositions while keeping classical network metrics constant. Using our approach, we show that higher-order structure realised either through the introduction of loops of different sizes or by generating networks based on different subgraphs but with identical degree distribution and clustering, leads to non-negligible differences in epidemic dynamics