Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

Microbial communities are complex dynamical systems harbouring many species interacting together to implement higher-level functions. Among these higher-level functions, conversion of organic matter into simpler building blocks by microbial communities underpins biogeochemical cycles and animal and plant nutrition, and is exploited in biotechnology. A prerequisite to predicting the dynamics and stability of community-mediated metabolic conversions is the development and calibration of appropriate mathematical models. Here, we present a generic, extendable thermodynamic model for community dynamics and calibrate a key parameter of this thermodynamic model, the minimum energy requirement associated with growth-supporting metabolic pathways, using experimental population dynamics data from synthetic communities composed of a sulfate reducer and two methanogens. Our findings show that accounting for thermodynamics is necessary in capturing the experimental population dynamics of these synthetic communities that feature relevant species using low energy growth pathways. Furthermore, they provide the first estimates for minimum energy requirements of methanogenesis (in the range of −30 kJ mol−1) and elaborate on previous estimates of lactate fermentation by sulfate reducers (in the range of −30 to −17 kJ mol−1 depending on the culture conditions). The open-source nature of the developed model and demonstration of its use for estimating a key thermodynamic parameter should facilitate further thermodynamic modelling of microbial communities

Irreducible MultiQutrit Correlations in Greenberger-Horne-Zeilinger Type States

Following the idea of the continuity approach in [D. L. Zhou, Phys. Rev. Lett. 101, 180505 (2008)], we obtain the degrees of irreducible multi-party correlations in two families of $n$-qutrit Greenberger-Horne-Zeilinger type states. For the pure states in one of the families, the irreducible 2-party, $n$-party and $(n-m)$-party ($0< m < n-2$) correlations are nonzero, which is different from the $n$-qubit case. We also derive the correlation distributions in the $n$-qutrit maximal slice state, which can be uniquely determined by its $(n-1)$-qutrit reduced density matrices among pure states. It is proved that there is no irreducible $n$-qutrit correlation in the maximal slice state. This enlightens us to give a discussion about how to characterize the pure states with irreducible $n$-party correlation in arbitrarily high-dimensional systems by the way of the continuity approach.Comment: 5p, no fi

Fast and robust population transfer in two-level quantum systems with dephasing noise and/or systematic frequency errors

We design, by invariant-based inverse engineering, driving fields that invert the population of a two-level atom in a given time, robustly with respect to dephasing noise and/or systematic frequency shifts. Without imposing constraints, optimal protocols are insensitive to the perturbations but need an infinite energy. For a constrained value of the Rabi frequency, a flat $\pi$ pulse is the least sensitive protocol to phase noise but not to systematic frequency shifts, for which we describe and optimize a family of protocols.Comment: 7 pages, 2 figure

Bell inequalities for three particles

We present tight Bell inequalities expressed by probabilities for three four- and five-dimensional systems. The tight structure of Bell inequalities for three $d$-dimensional systems (qudits) is proposed. Some interesting Bell inequalities of three qubits reduced from those of three qudits are also studied.Comment: 8 pages, 3 figures. Accepted for publication in Phys. Rev.

Quantum dense coding in multiparticle entangled states via local measurements

In this paper, we study quantum dense coding between two arbitrarily fixed particles in a (N+2)-particle maximally-entangled states through introducing an auxiliary qubit and carrying out local measurements. It is shown that the transmitted classical information amount through such an entangled quantum channel usually is less than two classical bits. However, the information amount may reach two classical bits of information, and the classical information capacity is independent of the number of the entangled particles in the initial entangled state under certain conditions. The results offer deeper insights to quantum dense coding via quantum channels of multi-particle entangled states.Comment: 3 pages, no figur

Asymptotic quasinormal modes of a coupled scalar field in the Gibbons-Maeda dilaton spacetime

Adopting the monodromy technique devised by Motl and Neitzke, we investigate analytically the asymptotic quasinormal frequencies of a coupled scalar field in the Gibbons-Maeda dilaton spacetime. We find that it is described by $e^{\beta \omega}=-[1+2\cos{(\frac{\sqrt{2\xi+1}}{2} \pi)}]-e^{-\beta_I \omega}[2+2\cos{(\frac{\sqrt{2\xi+1}}{2}\pi)}]$, which depends on the structure parameters of the background spacetime and on the coupling between the scalar and gravitational fields. As the parameters $\xi$ and $\beta_I$ tend to zero, the real parts of the asymptotic quasinormal frequencies becomes $T_H\ln{3}$, which is consistent with Hod's conjecture. When $\xi={91/18}$, the formula becomes that of the Reissner-Nordstr\"{o}m spacetime.Comment: 6 pages, 1 figur

Nanosecond electric pulses penetrate the nucleus and enhance speckle formation

Nanosecond electric pulses generate nanopores in the interior membranes of cells and modulate cellular functions. Here, we used confocal microscopy and flow cytometry to observe Smith antigen antibody (Y12) binding to nuclear speckles, known as small nuclear ribonucleoprotein particles (snRNPs) or intrachromatin granule clusters (IGCs), in Jurkat cells following one or five 10 ns, 150 kV/cm pulses. Using confocal microscopy and flow cytometry, we observed changes in nuclear speckle labeling that suggested a disruption of pre-messenger RNA splicing mechanisms. Pulse exposure increased the nuclear speckled substructures by 2.5-fold above basal levels while the propidium iodide (PI) uptake in pulsed cells was unchanged. The resulting nuclear speckle changes were also cell cycle dependent. These findings suggest that 10 ns pulses directly influenced nuclear processes, such as the changes in the nuclear RNA–protein complexes

Detecting Full N-Particle Entanglement in Arbitrarily High-Dimensional Systems with Bell-Type Inequality

We derive a set of Bell-type inequalities for arbitrarily high-dimensional systems, based on the assumption of partial separability in the hybrid local-nonlocal hidden variable model. Partially entangled states would not violate the inequalities, and thus upon violation, these Bell-type inequalities are sufficient conditions to detect the full $N$-particle entanglement and validity of the hybrid local-nonlocal hidden variable description.Comment: 6 page

Quantum nonlocality of Heisenberg XX model with Site-dependent Coupling Strength

We show that the generalized Bell inequality is violated in the extended Heisenberg model when the temperature is below a threshold value. The threshold temperature values are obtained by constructing exact solutions of the model using the temperature-dependent correlation functions. The effect due to the presence of external magnetic field is also illustrated.Comment: 10 pages and 2 figures, published versio

Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer

Methane producing microbial communities are of ecological and biotechnological interest. Syntrophic interactions among sulphate reducers and aceto/hydrogenotrophic and obligate hydrogenotrophic methanogens form a key component of these communities, yet, the impact of these different syntrophic routes on methane production and their stability against sulphate availability are not well understood. Here, we construct model synthetic communities using a sulphate reducer and two types of methanogens representing different methanogenesis routes. We find that tri-cultures with both routes increase methane production by almost two-fold compared to co-cultures, and are stable in the absence of sulphate. With increasing sulphate, system stability and productivity decreases, and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate. We show that this is due to a shift in these methanogens’ metabolism towards co-utilisation of hydrogen with acetate. These findings indicate the important role of hydrogen dynamics in the stability and productivity of syntrophic communities