Quasi-one and two-dimensional transitions of gases adsorbed on nanotube bundles

Grand canonical Monte Carlo simulations have been performed to determine the adsorption behavior of Ar and Kr atoms on the exterior surface of a rope (bundle) consisting of many carbon nanotubes. The computed adsorption isotherms reveal phase transitions associated with the successive creation of quasi-one dimensional lines of atoms near and parallel to the intersection of two adjacent nanotubes.Comment: 12 pages, 6 figures, submitted to J. Chem. Phy

Absolute protein quantification using fluorescence measurements with FPCountR

This paper presents a generalisable method for the calibration of fluorescence readings on microplate readers, in order to convert arbitrary fluorescence units into absolute units. FPCountR relies on the generation of bespoke fluorescent protein (FP) calibrants, assays to determine protein concentration and activity, and a corresponding analytical workflow. We systematically characterise the assay protocols for accuracy, sensitivity and simplicity, and describe an ‘ECmax’ assay that outperforms the others and even enables accurate calibration without requiring the purification of FPs. To obtain cellular protein concentrations, we consider methods for the conversion of optical density to either cell counts or alternatively to cell volumes, as well as examining how cells can interfere with protein counting via fluorescence quenching, which we quantify and correct for the first time. Calibration across different instruments, disparate filter sets and mismatched gains is demonstrated to yield equivalent results. It also reveals that mCherry absorption at 600 nm does not confound cell density measurements unless expressed to over 100,000 proteins per cell. FPCountR is presented as pair of open access tools (protocol and R package) to enable the community to use this method, and ultimately to facilitate the quantitative characterisation of synthetic microbial circuits

Comparative study of many-body perturbation theory and time-dependent density functional theory in the out-of-equilibrium Anderson model

We study time-dependent electron transport through an Anderson model. The electronic interactions on the impurity site are included via the self-energy approximations at Hartree-Fock (HF), second Born (2B), GW, and T-Matrix level as well as within a time-dependent density functional (TDDFT) scheme based on the adiabatic Bethe-Ansatz local density approximation (ABALDA) for the exchange correlation potential. The Anderson model is driven out of equilibrium by applying a bias to the leads and its nonequilibrium dynamics is determined by real-time propagation. The time-dependent currents and densities are compared to benchmark results obtained with the time-dependent density matrix renormalization group (tDMRG) method. Many-body perturbation theory beyond HF gives results in close agreement with tDMRG especially within the 2B approximation. We find that the TDDFT approach with the ABALDA approximation produces accurate results for the densities on the impurity site but overestimates the currents. This problem is found to have its origin in an overestimation of the lead densities which indicates that the exchange correlation potential must attain nonzero values in the leads.Comment: 11 pages, 9 figure

Quantum states and specific heat of low-density He gas adsorbed within the carbon nanotube interstitial channels: Band structure effects and potential dependence

We calculate the energy-band structure of a He atom trapped within the interstitial channel between close-packed nanotubes within a bundle and its influence on the specific heat of the adsorbed gas. A robust prediction of our calculations is that the contribution of the low-density adsorbed gas to the specific heat of the nanotube material shows pronounced nonmonotonic variations with temperature. These variations are shown to be closely related to the band gaps in the adsorbate density of states

Quasi one dimensional 4^4He inside carbon nanotubes

We report results of diffusion Monte Carlo calculations for both $^4$He absorbed in a narrow single walled carbon nanotube (R = 3.42 \AA) and strictly one dimensional $^4$He. Inside the tube, the binding energy of liquid $^4$He is approximately three times larger than on planar graphite. At low linear densities, $^4$He in a nanotube is an experimental realization of a one-dimensional quantum fluid. However, when the density increases the structural and energetic properties of both systems differ. At high density, a quasi-continuous liquid-solid phase transition is observed in both cases.Comment: 11 pages, 3ps figures, to appear in Phys. Rev. B (RC

Approximations for many-body Green's functions: insights from the fundamental equations

Several widely used methods for the calculation of band structures and photo emission spectra, such as the GW approximation, rely on Many-Body Perturbation Theory. They can be obtained by iterating a set of functional differential equations relating the one-particle Green's function to its functional derivative with respect to an external perturbing potential. In the present work we apply a linear response expansion in order to obtain insights in various approximations for Green's functions calculations. The expansion leads to an effective screening, while keeping the effects of the interaction to all orders. In order to study various aspects of the resulting equations we discretize them, and retain only one point in space, spin, and time for all variables. Within this one-point model we obtain an explicit solution for the Green's function, which allows us to explore the structure of the general family of solutions, and to determine the specific solution that corresponds to the physical one. Moreover we analyze the performances of established approaches like $GW$ over the whole range of interaction strength, and we explore alternative approximations. Finally we link certain approximations for the exact solution to the corresponding manipulations for the differential equation which produce them. This link is crucial in view of a generalization of our findings to the real (multidimensional functional) case where only the differential equation is known.Comment: 17 pages, 7 figure

Resource-aware whole-cell model of division of labour in a two-strain consortium for complex substrate degradation

Background Low-cost sustainable feedstocks are essential for commercially viable biotechnologies. These feedstocks, often derived from plant or food waste, contain a multitude of different complex biomolecules which require multiple enzymes to hydrolyse and metabolise. Current standard biotechnology uses monocultures in which a single host expresses all the proteins required for the consolidated bioprocess. However, these hosts have limited capacity for expressing proteins before growth is impacted. This limitation may be overcome by utilising division of labour (DOL) in a consortium, where each member expresses a single protein of a longer degradation pathway. Results Here, we model a two-strain consortium, with one strain expressing an endohydrolase and a second strain expressing an exohydrolase, for cooperative degradation of a complex substrate. Our results suggest that there is a balance between increasing expression to enhance degradation versus the burden that higher expression causes. Once a threshold of burden is reached, the consortium will consistently perform better than an equivalent single-cell monoculture. Conclusions We demonstrate that resource-aware whole-cell models can be used to predict the benefits and limitations of using consortia systems to overcome burden. Our model predicts the region of expression where DOL would be beneficial for growth on starch, which will assist in making informed design choices for this, and other, complex-substrate degradation pathways

Two wheeled lunar dumptruck

The design of a two wheel bulk material transport vehicle is described in detail. The design consists of a modified cylindrical bowl, two independently controlled direct drive motors, and two deformable wheels. The bowl has a carrying capacity of 2.8 m (100 ft) and is constructed of aluminum. The low speed, high HP motors are directly connected to the wheels, thus yielding only two moving parts. The wheels, specifically designed for lunar applications, utilize the chevron tread pattern for optimum traction. The vehicle is maneuvered by varying the relative angular velocities of the wheels. The bulk material being transported is unloaded by utilizing the motors to oscillate the bowl back and forth to a height at which dumping is achieved. The analytical models were tested using a scaled prototype of the lunar transport vehicle. The experimental data correlated well with theoretical predictions. Thus, the design established provides a feasible alternative for the handling of bulk material on the moon

Radio-Frequency Spectroscopy of Ultracold Fermions

Radio-frequency techniques were used to study ultracold fermions. We observed the absence of mean-field "clock" shifts, the dominant source of systematic error in current atomic clocks based on bosonic atoms. This is a direct consequence of fermionic antisymmetry. Resonance shifts proportional to interaction strengths were observed in a three-level system. However, in the strongly interacting regime, these shifts became very small, reflecting the quantum unitarity limit and many-body effects. This insight into an interacting Fermi gas is relevant for the quest to observe superfluidity in this system.Comment: 6 pages, 6 figure

Uptake of gases in bundles of carbon nanotubes

Model calculations are presented which predict whether or not an arbitrary gas experiences significant absorption within carbon nanotubes and/or bundles of nanotubes. The potentials used in these calculations assume a conventional form, based on a sum of two-body interactions with individual carbon atoms; the latter employ energy and distance parameters which are derived from empirical combining rules. The results confirm intuitive expectation that small atoms and molecules are absorbed within both the interstitial channels and the tubes, while large atoms and molecules are absorbed almost exclusively within the tubes.Comment: 9 pages, 12 figures, submitted to PRB Newer version (8MAR2K). There was an error in the old one (23JAN2K). Please download thi