The Limiting Speed of the Bacterial Flagellar Motor

Recent experiments on the bacterial flagellar motor have shown that the structure of this nanomachine, which drives locomotion in a wide range of bacterial species, is more dynamic than previously believed. Specifically, the number of active torque-generating units (stators) was shown to vary across applied loads. This finding invalidates the experimental evidence reporting that limiting (zero-torque) speed is independent of the number of active stators. Here, we propose that, contrary to previous assumptions, the maximum speed of the motor is not universal, but rather increases as additional torque-generators are recruited. This result arises from our assumption that stators disengage from the motor for a significant portion of their mechanochemical cycles at low loads. We show that this assumption is consistent with current experimental evidence and consolidate our predictions with arguments that a processive motor must have a high duty ratio at high loads.Comment: 8 pages, 3 figures (main text); 7 pages, 3 figures (supplementary

Rapid rotation of micron and submicron dielectric particles measured using optical tweezers

We demonstrate the use of a laser trap (‘optical tweezers’) and back-focal-plane position detector to measure rapid rotation in aqueous solution of single particles with sizes in the vicinity of 1 μm. Two types of rotation were measured: electrorotation of polystyrene microspheres and rotation of the flagellar motor of the bacterium Vibrio alginolyticus. In both cases, speeds in excess of 1000 Hz (rev s−1) were measured. Polystyrene beads of diameter about 1 μm labelled with smaller beads were held at the centre of a microelectrode array by the optical tweezers. Electrorotation of the labelled beads was induced by applying a rotating electric field to the solution using microelectrodes. Electrorotation spectra were obtained by varying the frequency of the applied field and analysed to obtain the surface conductance of the beads. Single cells of V. alginolyticus were trapped and rotation of the polar sodium-driven flagellar motor was measured. Cells rotated more rapidly in media containing higher concentrations of Na+, and photodamage caused by the trap was considerably less when the suspending medium did not contain oxygen. The technique allows single-speed measurements to be made in less than a second and separate particles can be measured at a rate of several per minute

Mechanics of torque generation in the bacterial flagellar motor

The bacterial flagellar motor (BFM) is responsible for driving bacterial locomotion and chemotaxis, fundamental processes in pathogenesis and biofilm formation. In the BFM, torque is generated at the interface between transmembrane proteins (stators) and a rotor. It is well-established that the passage of ions down a transmembrane gradient through the stator complex provides the energy needed for torque generation. However, the physics involved in this energy conversion remain poorly understood. Here we propose a mechanically specific model for torque generation in the BFM. In particular, we identify two fundamental forces involved in torque generation: electrostatic and steric. We propose that electrostatic forces serve to position the stator, while steric forces comprise the actual 'power stroke'. Specifically, we predict that ion-induced conformational changes about a proline 'hinge' residue in an $\alpha$-helix of the stator are directly responsible for generating the power stroke. Our model predictions fit well with recent experiments on a single-stator motor. Furthermore, we propose several experiments to elucidate the torque-speed relationship in motors where the number of stators may not be constant. The proposed model provides a mechanical explanation for several fundamental features of the flagellar motor, including: torque-speed and speed-ion motive force relationships, backstepping, variation in step sizes, and the puzzle of swarming experiments

Exponential improvement in precision for simulating sparse Hamiltonians

We provide a quantum algorithm for simulating the dynamics of sparse Hamiltonians with complexity sublogarithmic in the inverse error, an exponential improvement over previous methods. Specifically, we show that a $d$-sparse Hamiltonian $H$ acting on $n$ qubits can be simulated for time $t$ with precision $\epsilon$ using $O\big(\tau \frac{\log(\tau/\epsilon)}{\log\log(\tau/\epsilon)}\big)$ queries and $O\big(\tau \frac{\log^2(\tau/\epsilon)}{\log\log(\tau/\epsilon)}n\big)$ additional 2-qubit gates, where $\tau = d^2 \|{H}\|_{\max} t$. Unlike previous approaches based on product formulas, the query complexity is independent of the number of qubits acted on, and for time-varying Hamiltonians, the gate complexity is logarithmic in the norm of the derivative of the Hamiltonian. Our algorithm is based on a significantly improved simulation of the continuous- and fractional-query models using discrete quantum queries, showing that the former models are not much more powerful than the discrete model even for very small error. We also simplify the analysis of this conversion, avoiding the need for a complex fault correction procedure. Our simplification relies on a new form of "oblivious amplitude amplification" that can be applied even though the reflection about the input state is unavailable. Finally, we prove new lower bounds showing that our algorithms are optimal as a function of the error.Comment: v1: 27 pages; Subsumes and improves upon results in arXiv:1308.5424. v2: 28 pages, minor change

Simulating Hamiltonian dynamics with a truncated Taylor series

We describe a simple, efficient method for simulating Hamiltonian dynamics on a quantum computer by approximating the truncated Taylor series of the evolution operator. Our method can simulate the time evolution of a wide variety of physical systems. As in another recent algorithm, the cost of our method depends only logarithmically on the inverse of the desired precision, which is optimal. However, we simplify the algorithm and its analysis by using a method for implementing linear combinations of unitary operations to directly apply the truncated Taylor series.Comment: 5 page

Detection of Campylobacter concisus and other Campylobacter species in colonic biopsies from adults with ulcerative colitis

Peer reviewedPublisher PD

Vertical Excavation below Footing Solved by Compaction Grouting

One of the problems regularly facing engineers in designing additions to buildings or other structures is dealing with excavating for footings directly adjoining existing footings but at a deeper level. This was accomplished in sandy soils economically and quickly for a noted Conference Center in 1983 by using compaction grouting. Compaction piles were utilized to pick up existing loads as well as the horizontal loads which would normally allow the building to tip, settle and crack. We believe this was the first use of compaction piles as anchor piles to pick up horizontal loads. By using this process, the sandy soils along the excavation stood without other support when excavating with a backhoe. The paper presents the criteria used in developing this method, summarizes the critical loads, and explains the operation. There has been no settlement at the site

Controlled delivery of membrane proteins to artificial lipid bilayers by nystatin-ergosterol modulated vesicle fusion

The study of ion channels and other membrane proteins and their potential use as biosensors and drug screening targets require their reconstitution in an artificial membrane. These applications would greatly benefit from microfabricated devices in which stable artificial lipid bilayers can be rapidly and reliably formed. However, the amount of protein delivered to the bilayer must be carefully controlled. A vesicle fusion technique is investigated where composite ion channels of the polyene antibiotic nystatin and the sterol ergosterol are employed to render protein-carrying vesicles fusogenic After fusion with an ergosterol-free artificial bilayer the nystatin-ergosterol channels do not dissociate immediately and thus cause a transient current signal that marks the vesicle fusion event. Experimental pitfalls of this method were identified, the influence of the nystatin and ergosterol concentration on the fusion rate and the shape of the fusion event marker was explored, and the number of different lipid was reduced. Under these conditions, the B-amyloid peptide could be delivered in a controlled manner to a standard planar bilayer. Additionally, the electrical recordings were obtained of vesicles fusing with a planar lipid bilayer in a microfabricated device, demonstrating the suitability of nystatin-ergosterol modulated vesicle fusion for protein delivery within microsystems

Requirements for a Nutrition Education Demonstrator

[Context and Motivation] Development of innovative ICT-based applications is a complex process involving collaboration of all relevant disciplines. This complexity arises due to differences in terminology, knowledge and often also the ways of working between developers in the disciplines involved. [Question/problem] Advances in each discipline bring a rich design environment of theories, models, methods and techniques. Making a selection from these makes the development of distributed applications very challenging, often requiring a holistic approach to address the needs of the disciplines involved. This paper describes early stage requirements acquisition of a mobile nutrition education demonstrator which supports overweight persons in adopting healthier dietary behaviour. [Principal idea/results] We present a novel way to combine and use known requirements acquisition methods involving a two stage user needs analysis based on scenarios which apply a theory-based model of behavioural change and are onstructed in two phases. The first phase scenarios specify an indicative description reflecting the use of the transtheoretical model of behavioural change. In the second phase, a handshake protocol adds elements of optative system-oriented descriptions to the scenarios such that the intended system can support the indicative description. [Contribution] The holistic and phased approach separates design concerns to which each of the disciplines contributes with their own expertise and domain principles. It preserves the applied domain principles in the design and it bridges gaps in terminology, knowledge and ways of working