Stronger computational modelling of signalling pathways using both continuous and discrete-state methods

Starting from a biochemical signalling pathway model expresses in a process algebra enriched with quantitative information, we automatically derive both continuous-space and discrete-space representations suitable for numerical evaluation. We compare results obtained using approximate stochastic simulation thereby exposing a flaw in the use of the differentiation procedure producing misleading results

Factors that affect scrub practitioner non-technical skills: A literature review

Non-technical skills are the cognitive and interpersonal behaviours that compliment clinical competence in surgery. Effective use of non-technical skills is essential for scrub practice, because they facilitate anticipation of the surgeon’s requirements and promote appropriate communication behaviours. This literature review analyses the factors that may influence a scrub practitioner’s use of non-technical skills during surgery. Recommendations are made that are intended to improve their use by reducing behavioural variations during surgery

Variation of turbulent burning rate of methane, methanol, and iso-octane air mixtures with equivalence ratio at elevated pressure

Turbulent burning velocities for premixed methane, methanol, and iso-octane/air mixtures have been experimentally determined for an rms turbulent velocity of 2 m/s and pressure of 0.5 MPa for a wide range of equivalence ratios. Turbulent burning velocity data were derived using high-speed schlieren photography and transient pressure recording; measurements were processed to yield a turbulent mass rate burning velocity, utr. The consistency between the values derived using the two techniques, for all fuels for both fuel-lean and fuel-rich mixtures, was good. Laminar burning measurements were made at the same pressure, temperature, and equivalence ratios as the turbulent cases and laminar burning velocities and Markstein numbers were determined. The equivalence ratio (φ) for peak turbulent burning velocity proved not always coincident with that for laminar burning velocity for the same fuel; for isooctane, the turbulent burning velocity unexpectedly remained high over the range φ = 1 to 2. The ratio of turbulent to laminar burning velocity proved remarkably high for very rich iso-octane/air and lean methane/air mixtures

Inelastic final-state interaction

The final-state interaction in multichannel decay processes is sytematically studied with application to B decay in mind. Since the final-state inteaction is intrinsically interwoven with the decay interaction in this case, no simple phase theorem like "Watson's theorem" holds for experimentally observed final states. We first examine in detail the two-channel problem as a toy-model to clarify the issues and to remedy common mistakes made in earlier literature. Realistic multichannel problems are too challenging for quantitative analysis. To cope with mathematical complexity, we introduce a method of approximation that is applicable to the case where one prominant inelastic channel dominates over all others. We illustrate this approximation method in the amplitude of the decay B to pi K fed by the intermediate states of a charmed meson pair. Even with our approximation we need more accurate information of strong interactions than we have now. Nonethless we are able to obtain some insight in the issue and draw useful conclusions on general fearyres on the strong phases.Comment: The published version. One figure correcte

Stochastic modeling of cargo transport by teams of molecular motors

Many different types of cellular cargos are transported bidirectionally along microtubules by teams of molecular motors. The motion of this cargo-motors system has been experimentally characterized in vivo as processive with rather persistent directionality. Different theoretical approaches have been suggested in order to explore the origin of this kind of motion. An effective theoretical approach, introduced by M\"uller et al., describes the cargo dynamics as a tug-of-war between different kinds of motors. An alternative approach has been suggested recently by Kunwar et al., who considered the coupling between motor and cargo in more detail. Based on this framework we introduce a model considering single motor positions which we propagate in continuous time. Furthermore, we analyze the possible influence of the discrete time update schemes used in previous publications on the system's dynamic.Comment: Cenference proceedings - Traffic and Granular Flow 1

The detection of geothermal areas from Skylab thermal data

Skylab-4 X-5 thermal data of the geysers area was analyzed to determine the feasibility of using midday Skylab images to detect geothermal areas. The hottest ground areas indicated on the Skylab image corresponded to south-facing barren or sparsely vegetated slopes. A geothermal area approximately 15 by 30 m coincided with one of the hottest areas indicated by Skylab. This area could not be unambiguously distinguished from the other areas which are believed to be hotter than their surroundings as a result of their topography, and micrometeorological conditions. A simple modification of a previous thermal model was performed and the predicted temperatures for the hottest slopes using representative values was in general agreement with the observed data. It is concluded that data from a single midday Skylab pass cannot be used to locate geothermal areas

Sampling rare switching events in biochemical networks

Bistable biochemical switches are ubiquitous in gene regulatory networks and signal transduction pathways. Their switching dynamics, however, are difficult to study directly in experiments or conventional computer simulations, because switching events are rapid, yet infrequent. We present a simulation technique that makes it possible to predict the rate and mechanism of flipping of biochemical switches. The method uses a series of interfaces in phase space between the two stable steady states of the switch to generate transition trajectories in a ratchet-like manner. We demonstrate its use by calculating the spontaneous flipping rate of a symmetric model of a genetic switch consisting of two mutually repressing genes. The rate constant can be obtained orders of magnitude more efficiently than using brute-force simulations. For this model switch, we show that the switching mechanism, and consequently the switching rate, depends crucially on whether the binding of one regulatory protein to the DNA excludes the binding of the other one. Our technique could also be used to study rare events and non-equilibrium processes in soft condensed matter systems.Comment: 9 pages, 6 figures, last page contains supplementary informatio

Negotiated control between the manual and visual systems for visually guided hand reaching movements

Abstract Background Control of reaching movements for manual work, vehicle operation, or interactions with manual interfaces requires concurrent gaze control for visual guidance of the hand. We hypothesize that reaching movements are based on negotiated strategies to resolve possible conflicting demands placed on body segments shared by the visual (gaze) and manual (hand) control systems. Further, we hypothesize that a multiplicity of possible spatial configurations (redundancy) in a movement system enables a resolution of conflicting demands that does not require sacrificing the goals of the two systems. Methods The simultaneous control of manual reach and gaze during seated reaching movements was simulated by solving an inverse kinematics model wherein joint trajectories were estimated from a set of recorded hand and head movements. A secondary objective function, termed negotiation function, was introduced to describe a means for the manual reach and gaze directing systems to balance independent goals against (possibly competing) demands for shared resources, namely the torso movement. For both systems, the trade-off may be resolved without sacrificing goal achievement by taking advantage of redundant degrees of freedom. Estimated joint trajectories were then compared to joint movement recordings from ten participants. Joint angles were predicted with and without the negotiation function in place, and model accuracy was determined using the root-mean-square errors (RMSEs) and differences between estimated and recorded joint angles. Results The prediction accuracy was generally improved when negotiation was included: the negotiated control reduced RMSE by 16% and 30% on average when compared to the systems with only manual or visual control, respectively. Furthermore, the RMSE in the negotiated control system tended to improve with torso movement amplitude. Conclusions The proposed model describes how multiple systems cooperate to perform goal-directed human movements when those movements draw upon shared resources. Allocation of shared resources can be undertaken by a negotiation process that is aware of redundancies and the existence of multiple solutions within the individual systems.http://deepblue.lib.umich.edu/bitstream/2027.42/134579/1/12984_2012_Article_626.pd