Modeling ion channel dynamics through reflected stochastic differential equations

Ion channels are membrane proteins that open and close at random and play a vital role in the electrical dynamics of excitable cells. The stochastic nature of the conformational changes these proteins undergo can be significant, however current stochastic modeling methodologies limit the ability to study such systems. Discrete-state Markov chain models are seen as the "gold standard," but are computationally intensive, restricting investigation of stochastic effects to the single-cell level. Continuous stochastic methods that use stochastic differential equations (SDEs) to model the system are more efficient but can lead to simulations that have no biological meaning. In this paper we show that modeling the behavior of ion channel dynamics by a reflected SDE ensures biologically realistic simulations, and we argue that this model follows from the continuous approximation of the discrete-state Markov chain model. Open channel and action potential statistics from simulations of ion channel dynamics using the reflected SDE are compared with those of a discrete-state Markov chain method. Results show that the reflected SDE simulations are in good agreement with the discrete-state approach. The reflected SDE model therefore provides a computationally efficient method to simulate ion channel dynamics while preserving the distributional properties of the discrete-state Markov chain model and also ensuring biologically realistic solutions. This framework could easily be extended to other biochemical reaction networks. © 2012 American Physical Society.

Image-based visual servoing for the super-orbital re-entry of Hayabusa spacecraft

This paper presents an image-based visual servoing system that was used to track the atmospheric Earth re-entry of Hayabusa. The primary aim of this ground based tracking platform was to record the emission spectrum radiating from the superheated gas of the shock layer and the surface of the heat shield during re-entry. To the author's knowledge, this is the first time that a visual servoing system has successfully tracked a super-orbital re-entry of a spacecraft and recorded its pectral signature. Furthermore, we improved the system by including a simplified dynamic model for feed-forward control and demonstrate improved tracking performance on the International Space Station (ISS). We present comparisons between simulation and experimental results on different target trajectories including tracking results from Hayabusa and ISS. The required performance for tracking both spacecraft is demanding when combined with a narrow field of view (FOV). We also briefly discuss the preliminary results obtained from the spectroscopy of the Hayabusa's heat shield during re-entry.

Group dynamics and software engineering

This paper reports on an experiment that was conducted to determine the extent to which group dynamics impacts on the effectiveness of software development teams. The experiment was conducted on software engineering project students at the Queensland University of Technology (QUT).

Stigmergy in Web 2.0 : a model for site dynamics

Building Web 2.0 sites does not necessarily ensure the success of the site. We aim to better understand what improves the success of a site by drawing insight from biologically inspired design patterns. Web 2.0 sites provide a mechanism for human interaction enabling powerful intercommunication between massive volumes of users. Early Web 2.0 site providers that were previously dominant are being succeeded by newer sites providing innovative social interaction mechanisms. Understanding what site traits contribute to this success drives research into Web sites mechanics using models to describe the associated social networking behaviour. Some of these models attempt to show how the volume of users provides a self-organising and self-contextualisation of content. One model describing coordinated environments is called stigmergy, a term originally describing coordinated insect behavior. This paper explores how exploiting stigmergy can provide a valuable mechanism for identifying and analysing online user behavior specifically when considering that user freedom of choice is restricted by the provided web site functionality. This will aid our building better collaborative Web sites improving the collaborative processes.

Detecting common dynamics in transitory components

This paper considers VECMs for variables exhibiting cointegration and common features in the transitory components. While the presence of cointegration between the permanent components of series reduces the rank of the long-run multiplier matrix, a common feature among the transitory components leads to a rank reduction in the matrix summarizing short-run dynamics. The common feature also implies that there exists linear combinations of the first-differenced variables in a cointegrated VAR that are white noise and traditional tests focus on testing for this characteristic. An alternative, however, is to test the rank of the short-run dynamics matrix directly. Consequently, we use the literature on testing the rank of a matrix to produce some alternative test statistics. We also show that these are identical to one of the traditional tests. The performance of the different methods is illustrated in a Monte Carlo analysis which is then used to re-examine an existing empirical study. Finally, this approach is applied to provide a check for the presence of common dynamics in DSGE models.

Dynamics of rod and cone photoreceptor interactions under mesopic light levels

Visual adaptation regulates contrast sensitivity during dynamically changing light conditions (Crawford, 1947; Hecht, Haig & Chase, 1937). These adaptation dynamics are unknown under dim (mesopic) light levels when the rod (R) and long (L), medium (M) and short (S) wavelength cone photoreceptor classes contribute to vision via interactions in shared non-opponent Magnocellular (MC), chromatically opponent Parvocellular (PC) and Koniocellular (KC) visual pathways (Dacey, 2000). This study investigated the time-course of adaptation and post-receptoral pathways mediating receptor specific rod and cone interactions under mesopic illumination. A four-primary photostimulator (Pokorny, Smithson & Quinlan, 2004) was used to independently control the activity of the four photoreceptor classes and their post-receptoral visual athways in human observers. In the first experiment, the contrast sensitivity and time-course of visual adaptation under mesopic illumination were measured for receptoral (L, S, R) and post-receptoral (LMS, LMSR, L-M) stimuli. An incremental (Rapid-ON) sawtooth conditioning pulse biased detection to ON-cells within the visual pathways and sensitivity was assayed relative to pulse onset using a briefly presented incremental probe that did not alter adaptation. Cone.Cone interactions with luminance stimuli (L cone, LMS, LMSR) reduced sensitivity by 15% and the time course of recovery was 25± 5ms-1 (μ ± SEM). PC mediated (+L-M) chromatic stimuli sensitivity loss was less (8%) than for luminance and recovery was slower (μ = 2.95 ± 0.05 ms-1), with KC mediated (S cone) chromatic stimuli showing a high sensitivity loss (38%) and the slowest recovery time (1.6 ± 0.2 ms-1). Rod-Rod interactions increased sensitivity by 20% and the time course of recovery was 0.7 ± 0.2 ms-1 (μ ± SD). Compared to these interaction types, Rod-Cone interactions reduced sensitivity to a lesser degree (5%) and showed the fastest recovery (μ = 43 ± 7 ms-1). In the second experiment, rod contribution to the magnocellular, parvocellular and koniocellular post-receptoral pathways under mesopic illumination was determined as a function of incremental stimulus duration and waveform (rectangular; sawtooth) using a rod colour match procedure (Cao, Pokorny & Smith, 2005; Cao, Pokorny, Smith & Zele, 2008a). For a 30% rod increment, a cone match required a decrease in [L/(L+M)] and an increase in [L+M] and [S/(L+M)], giving a greenish-blue and brighter appearance for probe durations of 75 ms or longer. Probe durations less than 75 ms showed an increase in [L+M] and no change in chromaticity [L/(L+M) or S/(L+M)], uggesting mediation by the MC pathway only for short duration rod stimuli. s We advance previous studies by determining the time-course and nature of photoreceptor specific retinal interactions in the three post-receptoral pathways under mesopic illumination. In the first experiment, the time-course of adaptation for ON cell processing was determined, revealing opponent cell facilitation in chromatic PC and KC pathways. The Rod-Rod and Rod-Cone data identify previously unknown interaction types that act to maintain contrast sensitivity during dynamically changing light conditions and improve the speed of light adaptation under mesopic light levels. The second experiment determined the degree of rod contribution to the inferred post-eceptoral pathways as a function of the temporal properties of the rod signal. r The understanding of the mechanisms underlying interactions between photoreceptors under mesopic illumination has implications for the study of retinal disease. Visual function has been shown to be reduced in persons with age-related maculopathy (ARM) risk genotypes prior to clinical signs of the disease (Feigl, Cao, Morris & Zele, 2011) and disturbances in rod-mediated adaptation have been shown in early phases of ARM (Dimitrov, Guymer, Zele, Anderson & Vingrys, 2008; Feigl, Brown, Lovie-Kitchin & Swann, 2005). Also, the understanding of retinal networks controlling vision enables the development of international lighting standards to optimise visual performance nder dim light levels (e.g. work-place environments, transportation).

Variations on a routine : how selection-adaptation-retention dynamics create variety in organisational routines

The question "what causes variety in organisational routines" is of considerable interest to organisational scholars, and one to which this thesis seeks to answer. To this end an evolutionary theory of change is advanced which holds that the dynamics of selection, adaptation and retention explain the creation of variety in organisational routines. A longitudinal, multi-level, multi-case analysis is undertaken in this thesis, using multiple data collection strategies. In each case, different types of variety were identified, according to a typology, together with how selection, adaptation and retention contribute to variety in a positive or negative sense. Methodologically, the thesis makes a contribution to our understanding of variety, as certain types of variety only become evident when examined by specific types of research design. The research also makes a theoretical contribution by explaining how selection, adaptation and retention individually and collectively contribute to variety in organisational routines. Moreover, showing that routines could be stable, diverse, adaptive and dynamic at the same time; is a significant, and novel, theoretical contribution.

Investigating the dynamics of the psychological contract : how and why individuals' contract beliefs change

The overall objective of this thesis is to explore how and why the content of individuals' psychological contracts changes over time. The contract is generally understood as "individual beliefs, shaped by the organisation, regarding the terms of an exchange agreement between individuals and their organisation" (Rousseau, 1995, p. 9). With an overall study sampling frame of 320 graduate organisational newcomers, a mixed method longitudinal research design comprised of three sequential, inter-related studies is employed in order to capture the change process. From the 15 semi-structured interviews conducted in Study 1, the key findings included identifying a relatively high degree of mutuality between employees' and their managers' reciprocal contract beliefs around the time of organisational entry. Also, at this time, individuals had developed specific components of their contract content through a mix of social network information (regarding broader employment expectations) and perceptions of various elements of their particular organisation's reputation (for more firm-specific expectations). Study 2 utilised a four-wave survey approach (available to the full sampling frame) over the 14 months following organisational entry to explore the 'shape' of individuals' contract change trajectories and the role of four theorised change predictors in driving these trajectories. The predictors represented an organisational-level informational cue (perceptions of corporate reputation), a dyadic-level informational cue (perceptions of manager-employee relationship quality) and two individual difference variables (affect and hardiness). Through the use of individual growth modelling, the findings showed differences in the general change patterns across contract content components of perceived employer (exhibiting generally quadratic change patterns) and employee (exhibiting generally no-change patterns) obligations. Further, individuals differentially used the predictor variables to construct beliefs about specific contract content. While both organisational- and dyadic-level cues were focused upon to construct employer obligation beliefs, organisational-level cues and individual difference variables were focused upon to construct employee obligation beliefs. Through undertaking 26 semi-structured interviews, Study 3 focused upon gaining a richer understanding of why participants' contracts changed, or otherwise, over the study period, with a particular focus upon the roles of breach and violation. Breach refers to an employee's perception that an employer obligation has not been met and violation refers to the negative and affective employee reactions which may ensue following a breach. The main contribution of these findings was identifying that subsequent to a breach or violation event a range of 'remediation effects' could be activated by employees which, depending upon their effectiveness, served to instigate either breach or contract repair or both. These effects mostly instigated broader contract repair and were generally cognitive strategies enacted by an individual to re-evaluate the breach situation and re-focus upon other positive aspects of the employment relationship. As such, the findings offered new evidence for a clear distinction between remedial effects which serve to only repair the breach (and thus the contract) and effects which only repair the contract more broadly; however, when effective, both resulted in individuals again viewing their employment relationships positively. Overall, in response to the overarching research question of this thesis, how and why individuals' psychological contract beliefs change, individuals do indeed draw upon various information sources, particularly at the organisational-level, as cues or guides in shaping their contract content. Further, the 'shapes' of the changes in beliefs about employer and employee obligations generally follow different, and not necessarily linear, trajectories over time. Finally, both breach and violation and also remedial actions, which address these occurrences either by remedying the breach itself (and thus the contract) or the contract only, play central roles in guiding individuals' contract changes to greater or lesser degrees. The findings from the thesis provide both academics and practitioners with greater insights into how employees construct their contract beliefs over time, the salient informational cues used to do this and how the effects of breach and violation can be mitigated through creating an environment which facilitates the use of effective remediation strategies.