Dynamical frustration of protein's environment at the nanoseconds time scale

A 21-residue peptide in explicit water has been simulated using classical molecular dynamics. The system's trajectory has been analysed with a novel approach that quantifies the process of how atom's environment trajectories are explored. The approach is based on the measure of Statistical Complexity that extracts complete dynamical information from the signal. The introduced characteristic quantifies the system's dynamics at the nanoseconds time scale. It has been found that the peptide exhibits nanoseconds long periods that significantly differ in the rates of the exploration of the dynamically allowed configurations of the environment. During these periods the rates remain the same but different from other periods and from the rate for water. Periods of dynamical frustration are detected when only limited routes in the space of possible trajectories of the surrounding atoms are realised.

Variable time-scale information processing

With the extensive use of pulse modulation methods in telecommunications, much work has been done in the search for a better utilisation of the transmission channel.The present research is an extension of these investigations. A new modulation method, 'Variable Time-Scale Information Processing', (VTSIP), is proposed.The basic principles of this system have been established, and the main advantages and disadvantages investigated. With the proposed system, comparison circuits detect the instants at which the input signal voltage crosses predetermined amplitude levels.The time intervals between these occurrences are measured digitally and the results are temporarily stored, before being transmitted.After reception, an inverse process enables the original signal to be reconstituted.The advantage of this system is that the irregularities in the rate of information contained in the input signal are smoothed out before transmission, allowing the use of a smaller transmission bandwidth. A disadvantage of the system is the time delay necessarily introduced by the storage process.Another disadvantage is a type of distortion caused by the finite store capacity.A simulation of the system has been made using a standard speech signal, to make some assessment of this distortion. It is concluded that the new system should be an improvement on existing pulse transmission systems, allowing the use of a smaller transmission bandwidth, but introducing a time delay.

Time scale analysis for fluidizedbedmeltgranulation III: binder solidification rate

In series I and II of this study ([Chua et al., 2010a] and [Chua et al., 2010b]), we discussed the time scale of granule–granule collision, droplet–granule collision and droplet spreading in Fluidized Bed Melt Granulation (FBMG). In this third one, we consider the rate at which binder solidifies. Simple analytical solution, based on classical formulation for conduction across a semi-infinite slab, was used to obtain a generalized equation for binder solidification time. A multi-physics simulation package (Comsol) was used to predict the binder solidification time for various operating conditions usually considered in FBMG. The simulation results were validated with experimental temperature data obtained with a high speed infrared camera during solidification of ‘macroscopic’ (mm scale) droplets. For the range of microscopic droplet size and operating conditions considered for a FBMG process, the binder solidification time was found to fall approximately between 10-3 and 10-1 s. This is the slowest compared to the other three major FBMG microscopic events discussed in this series (granule–granule collision, granule–droplet collision and droplet spreading).

Time scale analysis for fluidized bed melt granulation I: granule-granule and granule-droplet collision rates

Fluidized bed spray granulators (FBMG) are widely used in the process industry for particle size growth; a desirable feature in many products, such as granulated food and medical tablets. In this paper, the first in a series of four discussing the rate of various microscopic events occurring in FBMG, theoretical analysis coupled with CFD simulations have been used to predict granule–granule and droplet–granule collision time scales. The granule–granule collision time scale was derived from principles of kinetic theory of granular flow (KTGF). For the droplet–granule collisions, two limiting models were derived; one is for the case of fast droplet velocity, where the granule velocity is considerable lower than that of the droplet (ballistic model) and another for the case where the droplet is traveling with a velocity similar to the velocity of the granules. The hydrodynamic parameters used in the solution of the above models were obtained from the CFD predictions for a typical spray fluidized bed system. The granule–granule collision rate within an identified spray zone was found to fall approximately within the range of 10-2–10-3 s, while the droplet–granule collision was found to be much faster, however, slowing rapidly (exponentially) when moving away from the spray nozzle tip. Such information, together with the time scale analysis of droplet solidification and spreading, discussed in part II and III of this study, are useful for probability analysis of the various event occurring during a granulation process, which then lead to be better qualitative and, in part IV, quantitative prediction of the aggregation rate.

Time scale analysis for fluidizedbedmeltgranulation-II: binder spreading rate

The spreading time of liquid binder droplet on the surface a primary particle is analyzed for Fluidized Bed Melt Granulation (FBMG). As discussed in the first paper of this series (Chua et al., in press) the droplet spreading rate has been identified as one of the important parameters affecting the probability of particles aggregation in FBMG. In this paper, the binder droplet spreading time has been estimated using Computational Fluid Dynamic modeling (CFD) based on Volume of Fluid approach (VOF). A simplified analytical solution has been developed and tested to explore its validity for predicting the spreading time. For the purpose of models validation, the droplet spreading evolution was recorded using a high speed video camera. Based on the validated model, a generalized correlative equation for binder spreading time is proposed. For the operating conditions considered here, the spreading time for Polyethylene Glycol (PEG1500) binder was found to fall within the range of 10-2 to 10-5 s. The study also included a number of other common binders used in FBMG. The results obtained here will be further used in paper III, where the binder solidification rate is discussed.

Characterization of human mesenchymal stem cells from multiple donors and the implications for large scale bioprocess development

Cell-based therapies have the potential to contribute to global healthcare, whereby the use of living cells and tissues can be used as medicinal therapies. Despite this potential, many challenges remain before the full value of this emerging field can be realized. The characterization of input material for cell-based therapy bioprocesses from multiple donors is necessary to identify and understand the potential implications of input variation on process development. In this work, we have characterized bone marrow derived human mesenchymal stem cells (BM-hMSCs) from multiple donors and discussed the implications of the measurable input variation on the development of autologous and allogeneic cell-based therapy manufacturing processes. The range of cumulative population doublings across the five BM-hMSC lines over 30 days of culture was 5.93, with an 18.2% range in colony forming efficiency at the end of the culture process and a 55.1% difference in the production of interleukin-6 between these cell lines. It has been demonstrated that this variation results in a range in the process time between these donor hMSC lines for a hypothetical product of over 13 days, creating potential batch timing issues when manufacturing products from multiple patients. All BM-hMSC donor lines demonstrated conformity to the ISCT criteria but showed a difference in cell morphology. Metabolite analysis showed that hMSCs from the different donors have a range in glucose consumption of 26.98 pmol cell−1 day−1, Lactate production of 29.45 pmol cell−1 day−1 and ammonium production of 1.35 pmol cell−1 day−1, demonstrating the extent of donor variability throughout the expansion process. Measuring informative product attributes during process development will facilitate progress towards consistent manufacturing processes, a critical step in the translation cell-based therapies.

Real-time control of a Tokamak plasma using neural networks

This paper presents results from the first use of neural networks for the real-time feedback control of high temperature plasmas in a Tokamak fusion experiment. The Tokamak is currently the principal experimental device for research into the magnetic confinement approach to controlled fusion. In the Tokamak, hydrogen plasmas, at temperatures of up to 100 Million K, are confined by strong magnetic fields. Accurate control of the position and shape of the plasma boundary requires real-time feedback control of the magnetic field structure on a time-scale of a few tens of microseconds. Software simulations have demonstrated that a neural network approach can give significantly better performance than the linear technique currently used on most Tokamak experiments. The practical application of the neural network approach requires high-speed hardware, for which a fully parallel implementation of the multi-layer perceptron, using a hybrid of digital and analogue technology, has been developed.

Employee social responsibility:development of an ESR measure and a multi-level investigation of antecedent and boundary conditions

The following thesis instigates the discussion on corporate social responsibility (CSR) through a review of literature on the conceptualisation, determinants, and remunerations of organisational CSR engagement. The case is made for the need to draw attention to the micro-levels of CSR, and consequently focus on employee social responsibility at multiple levels of analysis. In order to further research efforts in this area, the prerequisite of an employee social responsibility behavioural measurement tool is acknowledged. Accordingly, the subsequent chapters outline the process of scale development and validation, resulting in a robust, reliable and valid employee social responsibility scale. This scale is then put to use in a field study, and the noteworthy roles of the antecedent and boundary conditions of transformational leadership, assigned CSR priority, and CSR climate are confirmed at the group and individual level. Directionality of these relationships is subsequently alluded to in a time-lagged investigation, set within a simulated business environment. The thesis collates and discusses the contributions of the findings from the research series, which highlight a consistent three-way interaction effect of transformational leadership, assigned CSR priority and CSR climate. Specifically, efforts are made to outline various avenues for future research, given the infancy of the micro-level study of employee social responsibility.

Complex temporal patterns in molecular dynamics:a direct measure of the phase-space exploration by the trajectory at macroscopic time scales

Computer simulated trajectories of bulk water molecules form complex spatiotemporal structures at the picosecond time scale. This intrinsic complexity, which underlies the formation of molecular structures at longer time scales, has been quantified using a measure of statistical complexity. The method estimates the information contained in the molecular trajectory by detecting and quantifying temporal patterns present in the simulated data (velocity time series). Two types of temporal patterns are found. The first, defined by the short-time correlations corresponding to the velocity autocorrelation decay times (â‰0.1â€ps), remains asymptotically stable for time intervals longer than several tens of nanoseconds. The second is caused by previously unknown longer-time correlations (found at longer than the nanoseconds time scales) leading to a value of statistical complexity that slowly increases with time. A direct measure based on the notion of statistical complexity that describes how the trajectory explores the phase space and independent from the particular molecular signal used as the observed time series is introduced. © 2008 The American Physical Society.

Purification of plasmid DNA for use in human gene therapy

Two key issues defined the focus of this research in manufacturing plasmid DNA for use In human gene therapy. First, the processing of E.coli bacterial cells to effect the separation of therapeutic plasmid DNA from cellular debris and adventitious material. Second, the affinity purification of the plasmid DNA in a Simple one-stage process. The need arises when considering the concerns that have been recently voiced by the FDA concerning the scalability and reproducibility of the current manufacturing processes in meeting the quality criteria of purity, potency, efficacy, and safety for a recombinant drug substance for use in humans. To develop a preliminary purification procedure, an EFD cross-flow micro-filtration module was assessed for its ability to effect the 20-fold concentration, 6-time diafiltration, and final clarification of the plasmid DNA from the subsequent cell lysate that is derived from a 1 liter E.coli bacterial cell culture. Historically, the employment of cross-flow filtration modules within procedures for harvesting cells from bacterial cultures have failed to reach the required standards dictated by existing continuous centrifuge technologies, frequently resulting in the rapid blinding of the membrane with bacterial cells that substantially reduces the permeate flux. By challenging the EFD module, containing six helical wound tubular membranes promoting centrifugal instabilities known as Dean vortices, with distilled water between the Dean number's of 187Dn and 818Dn,and the transmembrane pressures (TMP) of 0 to 5 psi. The data demonstrated that the fluid dynamics significantly influenced the permeation rate, displaying a maximum at 227Dn (312 Imh) and minimum at 818Dn (130 Imh) for a transmembrane pressure of 1 psi. Numerical studies indicated that the initial increase and subsequent decrease resulted from a competition between the centrifugal and viscous forces that create the Dean vortices. At Dean numbers between 187Dn and 227Dn , the forces combine constructively to increase the apparent strength and influence of the Dean vortices. However, as the Dean number in increases above 227 On the centrifugal force dominates the viscous forces, compressing the Dean vortices into the membrane walls and reducing their influence on the radial transmembrane pressure i.e. the permeate flux reduced. When investigating the action of the Dean vortices in controlling tile fouling rate of E.coli bacterial cells, it was demonstrated that the optimum cross-flow rate at which to effect the concentration of a bacterial cell culture was 579Dn and 3 psi TMP, processing in excess of 400 Imh for 20 minutes (i.e., concentrating a 1L culture to 50 ml in 10 minutes at an average of 450 Imh). The data demonstrated that there was a conflict between the Dean number at which the shear rate could control the cell fouling, and the Dean number at which tile optimum flux enhancement was found. Hence, the internal geometry of the EFD module was shown to sub-optimal for this application. At 579Dn and 3 psi TMP, the 6-fold diafiltration was shown to occupy 3.6 minutes of process time, processing at an average flux of 400 Imh. Again, at 579Dn and 3 psi TMP the clarification of the plasmid from tile resulting freeze-thaw cell lysate was achieved at 120 Iml1, passing 83% (2,5 mg) of the plasmid DNA (6,3 ng μ-1 10.8 mg of genomic DNA (∼23,00 Obp, 36 ng μ-1 ), and 7.2 mg of cellular proteins (5-100 kDa, 21.4 ngμ-1 ) into the post-EFD process stream. Hence the EFD module was shown to be effective, achieving the desired objectives in approximately 25 minutes. On the basis of its ability to intercalate into low molecular weight dsDNA present in dilute cell lysates, and be electrophoresed through agarose, the fluorophore PicoGreen was selected for the development of a suitable dsDNA assay. It was assesseel for its accuracy, and reliability, In determining the concentration and identity of DNA present in samples that were eleclrophoresed through agarose gels. The signal emitted by intercalated PicoGreen was shown to be constant and linear, and that the mobility of the PicaGreen-DNA complex was not affected by the intercalation. Concerning the secondary purification procedure, various anion-exchange membranes were assessed for their ability to capture plasmid DNA from the post-EFD process stream. For a commercially available Sartorius Sartobind Q15 membrane, the reduction in the equilibriumbinding capacity for  ctDNA in buffer of increasing ionic demonstrated that DNA was being.adsorbed by electrostatic  interactions only. However, the problems associated with fluid distribution across the membrane demonstrated that the membrane housing was the predominant cause of the .erratic breakthrough curves. Consequently, this would need to be rectified before such a membrane could be integrated into the current system, or indeed be scaled beyond laboratory scale. However, when challenged with the process material, the data showed that considerable quantities of protein (1150 μg) were adsorbed preferentially to the plasmid DNA (44 μg). This was also shown for derived Pall Gelman UltraBind US450 membranes that had been functionalised by varying molecular weight poly-L~lysine and polyethyleneimine ligands. Hence the anion-exchange membranes were shown to be ineffective in capturing plasmid DNA from the process stream. Finally, work was performed to integrate a sequence-specific DNA·binding protein into a single-stage DNA chromatography, isolating plasmid DNA from E.coli cells whilst minimising the contamination from genomic DNA and cellular protein. Preliminary work demonstrated that the fusion protein was capable of isolating pUC19 DNA into which the recognition sequence for the fusion-protein had been inserted (pTS DNA) when in the presence of the conditioned process material. Althougth the pTS recognition sequence differs from native pUC19 sequences by only 2 bp, the fusion protein was shown to act as a highly selective affinity ligand for pTS DNA alone. Subsequently, the scale of the process was scaled 25-fold and positioned directly following the EFD system. In conclusion, the integration of the EFD micro-filtration system and zinc-finger affinity purification technique resulted in the capture of approximately 1 mg of plasmid DNA was purified from 1L of E.coli  culture in a simple two stage process, resulting in the complete removal of genomic DNA and 96.7% of cellular protein in less than 1 hour of process time.

Contact time periods in immunological synapse

This paper resolves the long standing debate as to the proper time scale τ of the onset of the immunological synapse bond, the noncovalent chemical bond defining the immune pathways involving T cells and antigen presenting cells. Results from our model calculations show τ to be of the order of seconds instead of minutes. Close to the linearly stable regime, we show that in between the two critical spatial thresholds defined by the integrin:ligand pair (Δ2∼ 40-45 nm) and the T-cell receptor TCR:peptide-major-histocompatibility-complex pMHC bond (Δ1∼ 14-15 nm), τ grows monotonically with increasing coreceptor bond length separation δ (= Δ2-Δ1∼ 26-30 nm) while τ decays with Δ1 for fixed Δ2. The nonuniversal δ-dependent power-law structure of the probability density function further explains why only the TCR:pMHC bond is a likely candidate to form a stable synapse.

Real-time high-resolution heterodyne-based measurements of spectral dynamics in fibre lasers

Conventional tools for measurement of laser spectra (e.g. optical spectrum analysers) capture data averaged over a considerable time period. However, the generation spectrum of many laser types may involve spectral dynamics whose relatively fast time scale is determined by their cavity round trip period, calling for instrumentation featuring both high temporal and spectral resolution. Such real-time spectral characterisation becomes particularly challenging if the laser pulses are long, or they have continuous or quasi-continuous wave radiation components. Here we combine optical heterodyning with a technique of spatiooral intensity measurements that allows the characterisation of such complex sources. Fast, round-trip-resolved spectral dynamics of cavity-based systems in real-time are obtained, with temporal resolution of one cavity round trip and frequency resolution defined by its inverse (85 ns and 24 MHz respectively are demonstrated). We also show how under certain conditions for quasi-continuous wave sources, the spectral resolution could be further increased by a factor of 100 by direct extraction of phase information from the heterodyned dynamics or by using double time scales within the spectrogram approach.

Are poor mathematics skills associated with visual deficits in temporal processing?

Developmental learning disabilities such as dyslexia and dyscalculia have a high rate of co-occurrence in pediatric populations, suggesting that they share underlying cognitive and neurophysiological mechanisms. Dyslexia and other developmental disorders with a strong heritable component have been associated with reduced sensitivity to coherent motion stimuli, an index of visual temporal processing on a millisecond time-scale. Here we examined whether deficits in sensitivity to visual motion are evident in children who have poor mathematics skills relative to other children of the same age. We obtained psychophysical thresholds for visual coherent motion and a control task from two groups of children who differed in their performance on a test of mathematics achievement. Children with math skills in the lowest 10% in their cohort were less sensitive than age-matched controls to coherent motion, but they had statistically equivalent thresholds to controls on a coherent form control measure. Children with mathematics difficulties therefore tend to present a similar pattern of visual processing deficit to those that have been reported previously in other developmental disorders. We speculate that reduced sensitivity to temporally defined stimuli such as coherent motion represents a common processing deficit apparent across a range of commonly co-occurring developmental disorders.

Sensitivity of peptide conformational dynamics on clustering of a classical molecular dynamics trajectory

We investigate the sensitivity of a Markov model with states and transition probabilities obtained from clustering a molecular dynamics trajectory. We have examined a 500 ns molecular dynamics trajectory of the peptide valine-proline-alanine-leucine in explicit water. The sensitivity is quantified by varying the boundaries of the clusters and investigating the resulting variation in transition probabilities and the average transition time between states. In this way, we represent the effect of clustering using different clustering algorithms. It is found that in terms of the investigated quantities, the peptide dynamics described by the Markov model is sensitive to the clustering; in particular, the average transition times are found to vary up to 46%. Moreover, inclusion of nonphysical sparsely populated clusters can lead to serious errors of up to 814%. In the investigation, the time step used in the transition matrix is determined by the minimum time scale on which the system behaves approximately Markovian. This time step is found to be about 100 ps. It is concluded that the description of peptide dynamics with transition matrices should be performed with care, and that using standard clustering algorithms to obtain states and transition probabilities may not always produce reliable results.

Transition metal ion coordination in hydrophilic polymer membranes

The research described within this thesis is concerned with the investigation of transition metal ion complexation within hydrophilic copolymer membranes. The membranes are copolymers of 4-methyl-4'-vinyl-2,2'-bipyridine, the 2-hydroxyethyl ester of 4,4'- dicarboxy-2,2'-bipyridine & bis-(5-vinylsalicylidene)ethylenediamine with 2-hydroxyethyl methacrylate. The effect of the polymer matrix on the formation and properties of transition metal iron complexes has been studied, specifically Cr(III) & Fe(II) salts for the bipyridyl- based copolymer membranes and Co(II), Ni(II) & Cu(II) salts for the salenH2- based copolymer membranes. The concomitant effect of complex formation on the properties of the polymer matrix have also been studied, e.g. on mechanical strength. A detailed body of work into the kinetics and thermodynamics for the formation of Cu(II) complexes in the salenH2- based copolymer membranes has been performed. The rate of complex formation is found to be very slow while the value of K for the equilibrium of complex formation is found to be unexpectedly small and shows a slight anion dependence. These phenomena are explained in terms of the effects of the heterogeneous phase provided by the polymer matrix. The transport of Cr(III) ions across uncomplexed and Cr(III)-pre-complexed bipyridyl-based membranes has been studied. In both cases, no Cr(III) coordination occurs within the time-scale of an experiment. Pre-complexation of the membrane does not lead to a change in the rate of permeation of Cr(III) ions. The transport of Co(II), Ni(II) & Cu(II) ions across salenH2- based membranes shows that there is no detectable lag-time in transport of the ions, despite independent evidence that complex formation within the membranes does occur. Finally, the synthesis of a number of functionalised ligands is described. Although they were found to be non-polymerisable by the methods employed in this research, they remain interesting ligands which provide a startmg pomt for further functionalisation.