Scale Free Bounds on the Amplification of Disturbances in Mass Chains

We give a method for designing a mechanical impedance to suppress the propagation of disturbances along a chain of masses. The key feature of our method is that it is scale free. This means that it can be used to give a single, fixed, design, with provable performance guarantees in mass chains of any length. We illustrate the approach by designing a bidirectional control law in a vehicle platoon in a manner that is independent of the number of vehicles in the platoon

Anomalous transport in the crowded world of biological cells

A ubiquitous observation in cell biology is that diffusion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarising their densely packed and heterogeneous structures. The most familiar phenomenon is a power-law increase of the MSD, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations, non-gaussian distributions of the displacements, heterogeneous diffusion, and immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarise some widely used theoretical models: gaussian models like FBM and Langevin equations for visco-elastic media, the CTRW model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Emphasis is put on the spatio-temporal properties of the transport in terms of 2-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even for identical MSDs. Then, we review the theory underlying common experimental techniques in the presence of anomalous transport: single-particle tracking, FCS, and FRAP. We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where model systems mimic physiological crowding conditions. Finally, computer simulations play an important role in testing the theoretical models and corroborating the experimental findings. The review is completed by a synthesis of the theoretical and experimental progress identifying open questions for future investigation.Comment: review article, to appear in Rep. Prog. Phy

Combustion and Society: A Fire-Centred History of Energy Use

Fire is a force that links everyday human activities to some of the most powerful energetic movements of the Earth. Drawing together the energy-centred social theory of Georges Bataille, the fire-centred environmental history of Stephen Pyne, and the work of a number of ‘pyrotechnology’ scholars, the paper proposes that the generalized study of combustion is a key to contextualizing human energetic practices within a broader ‘economy’ of terrestrial and cosmic energy flows. We examine the relatively recent turn towards fossil-fuelled ‘internal combustion’ in the light of a much longer human history of ‘broadcast’ burning of vegetation and of artisanal pyrotechnologies – the use of heat to transform diverse materials. A combustion-centred analysis, it is argued, brings human collective life into closer contact with the geochemical and geologic conditions of earthly existence, while also pointing to the significance of explorative, experimental and even playful dispositions towards energy and matter. © 2014, SAGE Publications. All rights reserved

Stabilisation of non-equilibrium melt in a linear polyethylene in the presence of reduced graphene oxide nanoplatelets

In this thesis, investigation on stabilisation of non-equilibrium melt in the presence of high aspect ratio reduced graphene oxide nanosheets (rGON) was carried out. The non-equilibrium melt was prepared by melting disentangled ultrahigh molecular weight polyethylene (UHMWPE) which was synthesised using homogeneous single-site catalytic system. Rheological analyses of the disentangled UHMWPE/rGON nanocomposites prepared by physical mixing conclusively demonstrate the transformation of the melt from non-equilibrium state to equilibrium state was suppressed when the filler was added. The suppression effect on the transformation reached maximum at a certain filler content and the non-equilibrium melt state was retained within the experimental time, indicating the existence of strong filler-chain interaction that hindered the chain thermodynamics. In order to have better understanding of the suppression on the transformation, thermal analysis was performed on the non-equilibrium melts to follow the influence of non-equilibrium polymer melt on crystallisation kinetics of disentangled UHMWPE with and without rGON. The analysis was carried out by means of differential scanning calorimetry (DSC), and the changes in enthalpic relaxation process were found in good agreement with the rheological response of the melts. Thermal analysis showed the presence of two endothermic peaks in a sample of non-equilibrium melt that was left to crystallise under isothermal condition after melting. The high temperature endothermic peak (141.5 °C) was related to melting of crystals obtained on crystallisation from the disentangled domains of the heterogeneous (non-equilibrium) polymer melt, whereas the low melting temperature endothermic peak was related to melting of crystals formed from entangled domains of the melt. It was further found that with increasing the annealing time in melt (160 °C), the enthalpy of the lower melting temperature peak increased at the expense of the higher melting temperature peak, confirming transformation of the non-equilibrium polymer melt to equilibrium melt state. The enthalpic relaxation process as a function of rGON showed that at the specific content of the filler, where the suppression of the transformation reached maximum, the high endothermic peak remained independent of the annealing time of the polymer melt at 160 °C. This observation strengthened the concept that in the presence of the filler, chain dynamics was arrested to an extent that the everlasting non-equilibrium melt state having lower entanglement density was retained facilitating crystal formation having high melting endothermic temperature. This unique property of the nanocomposites provokes potential in facilitating their processability and making high demanding products in more complex dimensions

Patterns, Processes, And Scale: An Evaluation Of Ecological And Biogeochemical Functions Across An Arctic Stream Network

Ecosystems are highly variable in space and time. Understanding how spatial and temporal scales influence the patterns and processes occurring across watersheds presents a fundamental challenge to aquatic ecologists. The goal of this research was to elucidate the importance of spatial scale on stream structure and function within the Oksrukuyik Creek, an Arctic watershed located on the North Slope of Alaska (68°36’N, 149°12’W). The studies that comprise this dissertation address issues of scale that affect our ability to assess ecosystem function, such as: methodologies used to scale ecosystem measurements, multiple interacting scales, translation between scales, and scale-dependencies. The first methodological study examined approaches used to evaluate chlorophyll a in ethanol extracts of aquatic biofilms. Quantification of chlorophyll a is essential to the study of aquatic ecosystems, yet differences in methodology may introduce significant errors to its determination that can lead to issues of comparability between studies. A refined analytical procedure for the determination of chlorophyll a was developed under common acidification concentrations at multiple common reaction times. The refined procedure was used to develop a series of predictive equations that could be used to correct and normalize previously evaluated chlorophyll a data. The predictive equations were validated using benthic periphyton samples from northern Alaska and northwestern Vermont, U.S.A. The second study examined interaction and translation between scales by examining how normalization approaches affect measurements of metabolism and nutrient uptake in stream sediment biofilms. The effect of particle size and heterogeneity on rates of biofilm metabolism and nutrient uptake was evaluated in colonized and native sediments normalized using two different scaling approaches. Functional rates were normalized by projected surface area and sediment surface area scaling approaches, which account for the surface area in plan view (looking top-down) and the total surface area of all sediment particles, respectively. Findings from this study indicated that rates of biogeochemical function in heterogeneous habitats were directly related to the total sediment surface area available for biofilm colonization. The significant interactions between sediment surface area and rates of respiration and nutrient uptake suggest that information about the size and distribution of sediment particles could substantially improve our ability to predict and scale measurements of important biogeochemical functions in streams. The final study examined how stream nutrient dynamics are influenced by the presence or absence of lakes across a variety of discharge conditions and how catchment characteristics can be used to predict stream nutrients. Concentrations of dissolved organic carbon (DOC) and other inorganic nutrients were significantly greater in streams without lakes than in streams in with lakes and DOC, total dissolved nitrogen (TDN), and soluble reactive phosphorus concentrations increased as a function of discharge. Catchment characteristic models explained between 20% and 76% of the variance of the nutrients measured. Organic nutrient models were driven by antecedent precipitation and watershed vegetation cover type while inorganic nutrients were driven by antecedent precipitation, landscape characteristics and reach vegetation cover types. The developed models contribute to existing and future understanding of the changing Arctic and lend new confidence to the prediction of nutrient dynamics in streams where lakes are present

Final report for research project with title: Dynamics of Electrically-Induced Flow of Viscoelastic Fluids (grant number: PE8/906)

The interaction of an externally applied electric _eld with a liquid can give rise to interesting ow instabilities and pattern formation. For example, it has been demonstrated that the application of an electric _eld to an initially at polymer-air or polymer-polymer interface may result in an electrohydrodynamic instability which leads to the formation of columnar structures. This phenomenon could be exploited in order to form well-controlled patterns at the microscale and nanoscale with many practical engineering applications. The scope of the present research project is to achieve fundamental understanding of the electrically-induced ow of viscoelastic liquid _lms and to investigate the e_ect of various factors (e.g. the complex uid rheology, the presence of surface active materials or free charge along the liquid-air or liquid-liquid interfaces, geometric con_guration, etc) that may play an important role in such a process. It is well known that the dynamics and stability of liquid _lms can be very rich and it is characteristic that despite the fact that the _rst attempts to address the stability of a simple system such as a clean (without surfactants) Newtonian liquid _lm under the e_ect of gravity appear in the literature in the late 50's full understanding of the underlying mechanisms was not achieved until recently. One of the goals of the present study was to expand our understanding on the stability of the liquid _lms in the presence of surface active materials (surfactants). The reason for this is threefold. On one hand, the interaction of a surfactant-ladden _lm with an electric _eld is of interest for controlled pattern formation at the micro- and nano-scale. For example, ionic surfactants may interact with the electric _eld thereby a_ecting interfacial concentration and imposing speci_c patterns in the liquid. On the other hand, surfactants attribute non-Newtonian properties to the liquid, because the free surface attains surface elasticity and surface viscosity. Also, at high surfactant concentrations, micelles may form in the bulk and complicate its rheological behavior, rendering the solution viscoelastic. Finally, the governing equation that describes the conservation of surfactant concentration along the interface is identical to the equation that describes the conservation of free charge in the case of dielectric materials. These systems share many similar characteristics and it is possible to draw conclusions from the analogy between them. To this end, we formulated the Orr-Sommerfeld equation for a surfactant-laden _lm with appropriate boundary conditions, and solved it numerically for arbitrary disturbances and analytically for long-wave disturbances. The results from our analysis demonstrate the signi_cant e_ect of surfactant solubility and sorption kinetics on the stability characteristics and provided useful insight in the non-linear dynamics of the ow. The results from this this work have been published to the Journal of Fluid Mechanics. In a subsequent paper that has also been submitted for publication to the Journal of Fluid Mechanics we have investigated the role of surfactants on the mechanism of the long-wave instability in liquid _lm ows. We have also made announcements to several local and international conferences. A second goal of this research project was to develop a robust numerical algorithm capable of handling the ow of viscoelastic material with large interfacial deformations….

Investigating the role of proteostasis pathways in regulating the intracellular inclusion formation of firefly luciferase: a model system to study protein aggregation in cells

The maintenance of cellular protein homeostasis, or proteostasis, is dependent upon a complex network of molecular chaperones, degradation machinery and other regulatory factors, which together act to keep the proteome soluble and functional. Disturbances to proteostasis can lead to protein aggregation and inclusion formation, processes associated with a variety of neurodegenerative disorders. The heat shock proteins (Hsps) are a superfamily of molecular chaperones that are dramatically upregulated in response to cellular stress. The Hsps can bind aggregation-prone proteins and either refold or traffic them for degradation. One class of Hsps, the DNAJBs, act as co-factors of the Hsp70 machine and have been previously identified as potent suppressors of disease-related protein aggregation. This has raised the potential of targeting DNAJB chaperone action in the context of protein aggregation associated with disease. In the work described in this thesis, a destabilised isoform of the protein firefly luciferase (R188Q/R261Q Fluc; FlucDM) was overexpressed in cells to assess how components of the proteostasis machinery engage with aggregation-prone proteins to prevent them from forming intracellular inclusions