Intermittent search strategies

This review examines intermittent target search strategies, which combine phases of slow motion, allowing the searcher to detect the target, and phases of fast motion during which targets cannot be detected. We first show that intermittent search strategies are actually widely observed at various scales. At the macroscopic scale, this is for example the case of animals looking for food ; at the microscopic scale, intermittent transport patterns are involved in reaction pathway of DNA binding proteins as well as in intracellular transport. Second, we introduce generic stochastic models, which show that intermittent strategies are efficient strategies, which enable to minimize the search time. This suggests that the intrinsic efficiency of intermittent search strategies could justify their frequent observation in nature. Last, beyond these modeling aspects, we propose that intermittent strategies could be used also in a broader context to design and accelerate search processes.Comment: 72 pages, review articl

Motion of Particles as a Probe: Dynamics and Assembly in Gel Networks/Aqueous Media

Nanoparticles are of great interest with a wide variety of potential applications due to their unexpected but interesting physical properties which are different from bulk state, enable small length scale-driven transport through complex materials, and provide the building units for well-ordered structures. Observing the motion of nanoparticles provides information about surrounding microstructures, flow dynamics, and assembly processes by virtue of fluorescence of nanoparticles. However, the proper control of surface chemistry and the fluorescence of particles are both paramount and challenging to allow particles to be used in a quantitative and robust manner. This thesis describes the use of precisely-defined particles for characterizing and building complex structures. The research exploits advantages of the particle dynamics in three distinct studies: i) the tracking of single CdSe/ZnS core/shell QDs to characterize complex structures of hydrogels, ii) the transformation of dispersed QDs in bulk phase into unique ring assemblies at the air/liquid interface, and iii) the mapping of flow dynamics within an evaporating droplet. Chapter 2 describes the diffusion dynamics of single quantum dots (QDs) within polyacrylamide (PAAm) hydrogels to characterize the structural heterogeneity of gel networks by employing the single particle tracking (SPT) technique. Due to their photo-stable and highly fluorescent emission and its small size (4- 10 nm), individual QDs can be tracked by a fluorescence microscopy as they find pathways through structurally complex gel networks. This tracking provides information about spatiotemporal dynamics. The anomalous diffusion dynamics revealed by the motion of single QDs suggests that the structural heterogeneities of PAAm gels develop with increasing cross-linker content, and the length scales discovered are in a good agreement with the correlation length scale reported in the previous light scattering studies. Chapter 3 describes the assembly of QD rings at the air/water interface by ‘2-D Pickering emulsions’. This work emanated from the unexpected observation of QD rings on the droplet of QD solutions. These rings form from QDs adsorbed to the interfacial line of surfactant islands assembled at the interface, and the QDs mark islands, appearing as rings. This island assembly was found to occur only at a specific range of surfactant concentrations due to the phase transition. Uniformly dispersed QDs in the bulk phase affording the ring patterns exclusively at the air/water interface provides insight that the thermodynamic driving force arises at the interfacial line between three phases (air/water/surfactant islands). Finally, Chapter 4 details the radial flow dynamics within an evaporating droplet with a pinned contact line is investigated. By suspending and tracking fluorescent latex beads, the flow dynamics are quantified as a function of contact angle. This phenomenon, commonly called the “coffee ring effect”, is advantageous for patterning and depositing suspended solutes on substrates. To develop evaporative assembly as a scalable process, it is particularly important to understand the effect of contact angle on radial velocity. By tracking the motion of suspended particles in a droplet, we experimentally measured the flow dynamics, specifically the height averaged radial velocity, within an evaporating droplet in the range of contact angles 5-50o. We found that our experimental results are in a good agreement with the analytical prediction by Hu and Larson. Following the analytical predictions, we modified the original equation to a simplified equation that directly links radial velocity to contact angle and evaporation rate. This study provides insight into the manipulation of evaporative assembly processes on different substrates in terms of assembly kinetics and structural dimensions

Statistical imaging of transport in complex fluids: a journey from entangled polymers to living cells

Combining advanced fluorescence imaging, single particle tracking, and quantitative analysis in the framework of statistical mechanics, we studied several transport phenomena in complex fluids with nanometer and millisecond resolution. On the list are diffusion of nanoparticles and vesicles in crowded environments, reptational motion of polymers in entangled semidilute solutions, and active endosome transport along microtubules in living cells. We started from individual trajectories, and then converged statistically to aggregate properties of interests, with special emphasis on the fluctuations buried under the classic mean-field descriptions. The unified scientific theme behind these diversified subjects is to examine, with experiments designed as direct as possible, the commonly believed fundamental assumptions in those fields, such as Gaussian displacements in Fickian diffusion, harmonic confining potential of virtual tubes in polymer entanglements, and bidirectional motion of active intra-cellular transport. This series of efforts led us to discoveries of new phenomena, mechanisms, and concepts. This route, we termed as ???statistical imaging???, is expected to be widely useful at studying dynamic processes, especially in those emerging fields at the overlap of physics and biology

Gas transfer through clay barriers

Gas transport through clay-rocks can occur by different processes that can be basically subdivided into pressure-driven flow of a bulk gas phase and transport of dissolved gas either by molecular diffusion or advective water flow (Figure 1, Marschall et al., 2005). The relative importance of these transport mechanisms depends on the boundary conditions and the scale of the system. Pressure-driven volume flow (“Darcy flow”) of gas is the most efficient transport mechanism. It requires, however, pressure gradients that are sufficiently large to overcome capillary forces in the typically water-saturated rocks (purely gas-saturated argillaceous rocks are not considered in the present context). These pressure gradients may form as a consequence of the gravity field (buoyancy, compaction) or by gas generation processes (thermogenic, microbial, radiolytic). Dissolved gas may be transported by water flow along a hydraulic gradient. This process is not affected by capillary forces but constrained by the solubility of the gas. It has much lower transport efficiency than bulk gas phase flow. Molecular diffusion of dissolved gas, finally, is occurring essentially without constraints, ubiquitously and perpetually. Effective diffusion distances are, however, proportional to the square root of time, which limits the relevance of this transport process to the range of tens to hundreds of metres on a geological time scale (millions of years). 2 Process understanding and the quantification of the controlling parameters, like diffusion coefficients, capillary gas breakthrough pressures and effective gas permeability coefficients, is of great importance for up-scaling purposes in different research disciplines and applications. During the past decades, gas migration through fully water-saturated geological clay-rich barriers has been investigated extensively (Thomas et al., 1968, Pusch and Forsberg, 1983; Horseman et al., 1999; Galle, 2000; Hildenbrand et al., 2002; Marschall et al., 2005; Davy et al., 2009; Harrington et al., 2009, 2012a, 2014). All of these studies aimed at the analysis of experimental data determined for different materials (rocks of different lithotype, composition, compaction state) and pressure/temperature conditions. The clay-rocks investigated in these studies, ranged from unconsolidated to indurated clays and shales, all characterised by small pores (2-100 nm) and very low hydraulic conductivity (K < 10-12 m·s-1) or permeability coefficients (k < 10-19 m²). Studies concerning radioactive waste disposal include investigations of both the natural host rock formation and synthetic/engineered backfill material at a depth of a few hundred meters (IAEA, 2003, 2009). Within a geological disposal facility, hydrogen is generated by anaerobic corrosion of metals and through radiolysis of water (Rodwell et al., 1999; Yu and Weetjens, 2009). Additionally, methane and carbon dioxide are generated by microbial degradation of organic wastes (Rodwell et al., 1999; Ortiz et al., 2002; Johnson, 2006; Yu and Weetjens, 2009). The focus of carbon capture and storage (CCS) studies is on the analysis of the long-term sealing efficiency of lithologies above depleted reservoirs or saline aquifers, typically at larger depths (hundreds to thousands of meters). During the last decade, several studies were published on the sealing integrity of clay-rocks to carbon dioxide (Hildenbrand et al., 2004; Li et al., 2005; Hangx et al., 2009; Harrington et al., 2009; Skurtveit et al., 2012; Amann-Hildenbrand et al., 2013). In the context of petroleum system analysis, a significant volume of research has been undertaken regarding gas/oil expulsion mechanisms from sources rocks during burial history (Tissot & Pellet, 1971; Appold & Nunn, 2002), secondary migration (Luo et al., 2008) and the capillary sealing capacity of caprocks overlying natural gas accumulations (Berg, 1975; Schowalter, 1979; Krooss, 1992; Schlömer and Kross, 2004; Li et al., 2005; Berne et al., 2010). Recently, more attention has been paid to investigations of the transport efficiency of shales in the context of oil/gas shale production (Bustin et al., 2008; Eseme et al., 2012; Amann-Hildenbrand et al., 2012; Ghanizadeh et al., 2013, 2014). Analysis of the migration mechanisms within partly unlithified strata becomes important when explaining the 3 origin of overpressure zones, sub-seafloor gas domes and gas seepages (Hovland & Judd, 1988; Boudreau, 2012). The conduction of experiments and data evaluation/interpretation requires a profound process understanding and a high level of experience. The acquisition and preparation of adequate samples for laboratory experiments usually constitutes a major challenge and may have serious impact on the representativeness of the experimental results. Information on the success/failure rate of the sample preparation procedure should therefore be provided. Sample specimens “surviving” this procedure are subjected to various experimental protocols to derive information on their gas transport properties. The present overview first presents the theoretical background of gas diffusion and advective flow, each followed by a literature review (sections 2 and 3). Different experimental methods are described in sections 4.1 and 4.2. Details are provided on selected experiments performed at the Belgian Nuclear Research Centre (SCK-CEN, Belgium), Ecole Centrale de Lille (France), British Geological Survey (UK), and at RWTH-Aachen University (Germany) (section 4.3). Experimental data are discussed with respect to different petrophysical parameters outlined above: i) gas diffusion, ii) evolution of gas breakthrough, iii) dilation-controlled flow, and iv) effective gas permeability after breakthrough. These experiments were conducted under different pressure and temperature conditions, depending on sample type, burial depth and research focus (e.g. radioactive waste disposal, natural gas exploration, or carbon dioxide storage). The interpretation of the experimental results can be difficult and sometimes a clear discrimination between different mechanisms (and the controlling parameters) is not possible. This holds, for instance, for gas breakthrough experiments where the observed transport can be interpreted as intermittent, continuous, capillary- or dilation-controlled flow. Also, low gas flow rates through samples on the length-scale of centimetres can be equally explained by effective two-phase flow or diffusion of dissolved gas

Modelling and engineering artificial burnt-bridge ratchet molecular motors

Nature has evolved many mechanisms for achieving directed motion on the subcellular level. The burnt-bridge ratchet (BBR) is one mechanism used to accomplish superdiffusive motion over long distances via the successive cleavage of surface-bound energy-rich substrate sites. The BBR mechanism is utilized throughout Nature: it can be found in bacteria, plants, mammals, arthropods (for example Crustaceans and Cheliceratans), as well as non-life forms such as influenza. Motivated to understand how fundamental engineering principles alter BBR kinetics, we have built both computer models and synthetic experimental systems to understand BBR kinetics. By exploring the dynamics of BBRs through simulation we find that their motor-like properties are highly dependent on the number of catalytic legs, the distance that the legs can reach from the central hub, and the hub topology. We further explore how design features in the underlying landscape affect BBR dynamics. We find that reducing the landscape from two- to one-dimensional increases superdiffusivity but leads to a loss in processivity. We also find that landscape elasticity affects all motor-like dynamical properties of BBRs: there are different optimal stiffnesses for distinct dynamical characteristics. For a spherical-hub BBR, speed, processivity, and persistence length are optimized at high, intermediate and soft stiffnesses, respectively, while rolling is also optimized at a high surface stiffness. Towards our development of a novel micron-sized protein-based BBR in the lab, we develop a new surface chemistry passivation technique and apply it to the surface of nanowires, turning an array of waveguiding nanowires into a high-throughput biosensing assay. In a separate assay, our protein-based BBR, which we call the lawnmower, is implemented in two dimensions on glass cover slips prepared with our surface chemistry (which serves as the lawn). We find the lawnmower dynamics reproduce key observations found in other similar systems, such as saltatory motion and broadly varying anomalously diffusive behaviour. The successful implementation of the lawnmower marks the first demonstration of an artificial protein-based molecular motor

A Literature Review and Transport Modelling of Nanoparticles for Enhanced Oil Recovery

Master's thesis in Petroleum engineeringNanotechnology has been envisioned to transform every sector of industries, particularly in the petroleum industry. Numerous researches, especially on nano-EOR, have been done in the past few years and shown promising results for improving oil recovery. Injected nanoparticles (NPs) are believed to be able to form adsorption layers on the top of grain surface. The adsorptions layers then alter the wettability of the rock and reduce the interfacial tension. Due to the importance of the adsorption, numerous theoretical studies were performed to simulate the transport behavior of NPs in the porous media. The purpose of this thesis is to i) review the state-of-the-art progress of nanoparticles application in the petroleum industry especially in EOR, and ii) simulate the transport and adsorption of nanoparticles in the porous media. Literatures show that various types of nanoparticles can improve oil recovery through several mechanisms such as wettability alteration, interfacial tension reduction, disjoining pressure and mobility control. Parameters such as salinity, temperature, size, and concentration are substantial for nano-EOR. Several experiments indicate that NPs can improve the oil recovery significantly up to 20% after the primary recovery period. Classical Advection-Dispersion Equation (ADE) is commonly used to simulate particles flow in the porous media, but it fails to simulate NPs flow due to the adsorption that occurs. The colloidal filtration theory (CFT) is used in the study to accommodate the adsorption. Several modifications on CFT, such as dual site model (ISTM), increase the number of unknown variables that reduce the efficiency and the accuracy of the model. Therefore, a simple modified linear adsorption model (ML) is proposed by the author, followed by parameter sensitivity study to reduce the unknown parameters and understand each parameter affecting on the model. The simulation result indicates that CFT model is unable to predict the effluent history data. Differently, ML model demonstrates that it can predict the effluent history quite well. The comparison with ISTM indicates that both can simulate the behavior of NPs, and our ML model gives slightly better result than ISTM model. Therefore, the transport and adsorption of NPs can be predicted by the simple linear adsorption model

KT-SCALE INTERACTIONS OF ETHYLENE OXIDE AND ZWITTERIONIC COPOLYMERS WITH BLOOD PROTEINS AND MUCUS

Mucus linings and immune system protein coronas limit entry, targeting, and bioavailability of therapeutics. A common strategy to circumvent these barriers is to sterically stabilize therapeutics. This approach is based on fundamental work in colloid science but is often neglected in terms of mechanisms and interactions with biological macromolecules such as mucus and immune system proteins. A challenge is to understand polymer interactions and architectures in face of mucus and blood proteins to assess their stability to design colloidal therapeutics with enhanced bioavailability, safety, and targeting. In this dissertation, total internal reflection microscopy is used to directly, sensitively, and nonintrusively measure adsorbed PEG and zwitterionic (ZI) layer interactions against specific ions, proteins, and mucus. The use of TIRM offers kT-scale and nanometer resolution to offer unique insights needed for stabilizing colloidal therapeutics. For the first goal, we report direct measurements of solution behaviour of adsorbed PEG and ZI triblock copolymers as a function of specific ions. Our findings indicate qualitatively different and unique behavior for each polymer, where: PEO layers are [NaCl] independent but collapse with increasing [MgSO4]; PMAPS layers extend with increasing [NaCl] but becomes less repulsive with increasing [MgSO4], and PMPC layers are completely insensitive to both salts. A competition between solvated molecular interactions and structures explains the unique response of each polymer to non-specific and specific ion effects. For the second goal, we show how serum albumin and immunoglobin G, interact with PEG and ZI layers. Our results provide unambiguous evidence of exclusion of iii proteins from adsorbed PEG. Low molecular weight zwitterionic coatings were displaced by both BSA and IgG unlike PEG. Measured interactions and corresponding exclusion states were fitted theoretically to reflect penetration and exclusion of both proteins. Finally, we report kT-scale interactions of ZI and PEG coatings with mucin in various conditions such as low pH, mucolytic agents, and calcium chloride. Our results demonstrate that PEG and ZI coatings are repulsive towards mucin and provide a template for tuning polymer coatings to specifically adhere to mucus to achieve a balance of mucopenetration and mucoadhesion behavior for successful permeability through mucus

Molecular Motor Based on Single Chiral Tripodal Molecules Studied with STM

This work presents a single molecular motor driven by the current in an STM. Its chiral functional group is supposed to perform a rotation in a preferred direction, proven by Binomial tests to be statistically significant. The rotation is proposedly driven by the chiral-induced spin selectivity effect (CISS). However, the studies of the rotation on the dependence on the lateral tip position, voltage and current indicate that he CISS is unlikely to cause the preferred rotation direction