Oxygen transport and stem cell aggregation in stirred-suspension bioreactor cultures.

PubMed

Wu, Jincheng; Rostami, Mahboubeh Rahmati; Cadavid Olaya, Diana P; Tzanakakis, Emmanuel S

2014-01-01

Stirred-suspension bioreactors are a promising modality for large-scale culture of 3D aggregates of pluripotent stem cells and their progeny. Yet, cells within these clusters experience limitations in the transfer of factors and particularly O2 which is characterized by low solubility in aqueous media. Cultured stem cells under different O2 levels may exhibit significantly different proliferation, viability and differentiation potential. Here, a transient diffusion-reaction model was built encompassing the size distribution and ultrastructural characteristics of embryonic stem cell (ESC) aggregates. The model was coupled to experimental data from bioreactor and static cultures for extracting the effective diffusivity and kinetics of consumption of O2 within mouse (mESC) and human ESC (hESC) clusters. Under agitation, mESC aggregates exhibited a higher maximum consumption rate than hESC aggregates. Moreover, the reaction-diffusion model was integrated with a population balance equation (PBE) for the temporal distribution of ESC clusters changing due to aggregation and cell proliferation. Hypoxia was found to be negligible for ESCs with a smaller radius than 100 µm but became appreciable for aggregates larger than 300 µm. The integrated model not only captured the O2 profile both in the bioreactor bulk and inside ESC aggregates but also led to the calculation of the duration that fractions of cells experience a certain range of O2 concentrations. The approach described in this study can be employed for gaining a deeper understanding of the effects of O2 on the physiology of stem cells organized in 3D structures. Such frameworks can be extended to encompass the spatial and temporal availability of nutrients and differentiation factors and facilitate the design and control of relevant bioprocesses for the production of stem cell therapeutics.

Influence of surface coating on the intracellular behaviour of gold nanoparticles: a fluorescence correlation spectroscopy study.

PubMed

Silvestri, A; Di Silvio, D; Llarena, I; Murray, R A; Marelli, M; Lay, L; Polito, L; Moya, S E

2017-10-05

In the biomedical applications of nanoparticles (NPs), the proper choice of surface chemistry is a crucial aspect in their design. The nature of the coating can heavily impact the interaction of NPs with biomolecules, affect the state of aggregation, and ultimately determine their biological fate. As such, protein corona formation and the aggregation behaviour of gold NPs (Au NPs) are studied here. Au NPs are prepared with four distinct surface functionalisations, namely mercaptosuccinic acid (MSA), N-4-thiobutyroil glucosamine, HS-PEG 5000 and HS-alkyl-PEG 600 . Corona formation, aggregation, and the intracellular behaviour of the Au NPs are then investigated by means of Fluorescence Correlation Spectroscopy (FCS) in cell culture media and in live cells. To evaluate the state of aggregation and the formation of a protein corona, the Au NPs are incubated in cell media and the diffusion coefficient is determined via FCS. The in vitro behaviour is compared with the level of aggregation of the NPs in cells. Diffusion times of the NPs are estimated at different positions in the cell after a one hour incubation period. It is found that the majority of MSA and glucose-Au NPs are present inside the cell as slowly diffusing species with diffusion times (τ D ) greater than 6000 μs (hydrodynamic diameter >250 nm). PEGylated Au NPs adsorb a small amount of protein and manifest low agglomeration both in media and in living cells. In particular, the HS-alkyl-PEG 600 coating shows an excellent correlation between lower protein adsorption, 4-fold lower compared to the MSA coated NPs, and limited intracellular aggregation. In the case of single HS-alkyl-PEG 600 coated NPs, it is found that typical intracellular τ D values range from 500 to 1500 μs, indicating that these particles display reduced aggregation in the intracellular environment.

Aggregates and Superaggregates of Soot with Four Distinct Fractal Morphologies

NASA Technical Reports Server (NTRS)

Sorensen, C. M.; Kim, W.; Fry, D.; Chakrabarti, A.

2004-01-01

Soot formed in laminar diffusion flames of heavily sooting fuels evolves through four distinct growth stages which give rise to four distinct aggregate fractal morphologies. These results were inferred from large and small angle static light scattering from the flames, microphotography of the flames, and analysis of soot sampled from the flames. The growth stages occur approximately over four successive orders of magnitude in aggregate size. Comparison to computer simulations suggests that these four growth stages involve either diffusion limited cluster aggregation or percolation in either three or two dimensions.

Formation and Growth of Stacking Fault Tetrahedra in Ni via Vacancy Aggregation Mechanism

DOE PAGES

Aidhy, Dilpuneet S.; Lu, Chenyang; Jin, Ke; ...

2015-12-29

Using molecular dynamics simulations, the formation and growth of stacking fault tetrahedra (SFT) are captured by vacancy cluster diffusion and aggregation mechanisms in Ni. The vacancytetrahedron acts as a nucleation point for SFT formation. Simulations show that perfect SFT can grow to the next size perfect SFT via a vacancy aggregation mechanism. The stopping and range of ions in matter (SRIM) calculations and transmission electron microscopy (TEM) observations reveal that SFT can form farther away from the initial cascade-event locations, indicating the operation of diffusion-based vacancy-aggregation mechanism.

Formation and Growth of Stacking Fault Tetrahedra in Ni via Vacancy Aggregation Mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aidhy, Dilpuneet S.; Lu, Chenyang; Jin, Ke

Using molecular dynamics simulations, the formation and growth of stacking fault tetrahedra (SFT) are captured by vacancy cluster diffusion and aggregation mechanisms in Ni. The vacancytetrahedron acts as a nucleation point for SFT formation. Simulations show that perfect SFT can grow to the next size perfect SFT via a vacancy aggregation mechanism. The stopping and range of ions in matter (SRIM) calculations and transmission electron microscopy (TEM) observations reveal that SFT can form farther away from the initial cascade-event locations, indicating the operation of diffusion-based vacancy-aggregation mechanism.

Methane Hydrate Formation in Thick Sand Reservoirs: Long-range Gas Transport or Short-range Methane Diffusion?

NASA Astrophysics Data System (ADS)

You, K.; Flemings, P. B.

2016-12-01

We developed two 2-D numerical models to simulate hydrate formation by long range methane gas transport and short-range methane diffusion. We interpret that methane hydrates in thick sands are most likely formed by long range gas transport where methane gas is transported upward into the hydrate stability zone (HSZ) under buoyancy and locally forms hydrate to its stability limit. In short-range methane diffusion, methane is generated locally by biodegradation of organic matter in mud and diffused into bounding sands where it forms hydrate. We could not simulate enough methane transport by diffusion to account for its observed concentration in thick sands. In our models, we include the capillary effect on dissolved methane solubility and on the hydrate phase boundary, sedimentation and different compaction in sand and mud, fracture generation as well as the fully coupled multiphase flow and multicomponent transport. We apply our models to a 12 meter-thick hydrate-bearing sand layer at Walker Ridge 313, Northern Gulf of Mexico. With the long-range gas transport, hydrate saturation is greater than 90% and salinity is increased from seawater to about 8 wt.% through the entire sand. With short-range diffusion, hydrate saturation is more than 90% at the sand base and is less than 10% in the overlying section; salinity is close to seawater when sand is deposited to 800 meter below seafloor by short-range methane diffusion. With short-range diffusion, the amount of hydrate formed is much less than that interpreted from the well log data. Two transient gas layers separated by a hydrate layer are formed from short-range diffusion caused by capillary effect. This could be interpreted as a double bottom simulating reflector. This study provides further insights into different hydrate formation mechanisms, and could serve as a base to confirm the hydrate formation mechanism in fields.

Interaction of lysozyme protein with different sized silica nanoparticles and their resultant structures

NASA Astrophysics Data System (ADS)

Yadav, Indresh; Aswal, V. K.; Kohlbrecher, J.

2016-05-01

The interaction of model protein-lysozyme with three different sized anionic silica nanoparticles has been studied by UV-vis spectroscopy, dynamic light scattering (DLS) and small-angle neutron scattering (SANS). The surface area and curvature of the nanoparticles change with size, which significantly influence their interaction with protein. The lysozyme adsorbs on the surface of the nanoparticles due to electrostatic attraction and leads to the phase transformation from one phase (clear) to two-phase (turbid) of the nanoparticle-protein system. The dominance of lysozyme induced short-range attraction over long-range electrostatic repulsion between nanoparticles is responsible for phase transformation and modeled by the two-Yukawa potential. The magnitude of the attractive interaction increases with the size of the nanoparticles as a result the phase transformation commences relatively at lower concentration of lysozyme. The structure of the nanoparticle-protein system in two-phase is characterized by the diffusion limited aggregate type of mass fractal morphology.

Interaction of lysozyme protein with different sized silica nanoparticles and their resultant structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yadav, Indresh, E-mail: iykumarindresh288@gmail.com; Aswal, V. K.; Kohlbrecher, J.

The interaction of model protein-lysozyme with three different sized anionic silica nanoparticles has been studied by UV-vis spectroscopy, dynamic light scattering (DLS) and small-angle neutron scattering (SANS). The surface area and curvature of the nanoparticles change with size, which significantly influence their interaction with protein. The lysozyme adsorbs on the surface of the nanoparticles due to electrostatic attraction and leads to the phase transformation from one phase (clear) to two-phase (turbid) of the nanoparticle-protein system. The dominance of lysozyme induced short-range attraction over long-range electrostatic repulsion between nanoparticles is responsible for phase transformation and modeled by the two-Yukawa potential. Themore » magnitude of the attractive interaction increases with the size of the nanoparticles as a result the phase transformation commences relatively at lower concentration of lysozyme. The structure of the nanoparticle-protein system in two-phase is characterized by the diffusion limited aggregate type of mass fractal morphology.« less

The Rejuvenating Effect in Hot Asphalt Recycling by Mortar Transfer Ratio and Image Analysis.

PubMed

Wang, Fusong; Wang, Zipeng; Li, Chao; Xiao, Yue; Wu, Shaopeng; Pan, Pan

2017-05-24

Using a rejuvenator to improve the performance of asphalt pavement is an effective and economic way of hot asphalt recycling. This research analyzes the rejuvenating effect on aged asphalt by means of a Mortar Transfer Ratio (MTR) test, which concerns the ratio of asphalt mortar that moves from recycled aggregates (RAP aggregates) to fresh added aggregates when aged asphalt is treated with a regenerating agent and comes into contact with fresh aggregates. The proposed MTR test analyzes the regeneration in terms of the softening degree on aged asphalt when the rejuvenator is applied. The covered area ratio is studied with an image analyzing tool to understand the possibility of mortar transferring from RAP aggregates to fresh aggregates. Additionally, a micro-crack closure test is conducted and observed through a microscope. The repairing ability and diffusion characteristics of micro-cracks can therefore be analyzed. The test results demonstrate that the proposed mortar transfer ratio is a feasible way to evaluate rejuvenator diffusion during hot recycling. The mortar transfer ratio and uncovered area ratio on fresh aggregates are compatible, and can be used to quantify the contribution of the rejuvenator. Within a certain temperature range, the diffusing effect of the rejuvenator is better when the diffusing temperature is higher. The diffusion time of the rejuvenator is optimum when diffusion occurs for 4-8 h. When the rejuvenator is properly applied, the rough and cracking surface can be repaired, resulting in better covered aggregates. The micro-closure analysis visually indicates that rejuvenators can be used to repair the RAP aggregates during hot recycling.

The Rejuvenating Effect in Hot Asphalt Recycling by Mortar Transfer Ratio and Image Analysis

PubMed Central

Wang, Fusong; Wang, Zipeng; Li, Chao; Xiao, Yue; Wu, Shaopeng; Pan, Pan

2017-01-01

Using a rejuvenator to improve the performance of asphalt pavement is an effective and economic way of hot asphalt recycling. This research analyzes the rejuvenating effect on aged asphalt by means of a Mortar Transfer Ratio (MTR) test, which concerns the ratio of asphalt mortar that moves from recycled aggregates (RAP aggregates) to fresh added aggregates when aged asphalt is treated with a regenerating agent and comes into contact with fresh aggregates. The proposed MTR test analyzes the regeneration in terms of the softening degree on aged asphalt when the rejuvenator is applied. The covered area ratio is studied with an image analyzing tool to understand the possibility of mortar transferring from RAP aggregates to fresh aggregates. Additionally, a micro-crack closure test is conducted and observed through a microscope. The repairing ability and diffusion characteristics of micro-cracks can therefore be analyzed. The test results demonstrate that the proposed mortar transfer ratio is a feasible way to evaluate rejuvenator diffusion during hot recycling. The mortar transfer ratio and uncovered area ratio on fresh aggregates are compatible, and can be used to quantify the contribution of the rejuvenator. Within a certain temperature range, the diffusing effect of the rejuvenator is better when the diffusing temperature is higher. The diffusion time of the rejuvenator is optimum when diffusion occurs for 4–8 h. When the rejuvenator is properly applied, the rough and cracking surface can be repaired, resulting in better covered aggregates. The micro-closure analysis visually indicates that rejuvenators can be used to repair the RAP aggregates during hot recycling. PMID:28772935

Condensation versus diffusion. A spatial-scale-independent theory of aggregate structures in edible oils: applications to model systems and commercial shortenings studied via rheology and USAXS

NASA Astrophysics Data System (ADS)

Pink, David A.; Peyronel, Fernanda; Quinn, Bonnie; Singh, Pratham; Marangoni, Alejandro G.

2015-09-01

Understanding how solid fats structures come about in edible oils and quantifying their structures is of fundamental importance in developing edible oils with pre-selected characteristics. We considered the great range of fractal dimensions, from 1.91 to 2.90, reported from rheological measurements. We point out that, if the structures arise via DLA/RLA or DLCA/RLCA, as has been established using ultra small angle x-ray scattering (USAXS), we would expect fractal dimensions in the range ~1.7 to 2.1, and ~2.5 or ~3.0. We present new data for commercial fats and show that the fractal dimensions deduced lie outside these values. We have developed a model in which competition between two processes can lead to the range of fractal dimensions observed. The two processes are (i) the rate at which the solid fat particles are created as the temperature is decreased, and (ii) the rate at which these particles diffuse, thereby meeting and forming aggregates. We assumed that aggregation can take place essentially isotropically and we identified two characteristic times: a time characterizing the rate of creation of solid fats, {τ\\text{create}}(T)\\equiv 1/{{R}S}(T) , where {{R}S}(T) is the rate of solid condensation (cm3 s-1), and the diffusion time of solid fats, {τ\\text{diff}}≤ft(T,{{c}S}\\right)=< {{r}2}> /6{D}≤ft(T,{{c}S}\\right) , where {D}≤ft(T,{{c}S}\\right) is their diffusion coefficient and < {{r}2}> is the typical average distance that fats must move in order to aggregate. The intent of this model is to show that a simple process can lead to a wide range of fractal dimensions. We showed that in the limit of very fast solid creation, {τ\\text{create}}\\ll {τ\\text{diff}} the fractal dimension is predicted to be that of DLCA, ~1.7, relaxing to that of RLCA, 2.0-2.1, and that in the limit of very slow solid creation, {τ\\text{create}}\\gg {τ\\text{diff}} , the fractal dimension is predicted to be that obtained via DLA, ~2.5, relaxing to that of RLA, 3.0. We predict that, given a system which satisfies our model assumptions and which can either be cooled rapidly or cooled slowly to yield fractal dimensions {{D}\\text{rapid}} and {{D}\\text{slow}}~ then {{D}\\text{rapid}}≤slant {{D}\\text{slow}} . This is supported by both rheological [1] and USAXS measurements [2, 3] even though the latter models do not conform to the assumptions of those presented here.

On the origin of the phase-space diffusion limit in (dis)ordered protein aggregation

NASA Astrophysics Data System (ADS)

Gadomski, A.; Siódmiak, J.; Santamaría-Holek, I.

2013-08-01

Derivation of a phase-space diffusion limit (D-L) allows to obtain a useful formula for a characteristic width of the macroion-channeling filter, controlling model (dis)ordered protein aggregations in a non-ideal aqueous solution. The channel’s width is estimated at the order of an inner half-width of the Stern-type double layer circumventing the growing object and depends in turn on an interplay of the local thermal and electrostatic conditions. The interfacial channeling effect manifests at the edge of biomolecular hydration-duration dependent (non)Markovianity of the system. The interface vs. solution aggregation late-time dynamics are discussed in such local (non)isothermal context with the aim to suggest their experimental assessment.

The balance between adaptation to catalysts and competition radius shapes the total wealth, time variability and inequality

NASA Astrophysics Data System (ADS)

Davidovich, Hadar; Louzoun, Yoram

2013-05-01

The globalization of modern markets has led to the emergence of competition between producers in ever growing distances. This opens the interesting question in population dynamics of the effect of long-range competition. We here study a model of non-local competition to test the effect of the competition radius on the wealth distribution, using the framework of a stochastic birth-death process, with non-local interactions. We show that this model leads to non-trivial dynamics that can have implications in other domains of physics. Competition is studied in the context of the catalyst induced growth of autocatalytic agents, representing the growth of capital in the presence of investment opportunities. These agents are competing with all other agents in a given radius on growth possibilities. We show that a large scale competition leads to an extreme localization of the agents, where typically a single aggregate of agents can survive within a given competition radius. The survival of these aggregates is determined by the diffusion rates of the agents and the catalysts. For high and low agent diffusion rates, the agent population is always annihilated, while for intermediate diffusion rates, a finite agent population persists. Increasing the catalyst diffusion rate always leads to a decrease in the average agent population density. The extreme localization of the agents leads to the emergence of intermittent fluctuations, when a large aggregate of agents disappear. As the competition radius increases, so does the average agent density and its spatial variance as well as the volatility.

Electrochemical deposition of layered copper thin films based on the diffusion limited aggregation

PubMed Central

Wei, Chenhuinan; Wu, Guoxing; Yang, Sanjun; Liu, Qiming

2016-01-01

In this work layered copper films with smooth surface were successfully fabricated onto ITO substrate by electrochemical deposition (ECD) and the thickness of the films was nearly 60 nm. The resulting films were characterized by SEM, TEM, AFM, XPS, and XRD. We have investigated the effects of potential and the concentration of additives and found that 2D dendritic-like growth process leaded the formation of films. A suitable growth mechanism based on diffusion limited aggregation (DLA) mechanism for the copper films formation is presented, which are meaningful for further designing homogeneous and functional films. PMID:27734900

Exciton-Induced Degradation of Carbazole-Based Host Materials and Its Role in the Electroluminescence Spectral Changes in Phosphorescent Organic Light Emitting Devices with Electrical Aging.

PubMed

Yu, Hyeonghwa; Zhang, Yingjie; Cho, Yong Joo; Aziz, Hany

2017-04-26

We investigate the origins of the long-wavelength bands that appear in the emission spectra of carbazole-based host materials and play a role in the electroluminescence (EL) spectral changes of phosphorescent organic light emitting devices (PhOLEDs) with electrical aging. 4,4'-Bis(carbazol-9-yl)biphenyl (CBP) is used as a model carbazole host material and is studied using photoluminescence, EL, and atomic force microscopy measurements under various stress scenarios in both single and bilayer devices and in combination with various electron transport layer (ETL) materials. Results show that exciton-induced morphological aggregation of CBP is behind the appearance of those long-wavelength bands and that complexation between the aggregated CBP molecules and ETL molecules plays a role in this phenomenon. Comparisons between the effects of exciton and thermal stress suggest that exciton-induced aggregation may be limited to short-range molecular ordering or pairing (e.g., dimer or trimer species formation) versus longer-range ordering (crystallization) in the case of thermal stress. The findings provide new insights into exciton-induced degradation in wide band gap host materials and its role in limiting the stability of PhOLEDs.

The narrow pulse approximation and long length scale determination in xenon gas diffusion NMR studies of model porous media

NASA Technical Reports Server (NTRS)

Mair, R. W.; Sen, P. N.; Hurlimann, M. D.; Patz, S.; Cory, D. G.; Walsworth, R. L.

2002-01-01

We report a systematic study of xenon gas diffusion NMR in simple model porous media, random packs of mono-sized glass beads, and focus on three specific areas peculiar to gas-phase diffusion. These topics are: (i) diffusion of spins on the order of the pore dimensions during the application of the diffusion encoding gradient pulses in a PGSE experiment (breakdown of the narrow pulse approximation and imperfect background gradient cancellation), (ii) the ability to derive long length scale structural information, and (iii) effects of finite sample size. We find that the time-dependent diffusion coefficient, D(t), of the imbibed xenon gas at short diffusion times in small beads is significantly affected by the gas pressure. In particular, as expected, we find smaller deviations between measured D(t) and theoretical predictions as the gas pressure is increased, resulting from reduced diffusion during the application of the gradient pulse. The deviations are then completely removed when water D(t) is observed in the same samples. The use of gas also allows us to probe D(t) over a wide range of length scales and observe the long time asymptotic limit which is proportional to the inverse tortuosity of the sample, as well as the diffusion distance where this limit takes effect (approximately 1-1.5 bead diameters). The Pade approximation can be used as a reference for expected xenon D(t) data between the short and the long time limits, allowing us to explore deviations from the expected behavior at intermediate times as a result of finite sample size effects. Finally, the application of the Pade interpolation between the long and the short time asymptotic limits yields a fitted length scale (the Pade length), which is found to be approximately 0.13b for all bead packs, where b is the bead diameter. c. 2002 Elsevier Sciences (USA).

The narrow pulse approximation and long length scale determination in xenon gas diffusion NMR studies of model porous media.

PubMed

Mair, R W; Sen, P N; Hürlimann, M D; Patz, S; Cory, D G; Walsworth, R L

2002-06-01

We report a systematic study of xenon gas diffusion NMR in simple model porous media, random packs of mono-sized glass beads, and focus on three specific areas peculiar to gas-phase diffusion. These topics are: (i) diffusion of spins on the order of the pore dimensions during the application of the diffusion encoding gradient pulses in a PGSE experiment (breakdown of the narrow pulse approximation and imperfect background gradient cancellation), (ii) the ability to derive long length scale structural information, and (iii) effects of finite sample size. We find that the time-dependent diffusion coefficient, D(t), of the imbibed xenon gas at short diffusion times in small beads is significantly affected by the gas pressure. In particular, as expected, we find smaller deviations between measured D(t) and theoretical predictions as the gas pressure is increased, resulting from reduced diffusion during the application of the gradient pulse. The deviations are then completely removed when water D(t) is observed in the same samples. The use of gas also allows us to probe D(t) over a wide range of length scales and observe the long time asymptotic limit which is proportional to the inverse tortuosity of the sample, as well as the diffusion distance where this limit takes effect (approximately 1-1.5 bead diameters). The Padé approximation can be used as a reference for expected xenon D(t) data between the short and the long time limits, allowing us to explore deviations from the expected behavior at intermediate times as a result of finite sample size effects. Finally, the application of the Padé interpolation between the long and the short time asymptotic limits yields a fitted length scale (the Padé length), which is found to be approximately 0.13b for all bead packs, where b is the bead diameter. c. 2002 Elsevier Sciences (USA).

Elasticity and critical bending moment of model colloidal aggregates.

PubMed

Pantina, John P; Furst, Eric M

2005-04-08

The bending mechanics of singly bonded colloidal aggregates are measured using laser tweezers. We find that the colloidal bonds are capable of supporting significant torques, providing a direct measurement of the tangential interactions between particles. A critical bending moment marks the limit of linear bending elasticity, past which small-scale rearrangements occur. These mechanical properties underlie the rheology and dynamics of colloidal gels formed by diffusion-limited cluster aggregation, and give critical insight into the contact interactions between Brownian particles.

Archean Earth Atmosphere Fractal Haze Aggregates: Light Scattering Calculations and the Faint Young Sun Paradox

NASA Astrophysics Data System (ADS)

Boness, D. A.; Terrell-Martinez, B.

2010-12-01

As part of an ongoing undergraduate research project of light scattering calculations involving fractal carbonaceous soot aggregates relevant to current anthropogenic and natural sources in Earth's atmosphere, we have read with interest a recent paper [E.T. Wolf and O.B Toon,Science 328, 1266 (2010)] claiming that the Faint Young Sun paradox discussed four decades ago by Carl Sagan and others can be resolved without invoking heavy CO2 concentrations as a greenhouse gas warming the early Earth enough to sustain liquid water and hence allow the origin of life. Wolf and Toon report that a Titan-like Archean Earth haze, with a fractal haze aggregate nature due to nitrogen-methane photochemistry at high altitudes, should block enough UV light to protect the warming greenhouse gas NH3 while allowing enough visible light to reach the surface of the Earth. To test this hypothesis, we have employed a rigorous T-Matrix arbitrary-particle light scattering technique, to avoid the simplifications inherent in Mie-sphere scattering, on haze fractal aggregates at UV and visible wavelenths of incident light. We generate these model aggregates using diffusion-limited cluster aggregation (DLCA) algorithms, which much more closely fit actual haze fractal aggregates than do diffusion-limited aggregation (DLA) algorithms.

A diffusion based long-range and steady chemical gradient generator on a microfluidic device for studying bacterial chemotaxis

NASA Astrophysics Data System (ADS)

Murugesan, Nithya; Singha, Siddhartha; Panda, Tapobrata; Das, Sarit K.

2016-03-01

Studies on chemotaxis in microfluidics device have become a major area of research to generate physiologically similar environment in vitro. In this work, a novel micro-fluidic device has been developed to study chemo-taxis of cells in near physiological condition which can create controllable, steady and long-range chemical gradients using various chemo-effectors in a micro-channel. Hydrogels like agarose, collagen, etc, can be used in the device to maintain exclusive diffusive flux of various chemical species into the micro-channel under study. Variations of concentrations and flow rates of Texas Red dextran in the device revealed that an increase in the concentration of the dye in the feed from 6 to 18 μg ml-1, causes a steeper chemical gradient in the device, whereas the flow rate of the dye has practically no effect on the chemical gradient in the device. This observation confirms that a diffusion controlled chemical gradient is generated in the micro-channel. Chemo-taxis of E. coli cells were studied under the steady gradient of a chemo-attractant and a chemo-repellent separately in the same chemical gradient generator. For sorbitol and NiSO4·6H2O, the bacterial cells exhibit a steady distribution in the micro channel after 1 h and 30 min, respectively. From the distribution of bacterial population chemo-tactic strength of the chemo-effectors was estimated for E. coli. In a long microfluidic channel, migration behavior of bacterial cells under diffusion controlled chemical gradient showed chemotaxis, random movement, aggregation, and concentration dependent reverse chemotaxis.

Nanomorphology Characteristics of Thermally Annealed Pre Encapsulated P3HT:PCBM Thin Films Using Atomic Force Microscopy

DTIC Science & Technology

2014-10-30

fib- rils aggregate in bundles with the fullerene as the anneal- ing temperature increases. This bundle formation or grain features could indicate a...the diffusion lengths of charge carriers (∼10 nm). Past work on these fullerene networks have shown that trap distribution in devices is broader for...aver- age distance between polymer and fullerene molecules. The size of crystallites perhaps reach an upper limit in the range of 150 "C; beyond this

Direct Imaging of Long-Range Exciton Transport in Quantum Dot Superlattices by Ultrafast Microscopy.

PubMed

Yoon, Seog Joon; Guo, Zhi; Dos Santos Claro, Paula C; Shevchenko, Elena V; Huang, Libai

2016-07-26

Long-range charge and exciton transport in quantum dot (QD) solids is a crucial challenge in utilizing QDs for optoelectronic applications. Here, we present a direct visualization of exciton diffusion in highly ordered CdSe QDs superlattices by mapping exciton population using ultrafast transient absorption microscopy. A temporal resolution of ∼200 fs and a spatial precision of ∼50 nm of this technique provide a direct assessment of the upper limit for exciton transport in QD solids. An exciton diffusion length of ∼125 nm has been visualized in the 3 ns experimental time window and an exciton diffusion coefficient of (2.5 ± 0.2) × 10(-2) cm(2) s(-1) has been measured for superlattices constructed from 3.6 nm CdSe QDs with center-to-center distance of 6.7 nm. The measured exciton diffusion constant is in good agreement with Förster resonance energy transfer theory. We have found that exciton diffusion is greatly enhanced in the superlattices over the disordered films with an order of magnitude higher diffusion coefficient, pointing toward the role of disorder in limiting transport. This study provides important understandings on energy transport mechanisms in both the spatial and temporal domains in QD solids.

A discrete three-layer stack aggregate of a linear porphyrin tetramer: solution-phase structure elucidation by NMR and X-ray scattering.

PubMed

Hutin, Marie; Sprafke, Johannes K; Odell, Barbara; Anderson, Harry L; Claridge, Tim D W

2013-08-28

Formation of stacked aggregates can dramatically alter the properties of aromatic π-systems, yet the solution-phase structure elucidation of these aggregates is often impossible because broad distributions of species are formed, giving uninformative spectroscopic data. Here, we show that a butadiyne-linked zinc porphyrin tetramer forms a remarkably well-defined aggregate, consisting of exactly three molecules, in a parallel stacked arrangement (in chloroform at room temperature; concentration 1 mM-0.1 μM). The aggregate has a mass of 14.7 kDa. Unlike most previously reported aggregates, it gives sharp NMR resonances and aggregation is in slow exchange on the NMR time scale. The structure was elucidated using a range of NMR techniques, including diffusion-editing, (1)H-(29)Si HMBC, (1)H-(1)H COSY, TOCSY and NOESY, and (1)H-(13)C edited HSQC spectroscopy. Surprisingly, the (1)H-(1)H COSY spectrum revealed many long-range residual dipolar couplings (RDCs), and detailed analysis of magnetic field-induced (1)H-(13)C RDCs provided further evidence for the structural model. The size and shape of the aggregate is supported by small-angle X-ray scattering (SAXS) data. It adopts a geometry that maximizes van der Waals contact between the porphyrins, while avoiding clashes between side chains. The need for interdigitation of the side chains prevents formation of stacks consisting of more than three layers. Although a detailed analysis has only been carried out for one compound (the tetramer), comparison with the NMR spectra of other oligomers indicates that they form similar three-layer stacks. In all cases, aggregation can be prevented by addition of pyridine, although at low pyridine concentrations, disaggregation takes many hours to reach equilibrium.

On the radiative properties of soot aggregates part 1: Necking and overlapping

NASA Astrophysics Data System (ADS)

Yon, J.; Bescond, A.; Liu, F.

2015-09-01

There is a strong interest in accurately modelling the radiative properties of soot aggregates (also known as black carbon particles) emitted from combustion systems and fires to gain improved understanding of the role of black carbon to global warming. This study conducted a systematic investigation of the effects of overlapping and necking between neighbouring primary particles on the radiative properties of soot aggregates using the discrete dipole approximation. The degrees of overlapping and necking are quantified by the overlapping and necking parameters. Realistic soot aggregates were generated numerically by constructing overlapping and necking to fractal aggregates formed by point-touch primary particles simulated using a diffusion-limited cluster aggregation algorithm. Radiative properties (differential scattering, absorption, total scattering, specific extinction, asymmetry factor and single scattering albedo) were calculated using the experimentally measured soot refractive index over the spectral range of 266-1064 nm for 9 combinations of the overlapping and necking parameters. Overlapping and necking affect significantly the absorption and scattering properties of soot aggregates, especially in the near UV spectrum due to the enhanced multiple scattering effects within an aggregate. By using correctly modified aggregate properties (fractal dimension, prefactor, primary particle radius, and the number of primary particle) and by accounting for the effects of multiple scattering, the simple Rayleigh-Debye-Gans theory for fractal aggregates can reproduce reasonably accurate radiative properties of realistic soot aggregates.

Diffusion in Jammed Particle Packs.

PubMed

Bolintineanu, Dan S; Grest, Gary S; Lechman, Jeremy B; Silbert, Leonardo E

2015-08-21

Using random walk simulations we explore diffusive transport through monodisperse sphere packings over a range of packing fractions ϕ in the vicinity of the jamming transition at ϕ(c). Various diffusion properties are computed over several orders of magnitude in both time and packing pressure. Two well-separated regimes of normal "Fickian" diffusion, where the mean squared displacement is linear in time, are observed. The first corresponds to diffusion inside individual spheres, while the latter is the long-time bulk diffusion. The intermediate anomalous diffusion regime and the long-time value of the diffusion coefficient are both shown to be controlled by particle contacts, which in turn depend on proximity to ϕ(c). The time required to recover normal diffusion t* scales as (ϕ-ϕ(c))(-0.5) and the long-time diffusivity D(∞)∼(ϕ-ϕ(c))0.5, or D(∞)∼1/t*. It is shown that the distribution of mean first passage times associated with the escape of random walkers between neighboring particles controls both t* and D(∞) in the limit ϕ→ϕ(c).

Nucleation of Organic Molecules via a Hot Precursor State: Pentacene on Amorphous Mica

PubMed Central

2013-01-01

Organic thin films have attracted considerable interest due to their applicability in organic electronics. The classical scenario for thin film nucleation is the diffusion-limited aggregation (DLA). Recently, it has been shown that organic thin film growth is better described by attachment-limited aggregation (ALA). However, in both cases, an unusual relationship between the island density and the substrate temperature was observed. Here, we present an aggregation model that goes beyond the classical DLA or ALA models to explain this behavior. We propose that the (hot) molecules impinging on the surface cannot immediately equilibrate to the substrate temperature but remain in a hot precursor state. In this state, the molecules can migrate considerable distances before attaching to a stable or unstable island. This results in a significantly smaller island density than expected by assuming fast equilibration and random diffusion. We have applied our model to pentacene film growth on amorphous Muscovite mica. PMID:24340130

Three-Dimensional Analytical Modeling of Diffusion-Limited Solute Transport.

DTIC Science & Technology

1986-07-01

displace- ment through an aggregated oxisol , Soil Sci. Soc. Am. J., 46, 471-476. Nkedi-Kizza, P., J. W. Biggar, H. M. Selim, M. Th. van Genuchten, P. J...aggregated oxisol , Water Resources Research, 20(8), 1123-1130. National Research Council (NRC), 1984. Groundwater Contamination, Panel on Groundwater

Abnormal growth kinetics of h-BN epitaxial monolayer on Ru(0001) enhanced by subsurface Ar species

NASA Astrophysics Data System (ADS)

Wei, Wei; Meng, Jie; Meng, Caixia; Ning, Yanxiao; Li, Qunxiang; Fu, Qiang; Bao, Xinhe

2018-04-01

Growth kinetics of epitaxial films often follows the diffusion-limited aggregation mechanism, which shows a "fractal-to-compact" morphological transition with increasing growth temperature or decreasing deposition flux. Here, we observe an abnormal "compact-to-fractal" morphological transition with increasing growth temperature for hexagonal boron nitride growth on the Ru(0001) surface. The unusual growth process can be explained by a reaction-limited aggregation (RLA) mechanism. Moreover, introduction of the subsurface Ar atoms has enhanced this RLA growth behavior by decreasing both reaction and diffusion barriers. Our work may shed light on the epitaxial growth of two-dimensional atomic crystals and help to control their morphology.

An exact and efficient first passage time algorithm for reaction-diffusion processes on a 2D-lattice

NASA Astrophysics Data System (ADS)

Bezzola, Andri; Bales, Benjamin B.; Alkire, Richard C.; Petzold, Linda R.

2014-01-01

We present an exact and efficient algorithm for reaction-diffusion-nucleation processes on a 2D-lattice. The algorithm makes use of first passage time (FPT) to replace the computationally intensive simulation of diffusion hops in KMC by larger jumps when particles are far away from step-edges or other particles. Our approach computes exact probability distributions of jump times and target locations in a closed-form formula, based on the eigenvectors and eigenvalues of the corresponding 1D transition matrix, maintaining atomic-scale resolution of resulting shapes of deposit islands. We have applied our method to three different test cases of electrodeposition: pure diffusional aggregation for large ranges of diffusivity rates and for simulation domain sizes of up to 4096×4096 sites, the effect of diffusivity on island shapes and sizes in combination with a KMC edge diffusion, and the calculation of an exclusion zone in front of a step-edge, confirming statistical equivalence to standard KMC simulations. The algorithm achieves significant speedup compared to standard KMC for cases where particles diffuse over long distances before nucleating with other particles or being captured by larger islands.

A new empirical potential energy function for Ar2

NASA Astrophysics Data System (ADS)

Myatt, Philip T.; Dham, Ashok K.; Chandrasekhar, Pragna; McCourt, Frederick R. W.; Le Roy, Robert J.

2018-06-01

A critical re-analysis of all available spectroscopic and virial coefficient data for Ar2 has been used to determine an improved empirical analytic potential energy function that has been 'tuned' to optimise its agreement with viscosity, diffusion and thermal diffusion data, and whose short-range behaviour is in reasonably good agreement with the most recent ab initio calculations for this system. The recommended Morse/long-range potential function is smooth and differentiable at all distances, and incorporates both the correct theoretically predicted long-range behaviour and the correct limiting short-range functional behaviour. The resulting value of the well depth is ? cm-1 and the associated equilibrium distance is re = 3.766 (±0.002) Å, while the 40Ar s-wave scattering length is -714 Å.

Synthesis of size controllable cu-phthalocyanine nanofibers by simple solvent diffusion method and their electrochemical properties.

PubMed

Gao, Junshan; Cheng, Chuanwei; Zhou, Xuechao; Li, Yingying; Xu, Xiaoqi; Du, Xiguang; Zhang, Haiqian

2010-02-15

Tetra (2-isopropyl-5-methylphenoxy) substituted Cu-phthalocyanine nanofibers were obtained in large scale by a simple solvent diffusion method. The sizes of the fibers can be finely tuned under different solvent temperature. FE-SEM micrographs indicate that the length of the fibers changed from several hundreds micrometers to several hundreds nanometers and the width changed from several micrometers to several decade nanometers. XRD measurement showed a highly long-range ordered lamellar arrangement of the substituted Cu-phthalocyanine molecules in the microfiber and the UV-vis absorption spectrum of the fibers indicated an H-aggregate of the phthalocyanine molecules. The CV curves elucidate the CuPc fibers can be fabricated Faraday pseudocapacitor. Crown Copyright 2009. Published by Elsevier Inc. All rights reserved.

Ultra small angle x-ray scattering in complex mixtures of triacylglycerols

NASA Astrophysics Data System (ADS)

Peyronel, Fernanda; Quinn, Bonnie; Marangoni, Alejandro G.; Pink, David A.

2014-11-01

Ultra-small angle x-ray scattering (USAXS) has been used to elucidate, in situ, the aggregation structure of unsheared model edible oils. Each system comprised one or two solid lipids and a combination of liquid lipids. The 3D nano- to micro-structures of each system were characterized. The length scale investigated, using the Bonse-Hart camera at beamline ID-15D at the Advanced Photon Source, ANL, ranged from 300 Å-10 µm. Using the Unified Fit model, level-1 analysis showed that the scatterers were 2D objects with either a smooth, a rough, or a diffuse surface. These 2D objects had an average radius of gyration Rg1 between 200-1500 Å. Level-2 analysis displayed a slope between -1 and -2. Use of the Guinier-Porod model gave s ≈ 1 thus showing that it was cylinders (TAGwoods) aggregating with fractal dimension 1 ≤ D2 ≤ 2. D2 = 1 is consistent with 1D structures formed from TAGwoods, while D2 = 2 implies that the TAGwoods had formed structures characteristic of diffusion or reaction limited cluster-cluster aggregation (DLCA/RLCA). These aggregates exhibited radii of gyration, Rg2, between 2500 and 6500 Å. Level-3 analyses showed diffuse surfaces, for most of the systems. These interpretations are in accord with theoretical models which studied crystalline nano-platelets (CNPs) coated with nano-scale layers arising from phase separation at the CNP surfaces. These layers could be due to either liquid-liquid phase separation with the CNPs coated, uniformly or non-uniformly, by a diffuse layer of TAGs, or solid-liquid phase separation with the CNPs coated by a rough layer of crystallites. A fundamental understanding of the self-organizing structures arising in these systems helps advance the characterization of fat crystal networks from nanometres to micrometres. This research can be used to design novel fat structures that use healthier fats via nano- and meso-scale structural engineering.

Lattice animals in diffusion limited binary colloidal system

NASA Astrophysics Data System (ADS)

Shireen, Zakiya; Babu, Sujin B.

2017-08-01

In a soft matter system, controlling the structure of the amorphous materials has been a key challenge. In this work, we have modeled irreversible diffusion limited cluster aggregation of binary colloids, which serves as a model for chemical gels. Irreversible aggregation of binary colloidal particles leads to the formation of a percolating cluster of one species or both species which are also called bigels. Before the formation of the percolating cluster, the system forms a self-similar structure defined by a fractal dimension. For a one component system when the volume fraction is very small, the clusters are far apart from each other and the system has a fractal dimension of 1.8. Contrary to this, we will show that for the binary system, we observe the presence of lattice animals which has a fractal dimension of 2 irrespective of the volume fraction. When the clusters start inter-penetrating, we observe a fractal dimension of 2.5, which is the same as in the case of the one component system. We were also able to predict the formation of bigels using a simple inequality relation. We have also shown that the growth of clusters follows the kinetic equations introduced by Smoluchowski for diffusion limited cluster aggregation. We will also show that the chemical distance of a cluster in the flocculation regime will follow the same scaling law as predicted for the lattice animals. Further, we will also show that irreversible binary aggregation comes under the universality class of the percolation theory.

Short-range, overpressure-driven methane migration in coarse-grained gas hydrate reservoirs

DOE PAGES

Nole, Michael; Daigle, Hugh; Cook, Ann E.; ...

2016-08-31

Two methane migration mechanisms have been proposed for coarse-grained gas hydrate reservoirs: short-range diffusive gas migration and long-range advective fluid transport from depth. Herein we demonstrate that short-range fluid flow due to overpressure in marine sediments is a significant additional methane transport mechanism that allows hydrate to precipitate in large quantities in thick, coarse-grained hydrate reservoirs. Two-dimensional simulations demonstrate that this migration mechanism, short-range advective transport, can supply significant amounts of dissolved gas and is unencumbered by limitations of the other two end-member mechanisms. Here, short-range advective migration can increase the amount of methane delivered to sands as compared tomore » the slow process of diffusion, yet it is not necessarily limited by effective porosity reduction as is typical of updip advection from a deep source.« less

Short-range, overpressure-driven methane migration in coarse-grained gas hydrate reservoirs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nole, Michael; Daigle, Hugh; Cook, Ann E.

Two methane migration mechanisms have been proposed for coarse-grained gas hydrate reservoirs: short-range diffusive gas migration and long-range advective fluid transport from depth. Herein we demonstrate that short-range fluid flow due to overpressure in marine sediments is a significant additional methane transport mechanism that allows hydrate to precipitate in large quantities in thick, coarse-grained hydrate reservoirs. Two-dimensional simulations demonstrate that this migration mechanism, short-range advective transport, can supply significant amounts of dissolved gas and is unencumbered by limitations of the other two end-member mechanisms. Here, short-range advective migration can increase the amount of methane delivered to sands as compared tomore » the slow process of diffusion, yet it is not necessarily limited by effective porosity reduction as is typical of updip advection from a deep source.« less

Congested Aggregation via Newtonian Interaction

NASA Astrophysics Data System (ADS)

Craig, Katy; Kim, Inwon; Yao, Yao

2018-01-01

We consider a congested aggregation model that describes the evolution of a density through the competing effects of nonlocal Newtonian attraction and a hard height constraint. This provides a counterpoint to existing literature on repulsive-attractive nonlocal interaction models, where the repulsive effects instead arise from an interaction kernel or the addition of diffusion. We formulate our model as the Wasserstein gradient flow of an interaction energy, with a penalization to enforce the constraint on the height of the density. From this perspective, the problem can be seen as a singular limit of the Keller-Segel equation with degenerate diffusion. Two key properties distinguish our problem from previous work on height constrained equations: nonconvexity of the interaction kernel (which places the model outside the scope of classical gradient flow theory) and nonlocal dependence of the velocity field on the density (which causes the problem to lack a comparison principle). To overcome these obstacles, we combine recent results on gradient flows of nonconvex energies with viscosity solution theory. We characterize the dynamics of patch solutions in terms of a Hele-Shaw type free boundary problem and, using this characterization, show that in two dimensions patch solutions converge to a characteristic function of a disk in the long-time limit, with an explicit rate on the decay of the energy. We believe that a key contribution of the present work is our blended approach, combining energy methods with viscosity solution theory.

On the radiative properties of soot aggregates - Part 2: Effects of coating

NASA Astrophysics Data System (ADS)

Liu, Fengshan; Yon, Jérôme; Bescond, Alexandre

2016-03-01

The effects of weakly absorbing material coating on soot have attracted considerable research attention in recent years due to the significant influence of such coating on soot radiative properties and the large differences predicted by different numerical models. Soot aggregates were first numerically generated using the diffusion limited cluster aggregation algorithm to produce fractal aggregates formed by log-normally distributed polydisperse spherical primary particles in point-touch. These aggregates were then processed by adding a certain amount of primary particle overlapping and necking to simulate the soot morphology observed from transmission electron microscopy images. After this process, a layer of WAM coating of different thicknesses was added to these more realistic soot aggregates. The radiative properties of these coated soot aggregates over the spectral range of 266-1064 nm were calculated by the discrete dipole approximation (DDA) using the spectrally dependent refractive index of soot for four aggregates containing Np=1, 20, 51 and 96 primary particles. The considered coating thicknesses range from 0% (no coating) up to 100% coating in terms of the primary particle diameter. Coating enhances both the particle absorption and scattering cross sections, with much stronger enhancement to the scattering one, as well as the asymmetry factor and the single scattering albedo. The absorption enhancement is stronger in the UV than in the visible and the near infrared. The simple corrections to the Rayleigh-Debye-Gans fractal aggregates theory for uncoated soot aggregates are found not working for coated soot aggregates. The core-shell model significantly overestimates the absorption enhancement by coating in the visible and the near infrared compared to the DDA results of the coated soot particle. Treating an externally coated soot aggregate as an aggregate formed by individually coated primary particles significantly underestimates the absorption enhancement by coating in the visible and the near infrared.

An exact and efficient first passage time algorithm for reaction–diffusion processes on a 2D-lattice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bezzola, Andri, E-mail: andri.bezzola@gmail.com; Bales, Benjamin B., E-mail: bbbales2@gmail.com; Alkire, Richard C., E-mail: r-alkire@uiuc.edu

2014-01-01

We present an exact and efficient algorithm for reaction–diffusion–nucleation processes on a 2D-lattice. The algorithm makes use of first passage time (FPT) to replace the computationally intensive simulation of diffusion hops in KMC by larger jumps when particles are far away from step-edges or other particles. Our approach computes exact probability distributions of jump times and target locations in a closed-form formula, based on the eigenvectors and eigenvalues of the corresponding 1D transition matrix, maintaining atomic-scale resolution of resulting shapes of deposit islands. We have applied our method to three different test cases of electrodeposition: pure diffusional aggregation for largemore » ranges of diffusivity rates and for simulation domain sizes of up to 4096×4096 sites, the effect of diffusivity on island shapes and sizes in combination with a KMC edge diffusion, and the calculation of an exclusion zone in front of a step-edge, confirming statistical equivalence to standard KMC simulations. The algorithm achieves significant speedup compared to standard KMC for cases where particles diffuse over long distances before nucleating with other particles or being captured by larger islands.« less

Colloidal Aggregate Structure under Shear by USANS

NASA Astrophysics Data System (ADS)

Chatterjee, Tirtha; van Dyk, Antony K.; Ginzburg, Valeriy V.; Nakatani, Alan I.

2015-03-01

Paints are complex formulations of polymeric binders, inorganic pigments, dispersants, surfactants, colorants, rheology modifiers, and other additives. A commercially successful paint exhibits a desired viscosity profile over a wide shear rate range from 10-5 s-1 for settling to >104 s-1 for rolling, and spray applications. Understanding paint formulation structure is critical as it governs the paint viscosity profile. However, probing paint formulation structure under shear is a challenging task due to the formulation complexity containing structures with different hierarchical length scales and their alterations under the influence of an external flow field. In this work mesoscale structures of paint formulations under shear are investigated using Ultra Small-Angle Neutron Scattering (rheo-USANS). Contrast match conditions were utilized to independently probe the structure of latex binder particle aggregates and the TiO2 pigment particle aggregates. Rheo-USANS data revealed that the aggregates are fractal in nature and their self-similarity dimensions and correlations lengths depend on the chemistry of the binder particles, the type of rheology modifier present and the shear stress imposed upon the formulation. These results can be explained in the framework of diffusion and reaction limited transient aggregates structure evolution under simple shear.

Numerical Simulations of Single and Multiple Scattering by Fractal Ice Clusters

NASA Technical Reports Server (NTRS)

Dlugach, Janna M.; Mishchenko, Michael I.; Mackowski, Daniel W.

2011-01-01

We consider the scattering model in the form of a vertically and horizontally homogeneous particulate slab of an arbitrary optical thickness composed of widely separated fractal aggregates built of small spherical ice monomers. The aggregates are generated by applying three different approaches, including simulated cluster-cluster aggregation (CCA) and diffusion-limited aggregation (DLA) procedures. Having in mind radar remote-sensing applications, we report and analyze the results of computations of the backscattering circular polarization ratio obtained using efficient superposition T-matrix and vector radiative-transfer codes. The computations have been performed at a wavelength of 12.6 cm for fractal aggregates with the following characteristics: monomer refractive index m=1.78+i0.003, monomer radius r=1 cm, monomer packing density p=0.2, overall aggregate radii R in the range 4<=R<=10 cm and fractal dimensions D(sub f) 2.5 and 3. We show that for aggregates generated with simulated CCA and DLA procedures, the respective values of the backscattering circular polarization ratio differ weakly for D(sub f) 2.5, but the differences can increase somewhat for D(sub f)3, especially in case of an optically semi-infinite medium. For aggregates with a spheroidal overall shape, the dependence of the circular polarization ratio on the cluster morphology can be quite significant and increases with increasing the aspect ratio of the circumscribing spheroid.

Absence of a charge diffusion pole at finite energies in an exactly solvable interacting flat-band model in d dimensions

NASA Astrophysics Data System (ADS)

Phillips, Philip W.; Setty, Chandan; Zhang, Shuyi

2018-05-01

Motivated by recent bounds for charge diffusion in critical matter, we investigate the following question: What sets the scale for the velocity for diffusing degrees of freedom in a scale-invariant system? To make our statements precise, we analyze the diffusion pole in an exactly solvable model for a Mott transition in the presence of a long-range interaction term. To achieve scale invariance, we limit our discussion to the flat-band regime. We find in this limit that the diffusion pole, which would normally obtain at finite energy, is pushed to zero energy, resulting in a vanishing of the diffusion constant. This occurs even in the presence of interactions in certain limits, indicating the robustness of this result to the inclusion of a scale in the problem. Consequently, scale invariance precludes any reasonable definition of the diffusion constant. Nonetheless, we do find that a scale can be defined, albeit irrelevant to diffusion, which is the product of the squared band velocity and the density of states.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Siqi; Senses, Erkan; Jiao, Yang

Nanoparticles functionalized with long polymer chains at low graft density are interesting systems to study structure–dynamic relationships in polymer nanocomposites since they are shown to aggregate into strings in both solution and melts and also into spheres and branched aggregates in the presence of free polymer chains. Our work investigates structure and entanglement effects in composites of polystyrene-grafted iron oxide nanoparticles by measuring particle relaxations using X-ray photon correlation spectroscopy. And for particles within highly ordered strings and aggregated systems, they experience a dynamically heterogeneous environment displaying hyperdiffusive relaxation commonly observed in jammed soft glassy systems. Furthermore, particle dynamics ismore » diffusive for branched aggregated structures which could be caused by less penetration of long matrix chains into brushes. These results suggest that particle motion is dictated by the strong interactions of chains grafted at low density with the host matrix polymer.« less

Ensemble and single particle fluorimetric techniques in concerted action to study the diffusion and aggregation of the glycine receptor α3 isoforms in the cell plasma membrane.

PubMed

Notelaers, Kristof; Smisdom, Nick; Rocha, Susana; Janssen, Daniel; Meier, Jochen C; Rigo, Jean-Michel; Hofkens, Johan; Ameloot, Marcel

2012-12-01

The spatio-temporal membrane behavior of glycine receptors (GlyRs) is known to be of influence on receptor homeostasis and functionality. In this work, an elaborate fluorimetric strategy was applied to study the GlyR α3K and L isoforms. Previously established differential clustering, desensitization and synaptic localization of these isoforms imply that membrane behavior is crucial in determining GlyR α3 physiology. Therefore diffusion and aggregation of homomeric α3 isoform-containing GlyRs were studied in HEK 293 cells. A unique combination of multiple diffraction-limited ensemble average methods and subdiffraction single particle techniques was used in order to achieve an integrated view of receptor properties. Static measurements of aggregation were performed with image correlation spectroscopy (ICS) and, single particle based, direct stochastic optical reconstruction microscopy (dSTORM). Receptor diffusion was measured by means of raster image correlation spectroscopy (RICS), temporal image correlation spectroscopy (TICS), fluorescence recovery after photobleaching (FRAP) and single particle tracking (SPT). The results show a significant difference in diffusion coefficient and cluster size between the isoforms. This reveals a positive correlation between desensitization and diffusion and disproves the notion that receptor aggregation is a universal mechanism for accelerated desensitization. The difference in diffusion coefficient between the clustering GlyR α3L and the non-clustering GlyR α3K cannot be explained by normal diffusion. SPT measurements indicate that the α3L receptors undergo transient trapping and directed motion, while the GlyR α3K displays mild hindered diffusion. These findings are suggestive of differential molecular interaction of the isoforms after incorporation in the membrane. Copyright © 2012 Elsevier B.V. All rights reserved.

Two-Dimensional Animal-Like Fractals in Thin Films

NASA Astrophysics Data System (ADS)

Gao, Hong-jun; Xue, Zeng-quan; Wu, Quan-de; Pang, Shi-jin

1996-02-01

We present a few unique animal-like fractal patterns in ionized-cluster-beam deposited fullerene-tetracyanoquinodimethane thin films. The fractal patterns consisting of animal-like aggregates such as "fishes" and "quasi-seahorses" have been characterized by transmission electron microscopy. The results indicate that the small aggregates of the animal-like body are composed of many single crystals whose crystalline directions are generally different. The formation of the fractal patterns can be attributed to the cluster-diffusion-limited aggregation.

Traveling front solutions to directed diffusion-limited aggregation, digital search trees, and the Lempel-Ziv data compression algorithm.

PubMed

Majumdar, Satya N

2003-08-01

We use the traveling front approach to derive exact asymptotic results for the statistics of the number of particles in a class of directed diffusion-limited aggregation models on a Cayley tree. We point out that some aspects of these models are closely connected to two different problems in computer science, namely, the digital search tree problem in data structures and the Lempel-Ziv algorithm for data compression. The statistics of the number of particles studied here is related to the statistics of height in digital search trees which, in turn, is related to the statistics of the length of the longest word formed by the Lempel-Ziv algorithm. Implications of our results to these computer science problems are pointed out.

Traveling front solutions to directed diffusion-limited aggregation, digital search trees, and the Lempel-Ziv data compression algorithm

NASA Astrophysics Data System (ADS)

Majumdar, Satya N.

2003-08-01

We use the traveling front approach to derive exact asymptotic results for the statistics of the number of particles in a class of directed diffusion-limited aggregation models on a Cayley tree. We point out that some aspects of these models are closely connected to two different problems in computer science, namely, the digital search tree problem in data structures and the Lempel-Ziv algorithm for data compression. The statistics of the number of particles studied here is related to the statistics of height in digital search trees which, in turn, is related to the statistics of the length of the longest word formed by the Lempel-Ziv algorithm. Implications of our results to these computer science problems are pointed out.

Direct Imaging of Frenkel Exciton Transport by Ultrafast Microscopy.

PubMed

Zhu, Tong; Wan, Yan; Huang, Libai

2017-07-18

Long-range transport of Frenkel excitons is crucial for achieving efficient molecular-based solar energy harvesting. Understanding of exciton transport mechanisms is important for designing materials for solar energy applications. One major bottleneck in unraveling of exciton transport mechanisms is the lack of direct measurements to provide information in both spatial and temporal domains, imposed by the combination of fast energy transfer (typically ≤1 ps) and short exciton diffusion lengths (typically ≤100 nm). This challenge requires developing experimental tools to directly characterize excitation energy transport, and thus facilitate the elucidation of mechanisms. To address this challenge, we have employed ultrafast transient absorption microscopy (TAM) as a means to directly image exciton transport with ∼200 fs time resolution and ∼50 nm spatial precision. By mapping population in spatial and temporal domains, such approach has unraveled otherwise obscured information and provided important parameters for testing exciton transport models. In this Account, we discuss the recent progress in imaging Frenkel exciton migration in molecular crystals and aggregates by ultrafast microscopy. First, we establish the validity of the TAM methods by imaging singlet and triplet exciton transport in a series of polyacene single crystals that undergo singlet fission. A new singlet-mediated triplet transport pathway has been revealed by TAM, resulting from the equilibrium between triplet and singlet exciton populations. Such enhancement of triplet exciton transport enables triplet excitons to migrate as singlet excitons and leads to orders of magnitude faster apparent triplet exciton diffusion rate in the picosecond and nanosecond time scales, favorable for solar cell applications. Next we discuss how information obtained by ultrafast microscopy can evaluate coherent effects in exciton transport. We use tubular molecular aggregates that could support large exciton delocalization sizes as a model system. The initial experiments measure exciton diffusion constants of 3-6 cm 2 s -1 , 3-5 times higher than the incoherent limit predicted by theory, suggesting that coherent effects play a role. In summary, combining ultrafast spectroscopic methods with microscopic techniques provides a direct approach for obtaining important parameters to unravel the underlying exciton transport mechanisms in molecular solids. We discuss future directions to bridge the gap in understanding of fundamental energy transfer theories to include coherent and incoherent effects. We are still in the infancy of ultrafast microscopy, and the vast potential is not limited to the systems discussed in this Account.

A Gossip-based Energy Efficient Protocol for Robust In-network Aggregation in Wireless Sensor Networks

NASA Astrophysics Data System (ADS)

Fauji, Shantanu

We consider the problem of energy efficient and fault tolerant in--network aggregation for wireless sensor networks (WSNs). In-network aggregation is the process of aggregation while collecting data from sensors to the base station. This process should be energy efficient due to the limited energy at the sensors and tolerant to the high failure rates common in sensor networks. Tree based in--network aggregation protocols, although energy efficient, are not robust to network failures. Multipath routing protocols are robust to failures to a certain degree but are not energy efficient due to the overhead in the maintenance of multiple paths. We propose a new protocol for in-network aggregation in WSNs, which is energy efficient, achieves high lifetime, and is robust to the changes in the network topology. Our protocol, gossip--based protocol for in-network aggregation (GPIA) is based on the spreading of information via gossip. GPIA is not only adaptive to failures and changes in the network topology, but is also energy efficient. Energy efficiency of GPIA comes from all the nodes being capable of selective message reception and detecting convergence of the aggregation early. We experimentally show that GPIA provides significant improvement over some other competitors like the Ridesharing, Synopsis Diffusion and the pure version of gossip. GPIA shows ten fold, five fold and two fold improvement over the pure gossip, the synopsis diffusion and Ridesharing protocols in terms of network lifetime, respectively. Further, GPIA retains gossip's robustness to failures and improves upon the accuracy of synopsis diffusion and Ridesharing.

Structure and Entanglement Factors on Dynamics of Polymer-Grafted Nanoparticles

DOE PAGES

Liu, Siqi; Senses, Erkan; Jiao, Yang; ...

2016-04-15

Nanoparticles functionalized with long polymer chains at low graft density are interesting systems to study structure–dynamic relationships in polymer nanocomposites since they are shown to aggregate into strings in both solution and melts and also into spheres and branched aggregates in the presence of free polymer chains. Our work investigates structure and entanglement effects in composites of polystyrene-grafted iron oxide nanoparticles by measuring particle relaxations using X-ray photon correlation spectroscopy. And for particles within highly ordered strings and aggregated systems, they experience a dynamically heterogeneous environment displaying hyperdiffusive relaxation commonly observed in jammed soft glassy systems. Furthermore, particle dynamics ismore » diffusive for branched aggregated structures which could be caused by less penetration of long matrix chains into brushes. These results suggest that particle motion is dictated by the strong interactions of chains grafted at low density with the host matrix polymer.« less

Island size distribution with hindered aggregation

NASA Astrophysics Data System (ADS)

González, Diego Luis; Camargo, Manuel; Sánchez, Julián A.

2018-05-01

We study the effect of hindered aggregation on the island formation processes for a one-dimensional model of epitaxial growth with arbitrary nucleus size i . In the proposed model, the attachment of monomers to islands is hindered by an aggregation barrier, ɛa, which decreases the hopping rate of monomers to the islands. As ɛa increases, the system exhibits a crossover between two different regimes; namely, from diffusion-limited aggregation to attachment-limited aggregation. The island size distribution, P (s ) , is calculated for different values of ɛa by a self-consistent approach involving the nucleation and aggregation capture kernels. The results given by the analytical model are compared with those from kinetic Monte Carlo simulations, finding a close agreement between both sets of data for all considered values of i and ɛa. As the aggregation barrier increases, the spatial effect of fluctuations on the density of monomers can be neglected and P (s ) smoothly approximates to the limit distribution P (s ) =δs ,i +1 . In the crossover regime the system features a complex and rich behavior, which can be explained in terms of the characteristic timescales of different microscopic processes.

Erysipelas in a free-ranging Hawaiian crow (Corvus hawaiiensis)

USGS Publications Warehouse

Work, Thierry M.; Ball, Donna; Wolcott, Mark

1999-01-01

We describe a case of erysipelas in a free-ranging endangered Hawaiian crow. The partially scavenged carcass exhibited gross emaciation and petechial hemorrhages in both lungs. Microscopy revealed multiple necrotic foci associated with gram-positive rods in the liver and adrenal, diffuse acute proximal tubular necrosis of kidney, diffuse necrosis and inflammation of proventricular mucosa associated with gram-positive rods, and multiple intravascular aggregates of gram-positive rods associated with thrombi. Culture of the kidney revealed the bacterium to be Erysipelothrix rhusiopathiae. The implications of this finding to free-ranging crows remain unclear.

A critical-like collective state leads to long-range cell communication in Dictyostelium discoideum aggregation

PubMed Central

De Palo, Giovanna; Yi, Darvin; Endres, Robert G.

2017-01-01

The transition from single-cell to multicellular behavior is important in early development but rarely studied. The starvation-induced aggregation of the social amoeba Dictyostelium discoideum into a multicellular slug is known to result from single-cell chemotaxis towards emitted pulses of cyclic adenosine monophosphate (cAMP). However, how exactly do transient, short-range chemical gradients lead to coherent collective movement at a macroscopic scale? Here, we developed a multiscale model verified by quantitative microscopy to describe behaviors ranging widely from chemotaxis and excitability of individual cells to aggregation of thousands of cells. To better understand the mechanism of long-range cell—cell communication and hence aggregation, we analyzed cell—cell correlations, showing evidence of self-organization at the onset of aggregation (as opposed to following a leader cell). Surprisingly, cell collectives, despite their finite size, show features of criticality known from phase transitions in physical systems. By comparing wild-type and mutant cells with impaired aggregation, we found the longest cell—cell communication distance in wild-type cells, suggesting that criticality provides an adaptive advantage and optimally sized aggregates for the dispersal of spores. PMID:28422986

Does Diffusion Sequester Heavy Metals in Old Contamination Soils?

NASA Astrophysics Data System (ADS)

Ma, J.; Jennings, A. A.

2002-12-01

Old soil contamination refers to soil contamination that has aged over a long period of time. For example, at some brownfields, the soil heavy metal contamination can be one hundred or more years old. When contamination is young, the heavy metals are bound relatively weakly to the soil. However, the speciation and/or mechanisms of association evolve with aging into much more stable forms. It also appears that the metals migrate deeper into the bulk soil matrix where they are less available to participate in surface-related phenomena. Previous research showed elevated heavy metal extraction result after the soil was pulverized, with all other experiment conditions remaining unchanged. This indicates the presence of sequestered heavy metal contamination within the large soil particles (aggregate). The mechanisms of sequestering are uncertain, but diffusion appears to be a major factor. There are two possible pathways of diffusion that can account for heavy metal sequestering: solid-state diffusion through the bulk aggregate or liquid-phase diffusion through micro-pores within the aggregate structure. The second diffusion mechanism can be coupled with sorption (or other surface-related phenomena) on the pore walls. The remediation of sequestered heavy metals is also impacted by diffusion. Grinding a soil significantly reduces its average particle size. This exposes more of its internal bulk volume to extraction and results in much shorter diffusion pathway for the sequestered heavy metals to be released. Evidence has illustrated that this both improves remediation efficiency and provides a method by which the degree of sequestering can be quantified. This paper will present the results of ongoing research that is developing methods to identify the mechanisms of, quantify the magnitude of and determine the relative importance of (i.e. risk analysis) heavy metals sequestered in old contamination soils.

Physicochemical characterization of coke-plant soil for the assessment of polycyclic aromatic hydrocarbon availability and the feasibility of phytoremediation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahn, S.; Werner, D.; Luthy, R.G.

Coke oven site soil was characterized to assess the particle association and availability of polycyclic aromatic hydrocarbons (PAHs). We identified various carbonaceous materials including coal, coke, pitch, and tar decanter sludge. Most of the PAHs were associated with the polymeric matrix of tar sludge or hard pitch as discrete particles, coatings on soil mineral particles, or complex aggregates. The PAH availability from these particles was very low due to hindered diffusive release from solid tar or pitch with apparent diffusivities of 6 x 10{sup -15} for phenanthrene, 3 x 10{sup -15} for pyrene, and 1 x 10{sup -15} cm{sup 2}/smore » for benzo(a)pyrene. Significant concentrations of PAHs were observed in the interior of solid tar aggregates with up to 40,000 mg/kg total PAHs. The release of PAHs from the interior of such particles requires diffusion over a substantial distance, and semipermeable membrane device tests confirmed a very limited availability of PAHs. These findings explain the results from three years of phytoremediation of the site soil, for which no significant changes in the total PAH concentrations were observed in the test plot samples. The observed low bioavailability of PAHs probably inhibited PAH phytoremediation, as diffusion-limited mass transfer would limit the release of PAHs to the aqueous phase.« less

Cell fiber-based three-dimensional culture system for highly efficient expansion of human induced pluripotent stem cells.

PubMed

Ikeda, Kazuhiro; Nagata, Shogo; Okitsu, Teru; Takeuchi, Shoji

2017-06-06

Human pluripotent stem cells are a potentially powerful cellular resource for application in regenerative medicine. Because such applications require large numbers of human pluripotent stem cell-derived cells, a scalable culture system of human pluripotent stem cell needs to be developed. Several suspension culture systems for human pluripotent stem cell expansion exist; however, it is difficult to control the thickness of cell aggregations in these systems, leading to increased cell death likely caused by limited diffusion of gases and nutrients into the aggregations. Here, we describe a scalable culture system using the cell fiber technology for the expansion of human induced pluripotent stem (iPS) cells. The cells were encapsulated and cultured within the core region of core-shell hydrogel microfibers, resulting in the formation of rod-shaped or fiber-shaped cell aggregations with sustained thickness and high viability. By encapsulating the cells with type I collagen, we demonstrated a long-term culture of the cells by serial passaging at a high expansion rate (14-fold in four days) while retaining its pluripotency. Therefore, our culture system could be used for large-scale expansion of human pluripotent stem cells for use in regenerative medicine.

Response of Microbial Soil Carbon Mineralization Rates to Oxygen Limitations

NASA Astrophysics Data System (ADS)

Keiluweit, M.; Denney, A.; Nico, P. S.; Fendorf, S. E.

2014-12-01

The rate of soil organic matter (SOM) mineralization is known to be controlled by climatic factors as well as molecular structure, mineral-organic associations, and physical protection. What remains elusive is to what extent oxygen (O2) limitations impact overall rates of microbial SOM mineralization (oxidation) in soils. Even within upland soils that are aerobic in bulk, factors limiting O2 diffusion such as texture and soil moisture can result in an abundance of anaerobic microsites in the interior of soil aggregates. Variation in ensuing anaerobic respiration pathways can further impact SOM mineralization rates. Using a combination of (first) aggregate model systems and (second) manipulations of intact field samples, we show how limitations on diffusion and carbon bioavailability interact to impose anaerobic conditions and associated respiration constraints on SOM mineralization rates. In model aggregates, we examined how particle size (soil texture) and amount of dissolved organic carbon (bioavailable carbon) affect O2 availability and distribution. Monitoring electron acceptor profiles (O2, NO3-, Mn and Fe) and SOM transformations (dissolved, particulate, mineral-associated pools) across the resulting redox gradients, we then determined the distribution of operative microbial metabolisms and their cumulative impact on SOM mineralization rates. Our results show that anaerobic conditions decrease SOM mineralization rates overall, but those are partially offset by the concurrent increases in SOM bioavailability due to transformations of protective mineral phases. In intact soil aggregates collected from soils varying in texture and SOM content, we mapped the spatial distribution of anaerobic microsites. Optode imaging, microsensor profiling and 3D tomography revealed that soil texture regulates overall O2 availability in aggregate interiors, while particulate SOM in biopores appears to control the fine-scale distribution of anaerobic microsites. Collectively, our results suggest that texture and particulate organic matter content are useful predictors for the impact of O2 limitations on SOM mineralization rates.

Growth pattern of the surface of fungus Aspergillus colony

NASA Astrophysics Data System (ADS)

Matsuura, Shu; Miyazima, Sasuke

1992-05-01

Aspergillus oryzae colonies were grown under various glucose concentrations, temperatures, and agar concentrations, and the effects on the pattern were investigated. Patterns of colony were found to vary from uniform to diffusion-limited aggregation type.

Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules

PubMed Central

Skolnick, Jeffrey

2016-01-01

An outstanding challenge in computational biophysics is the simulation of a living cell at molecular detail. Over the past several years, using Stokesian dynamics, progress has been made in simulating coarse grained molecular models of the cytoplasm. Since macromolecules comprise 20%-40% of the volume of a cell, one would expect that steric interactions dominate macromolecular diffusion. However, the reduction in cellular diffusion rates relative to infinite dilution is due, roughly equally, to steric and hydrodynamic interactions, HI, with nonspecific attractive interactions likely playing rather a minor role. HI not only serve to slow down long time diffusion rates but also cause a considerable reduction in the magnitude of the short time diffusion coefficient relative to that at infinite dilution. More importantly, the long range contribution of the Rotne-Prager-Yamakawa diffusion tensor results in temporal and spatial correlations that persist up to microseconds and for intermolecular distances on the order of protein radii. While HI slow down the bimolecular association rate in the early stages of lipid bilayer formation, they accelerate the rate of large scale assembly of lipid aggregates. This is suggestive of an important role for HI in the self-assembly kinetics of large macromolecular complexes such as tubulin. Since HI are important, questions as to whether continuum models of HI are adequate as well as improved simulation methodologies that will make simulations of more complex cellular processes practical need to be addressed. Nevertheless, the stage is set for the molecular simulations of ever more complex subcellular processes. PMID:27634243

Early-stage aggregation in three-dimensional charged granular gas.

PubMed

Singh, Chamkor; Mazza, Marco G

2018-02-01

Neutral grains made of the same dielectric material can attain considerable charges due to collisions and generate long-range interactions. We perform molecular dynamic simulations in three dimensions for a dilute, freely cooling granular gas of viscoelastic particles that exchange charges during collisions. As compared to the case of clustering of viscoelastic particles solely due to dissipation, we find that the electrostatic interactions due to collisional charging alter the characteristic size, morphology, and growth rate of the clusters. The average cluster size grows with time as a power law, whose exponent is relatively larger in the charged gas than the neutral case. The growth of the average cluster size is found to be independent of the ratio of characteristic Coulomb to kinetic energy, or equivalently, of the typical Bjerrum length. However, this ratio alters the crossover time of the growth. Both simulations and mean-field calculations based on Smoluchowski's equation suggest that a suppression of particle diffusion due to the electrostatic interactions helps in the aggregation process.

Early-stage aggregation in three-dimensional charged granular gas

NASA Astrophysics Data System (ADS)

Singh, Chamkor; Mazza, Marco G.

2018-02-01

Neutral grains made of the same dielectric material can attain considerable charges due to collisions and generate long-range interactions. We perform molecular dynamic simulations in three dimensions for a dilute, freely cooling granular gas of viscoelastic particles that exchange charges during collisions. As compared to the case of clustering of viscoelastic particles solely due to dissipation, we find that the electrostatic interactions due to collisional charging alter the characteristic size, morphology, and growth rate of the clusters. The average cluster size grows with time as a power law, whose exponent is relatively larger in the charged gas than the neutral case. The growth of the average cluster size is found to be independent of the ratio of characteristic Coulomb to kinetic energy, or equivalently, of the typical Bjerrum length. However, this ratio alters the crossover time of the growth. Both simulations and mean-field calculations based on Smoluchowski's equation suggest that a suppression of particle diffusion due to the electrostatic interactions helps in the aggregation process.

A generalized electrochemical aggregative growth mechanism.

PubMed

Ustarroz, Jon; Hammons, Joshua A; Altantzis, Thomas; Hubin, Annick; Bals, Sara; Terryn, Herman

2013-08-07

The early stages of nanocrystal nucleation and growth are still an active field of research and remain unrevealed. In this work, by the combination of aberration-corrected transmission electron microscopy (TEM) and electrochemical characterization of the electrodeposition of different metals, we provide a complete reformulation of the Volmer-Weber 3D island growth mechanism, which has always been accepted to explain the early stages of metal electrodeposition and thin-film growth on low-energy substrates. We have developed a Generalized Electrochemical Aggregative Growth Mechanism which mimics the atomistic processes during the early stages of thin-film growth, by incorporating nanoclusters as building blocks. We discuss the influence of new processes such as nanocluster self-limiting growth, surface diffusion, aggregation, and coalescence on the growth mechanism and morphology of the resulting nanostructures. Self-limiting growth mechanisms hinder nanocluster growth and favor coalescence driven growth. The size of the primary nanoclusters is independent of the applied potential and deposition time. The balance between nucleation, nanocluster surface diffusion, and coalescence depends on the material and the overpotential, and influences strongly the morphology of the deposits. A small extent of coalescence leads to ultraporous dendritic structures, large surface coverage, and small particle size. Contrarily, full recrystallization leads to larger hemispherical monocrystalline islands and smaller particle density. The mechanism we propose represents a scientific breakthrough from the fundamental point of view and indicates that achieving the right balance between nucleation, self-limiting growth, cluster surface diffusion, and coalescence is essential and opens new, exciting possibilities to build up enhanced supported nanostructures using nanoclusters as building blocks.

Thin film growth by 3D multi-particle diffusion limited aggregation model: Anomalous roughening and fractal analysis

NASA Astrophysics Data System (ADS)

Nasehnejad, Maryam; Nabiyouni, G.; Gholipour Shahraki, Mehran

2018-03-01

In this study a 3D multi-particle diffusion limited aggregation method is employed to simulate growth of rough surfaces with fractal behavior in electrodeposition process. A deposition model is used in which the radial motion of the particles with probability P, competes with random motions with probability 1 - P. Thin films growth is simulated for different values of probability P (related to the electric field) and thickness of the layer(related to the number of deposited particles). The influence of these parameters on morphology, kinetic of roughening and the fractal dimension of the simulated surfaces has been investigated. The results show that the surface roughness increases with increasing the deposition time and scaling exponents exhibit a complex behavior which is called as anomalous scaling. It seems that in electrodeposition process, radial motion of the particles toward the growing seeds may be an important mechanism leading to anomalous scaling. The results also indicate that the larger values of probability P, results in smoother topography with more densely packed structure. We have suggested a dynamic scaling ansatz for interface width has a function of deposition time, scan length and probability. Two different methods are employed to evaluate the fractal dimension of the simulated surfaces which are "cube counting" and "roughness" methods. The results of both methods show that by increasing the probability P or decreasing the deposition time, the fractal dimension of the simulated surfaces is increased. All gained values for fractal dimensions are close to 2.5 in the diffusion limited aggregation model.

A model for bacterial colonization of sinking aggregates.

PubMed

Bearon, R N

2007-01-01

Sinking aggregates provide important nutrient-rich environments for marine bacteria. Quantifying the rate at which motile bacteria colonize such aggregations is important in understanding the microbial loop in the pelagic food web. In this paper, a simple analytical model is presented to predict the rate at which bacteria undergoing a random walk encounter a sinking aggregate. The model incorporates the flow field generated by the sinking aggregate, the swimming behavior of the bacteria, and the interaction of the flow with the swimming behavior. An expression for the encounter rate is computed in the limit of large Péclet number when the random walk can be approximated by a diffusion process. Comparison with an individual-based numerical simulation is also given.

The Effect of Thermal Convection on Earth-Atmosphere CO2 Gas Exchange in Aggregated Soil

NASA Astrophysics Data System (ADS)

Ganot, Y.; Weisbrod, N.; Dragila, M. I.

2011-12-01

Gas transport in soils and surface-atmosphere gas exchange are important processes that affect different aspects of soil science such as soil aeration, nutrient bio-availability, sorption kinetics, soil and groundwater pollution and soil remediation. Diffusion and convection are the two main mechanisms that affect gas transport, fate and emissions in the soils and in the upper vadose zone. In this work we studied CO2 soil-atmosphere gas exchange under both day-time and night-time conditions, focusing on the impact of thermal convection (TCV) during the night. Experiments were performed in a climate-controlled laboratory. One meter long columns were packed with matrix of different grain size (sand, gravel and soil aggregates). Air with 2000 ppm CO2 was injected into the bottom of the columns and CO2 concentration within the columns was continuously monitored by an Infra Red Gas Analyzer. Two scenarios were compared for each soil: (1) isothermal conditions, representing day time conditions; and (2) thermal gradient conditions, i.e., atmosphere colder than the soil, representing night time conditions. Our results show that under isothermal conditions, diffusion is the major mechanism for surface-atmosphere gas exchange for all grain sizes; while under night time conditions the prevailing mechanism is dependent on the air permeability of the matrix: for sand and gravel it is diffusion, and for soil aggregates it is TCV. Calculated CO2 flux for the soil aggregates column shows that the TCV flux was three orders of magnitude higher than the diffusive flux.

Broadband classification and statistics of echoes from aggregations of fish measured by long-range, mid-frequency sonar.

PubMed

Jones, Benjamin A; Stanton, Timothy K; Colosi, John A; Gauss, Roger C; Fialkowski, Joseph M; Michael Jech, J

2017-06-01

For horizontal-looking sonar systems operating at mid-frequencies (1-10 kHz), scattering by fish with resonant gas-filled swimbladders can dominate seafloor and surface reverberation at long-ranges (i.e., distances much greater than the water depth). This source of scattering, which can be difficult to distinguish from other sources of scattering in the water column or at the boundaries, can add spatio-temporal variability to an already complex acoustic record. Sparsely distributed, spatially compact fish aggregations were measured in the Gulf of Maine using a long-range broadband sonar with continuous spectral coverage from 1.5 to 5 kHz. Observed echoes, that are at least 15 decibels above background levels in the horizontal-looking sonar data, are classified spectrally by the resonance features as due to swimbladder-bearing fish. Contemporaneous multi-frequency echosounder measurements (18, 38, and 120 kHz) and net samples are used in conjunction with physics-based acoustic models to validate this approach. Furthermore, the fish aggregations are statistically characterized in the long-range data by highly non-Rayleigh distributions of the echo magnitudes. These distributions are accurately predicted by a computationally efficient, physics-based model. The model accounts for beam-pattern and waveguide effects as well as the scattering response of aggregations of fish.

Non-Linear Dynamics of Saturn's Rings

NASA Astrophysics Data System (ADS)

Esposito, L. W.

2015-12-01

Non-linear processes can explain why Saturn's rings are so active and dynamic. Some of this non-linearity is captured in a simple Predator-Prey Model: Periodic forcing from the moon causes streamline crowding; This damps the relative velocity, and allows aggregates to grow. About a quarter phase later, the aggregates stir the system to higher relative velocity and the limit cycle repeats each orbit, with relative velocity ranging from nearly zero to a multiple of the orbit average: 2-10x is possible. Summary of Halo Results: A predator-prey model for ring dynamics produces transient structures like 'straw' that can explain the halo structure and spectroscopy: Cyclic velocity changes cause perturbed regions to reach higher collision speeds at some orbital phases, which preferentially removes small regolith particles; Surrounding particles diffuse back too slowly to erase the effect: this gives the halo morphology; This requires energetic collisions (v ≈ 10m/sec, with throw distances about 200km, implying objects of scale R ≈ 20km); We propose 'straw', as observed ny Cassini cameras. Transform to Duffing Eqn : With the coordinate transformation, z = M2/3, the Predator-Prey equations can be combined to form a single second-order differential equation with harmonic resonance forcing. Ring dynamics and history implications: Moon-triggered clumping at perturbed regions in Saturn's rings creates both high velocity dispersion and large aggregates at these distances, explaining both small and large particles observed there. This confirms the triple architecture of ring particles: a broad size distribution of particles; these aggregate into temporary rubble piles; coated by a regolith of dust. We calculate the stationary size distribution using a cell-to-cell mapping procedure that converts the phase-plane trajectories to a Markov chain. Approximating the Markov chain as an asymmetric random walk with reflecting boundaries allows us to determine the power law index from results of numerical simulations in the tidal environment surrounding Saturn. Aggregates can explain many dynamic aspects of the rings and can renew rings by shielding and recycling the material within them, depending on how long the mass is sequestered. We can ask: Are Saturn's rings a chaotic non-linear driven system?

Unusual properties of aqueous solutions of L-proline: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Civera, Monica; Sironi, Maurizio; Fornili, Sandro L.

2005-11-01

Aqueous solutions of the bioprotectant proline are simulated for solute molar fractions ranging from 2.0 × 10 -3 to 2.3 × 10 -1. Statistical analyses show that proline affects the water structure more strongly than glycine betaine and trimethylamine- N-oxide, two of the most effective bioprotectants widely diffuse in nature, and as strongly as tert-butyl alcohol, a protein denaturant which at high concentration self-aggregates. No evidence is found, however, that proline self-aggregates as it has been previously suggested to explain experimental findings on concentrated proline solutions. Nevertheless, the behavior of the diffusion coefficients of proline and water vs. solute concentration qualitatively agrees with such results.

Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Virk, Amninder; Stait-Gardner, Timothy; Willis, Scott; Torres, Allan; Price, William

2015-02-01

Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction). Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine) up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.

Dynamics of Phenanthrenequinone on Carbon Nano-Onion Surfaces Probed by Quasielastic Neutron Scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anjos, Daniela M; Mamontov, Eugene; Brown, Gilbert M

We used quasielastic neutron scattering (QENS) to study the dynamics of phenanthrenequinone (PQ) on the surface of onion-like carbon (OLC), or so called carbon onions, as a function of surface coverage and temperature. For both the high- and low-coverage samples, we observed two diffusion processes; a faster process and nearly an order of magnitude slower process. On the high-coverage surface, the slow diffusion process is of long-range translational character, whereas the fast diffusion process is spatially localized on the length scale of ~ 4.7 . On the low-coverage surface, both diffusion processes are spatially localized; on the same length scalemore » of ~ 4.7 for the fast diffusion and a somewhat larger length scale for the slow diffusion. Arrhenius temperature dependence is observed except for the long-range diffusion on the high-coverage surface. We attribute the fast diffusion process to the generic localized in-cage dynamics of PQ molecules, and the slow diffusion process to the long-range translational dynamics of PQ molecules, which, depending on the coverage, may be either spatially restricted, or long-range. On the low-coverage surface, uniform surface coverage is not attained, and the PQ molecules experience the effect of spatial constraints on their long-range translational dynamics. Unexpectedly, the dynamics of PQ molecules on OLC as a function of temperature and surface coverage bears qualitative resemblance to the dynamics of water molecules on oxide surfaces, including practically temperature-independent residence times for the low-coverage surface. The dynamics features that we observed may be universal across different classes of surface adsorbates.« less

Concentration-dependent changes in apparent diffusion coefficients as indicator for colloidal stability of protein solutions.

PubMed

Bauer, Katharina Christin; Göbel, Mathias; Schwab, Marie-Luise; Schermeyer, Marie-Therese; Hubbuch, Jürgen

2016-09-10

The colloidal stability of a protein solution during downstream processing, formulation, and storage is a key issue for the biopharmaceutical production process. Thus, knowledge about colloidal solution characteristics, such as the tendency to form aggregates or high viscosity, at various processing conditions is of interest. This work correlates changes in the apparent diffusion coefficient as a parameter of protein interactions with observed protein aggregation and dynamic viscosity of the respective protein samples. For this purpose, the diffusion coefficient, the protein phase behavior, and the dynamic viscosity in various systems containing the model proteins α-lactalbumin, lysozyme, and glucose oxidase were studied. Each of these experiments revealed a wide range of variations in protein interactions depending on protein type, protein concentration, pH, and the NaCl concentration. All these variations showed to be mirrored by changes in the apparent diffusion coefficient in the respective samples. Whereas stable samples with relatively low viscosity showed an almost linear dependence, the deviation from the concentration-dependent linearity indicated both an increase in the sample viscosity and probability of protein aggregation. This deviation of the apparent diffusion coefficient from concentration-dependent linearity was independent of protein type and solution properties for this study. Thus, this single parameter shows the potential to act as a prognostic tool for colloidal stability of protein solutions. Copyright © 2016 Elsevier B.V. All rights reserved.

Controlled Growth of Polypyrrole on Microelectrodes

NASA Astrophysics Data System (ADS)

Kannan, Bhuvaneswari; Williams, David E.; Travas-Sejdic, Jandranka

2009-07-01

Electrochemical growth of a conducting polymer generally leads to a microstructure which is an irregular assembly of irregular spheres, generally taken to be indicative of a diffusion-limited aggregation in which oligomers generated at or near the electrode aggregate into particles that in turn aggregate onto the electrode. We have explored the possibilities for controlling this growth mode by using short current pulses to form the polymer. We illustrate the alteration in growth morphology achievable by the use of different pulse sequences. In particular, we show the possibility to grow isolated dendrites (`nanowires') of conducting polymer on an electrode surface.

Random walk on lattices: Graph-theoretic approach to simulating long-range diffusion-attachment growth models

NASA Astrophysics Data System (ADS)

Limkumnerd, Surachate

2014-03-01

Interest in thin-film fabrication for industrial applications have driven both theoretical and computational aspects of modeling its growth. One of the earliest attempts toward understanding the morphological structure of a film's surface is through a class of solid-on-solid limited-mobility growth models such as the Family, Wolf-Villain, or Das Sarma-Tamborenea models, which have produced fascinating surface roughening behaviors. These models, however, restrict the motion of an incidence atom to be within the neighborhood of its landing site, which renders them inept for simulating long-distance surface diffusion such as that observed in thin-film growth using a molecular-beam epitaxy technique. Naive extension of these models by repeatedly applying the local diffusion rules for each hop to simulate large diffusion length can be computationally very costly when certain statistical aspects are demanded. We present a graph-theoretic approach to simulating a long-range diffusion-attachment growth model. Using the Markovian assumption and given a local diffusion bias, we derive the transition probabilities for a random walker to traverse from one lattice site to the others after a large, possibly infinite, number of steps. Only computation with linear-time complexity is required for the surface morphology calculation without other probabilistic measures. The formalism is applied, as illustrations, to simulate surface growth on a two-dimensional flat substrate and around a screw dislocation under the modified Wolf-Villain diffusion rule. A rectangular spiral ridge is observed in the latter case with a smooth front feature similar to that obtained from simulations using the well-known multiple registration technique. An algorithm for computing the inverse of a class of substochastic matrices is derived as a corollary.

Crystallization of DNA-coated colloids

PubMed Central

Wang, Yu; Wang, Yufeng; Zheng, Xiaolong; Ducrot, Étienne; Yodh, Jeremy S.; Weck, Marcus; Pine, David J.

2015-01-01

DNA-coated colloids hold great promise for self-assembly of programmed heterogeneous microstructures, provided they not only bind when cooled below their melting temperature, but also rearrange so that aggregated particles can anneal into the structure that minimizes the free energy. Unfortunately, DNA-coated colloids generally collide and stick forming kinetically arrested random aggregates when the thickness of the DNA coating is much smaller than the particles. Here we report DNA-coated colloids that can rearrange and anneal, thus enabling the growth of large colloidal crystals from a wide range of micrometre-sized DNA-coated colloids for the first time. The kinetics of aggregation, crystallization and defect formation are followed in real time. The crystallization rate exhibits the familiar maximum for intermediate temperature quenches observed in metallic alloys, but over a temperature range smaller by two orders of magnitude, owing to the highly temperature-sensitive diffusion between aggregated DNA-coated colloids. PMID:26078020

Continuum models of cohesive stochastic swarms: The effect of motility on aggregation patterns

NASA Astrophysics Data System (ADS)

Hughes, Barry D.; Fellner, Klemens

2013-10-01

Mathematical models of swarms of moving agents with non-local interactions have many applications and have been the subject of considerable recent interest. For modest numbers of agents, cellular automata or related algorithms can be used to study such systems, but in the present work, instead of considering discrete agents, we discuss a class of one-dimensional continuum models, in which the agents possess a density ρ(x,t) at location x at time t. The agents are subject to a stochastic motility mechanism and to a global cohesive inter-agent force. The motility mechanisms covered include classical diffusion, nonlinear diffusion (which may be used to model, in a phenomenological way, volume exclusion or other short-range local interactions), and a family of linear redistribution operators related to fractional diffusion equations. A variety of exact analytic results are discussed, including equilibrium solutions and criteria for unimodality of equilibrium distributions, full time-dependent solutions, and transitions between asymptotic collapse and asymptotic escape. We address the behaviour of the system for diffusive motility in the low-diffusivity limit for both smooth and singular interaction potentials and show how this elucidates puzzling behaviour in fully deterministic non-local particle interaction models. We conclude with speculative remarks about extensions and applications of the models.

Effects of ionic strength and temperature on the aggregation and deposition of multi-walled carbon nanotubes.

PubMed

Wang, Lixin; Yang, Xuezhi; Wang, Qi; Zeng, Yuxuan; Ding, Lei; Jiang, Wei

2017-01-01

The aggregation and deposition of carbon nanotubes (CNTs) determines their transport and fate in natural waters. Therefore, the aggregation kinetics of humic-acid treated multi-walled carbon nanotubes (HA-MWCNTs) was investigated by time-resolved dynamic light scattering in NaCl and CaCl 2 electrolyte solutions. Increased ionic strength induced HA-MWCNT aggregation due to the less negative zeta potential and the reduced electrostatic repulsion. The critical coagulation concentration (CCC) values of HA-MWCNTs were 80mmol/L in NaCl and 1.3mmol/L in CaCl 2 electrolyte, showing that Ca 2+ causes more serious aggregation than Na + . The aggregation behavior of HA-MWCNTs was consistent with Derjaguin-Landau-Verwey-Overbeek theory. The deposition kinetics of HA-MWCNTs was measured by the optical absorbance at 800nm. The critical deposition concentrations for HA-MWCNT in NaCl and CaCl 2 solutions were close to the CCC values, therefore the rate of deposition cannot be increased by changing the ionic strength in the diffusion-limited aggregation regime. The deposition process was correlated to the aggregation since larger aggregates increased gravitational deposition and decreased random Brownian diffusion. HA-MWCNTs hydrodynamic diameters were evaluated at 5, 15 and 25°C. Higher temperature caused faster aggregation due to the reduced electrostatic repulsion and increased random Brownian motion and collision frequency. HA-MWCNTs aggregate faster at higher temperature in either NaCl or CaCl 2 electrolyte due to the decreased electrostatic repulsion and increased random Brownian motion. Our results suggest that CNT aggregation and deposition are two correlated processes governed by the electrolyte, and CNT transport is favored at low ionic strength and low temperature. Copyright © 2016. Published by Elsevier B.V.

Optical characterization limits of nanoparticle aggregates at different wavelengths using approximate Bayesian computation

NASA Astrophysics Data System (ADS)

Eriçok, Ozan Burak; Ertürk, Hakan

2018-07-01

Optical characterization of nanoparticle aggregates is a complex inverse problem that can be solved by deterministic or statistical methods. Previous studies showed that there exists a different lower size limit of reliable characterization, corresponding to the wavelength of light source used. In this study, these characterization limits are determined considering a light source wavelength range changing from ultraviolet to near infrared (266-1064 nm) relying on numerical light scattering experiments. Two different measurement ensembles are considered. Collection of well separated aggregates made up of same sized particles and that of having particle size distribution. Filippov's cluster-cluster algorithm is used to generate the aggregates and the light scattering behavior is calculated by discrete dipole approximation. A likelihood-free Approximate Bayesian Computation, relying on Adaptive Population Monte Carlo method, is used for characterization. It is found that when the wavelength range of 266-1064 nm is used, successful characterization limit changes from 21-62 nm effective radius for monodisperse and polydisperse soot aggregates.

Long-range repulsion of colloids driven by ion exchange and diffusiophoresis

PubMed Central

Florea, Daniel; Musa, Sami; Huyghe, Jacques M. R.; Wyss, Hans M.

2014-01-01

Interactions between surfaces and particles in aqueous suspension are usually limited to distances smaller than 1 μm. However, in a range of studies from different disciplines, repulsion of particles has been observed over distances of up to hundreds of micrometers, in the absence of any additional external fields. Although a range of hypotheses have been suggested to account for such behavior, the physical mechanisms responsible for the phenomenon still remain unclear. To identify and isolate these mechanisms, we perform detailed experiments on a well-defined experimental system, using a setup that minimizes the effects of gravity and convection. Our experiments clearly indicate that the observed long-range repulsion is driven by a combination of ion exchange, ion diffusion, and diffusiophoresis. We develop a simple model that accounts for our data; this description is expected to be directly applicable to a wide range of systems exhibiting similar long-range forces. PMID:24748113

Statistical variances of diffusional properties from ab initio molecular dynamics simulations

NASA Astrophysics Data System (ADS)

He, Xingfeng; Zhu, Yizhou; Epstein, Alexander; Mo, Yifei

2018-12-01

Ab initio molecular dynamics (AIMD) simulation is widely employed in studying diffusion mechanisms and in quantifying diffusional properties of materials. However, AIMD simulations are often limited to a few hundred atoms and a short, sub-nanosecond physical timescale, which leads to models that include only a limited number of diffusion events. As a result, the diffusional properties obtained from AIMD simulations are often plagued by poor statistics. In this paper, we re-examine the process to estimate diffusivity and ionic conductivity from the AIMD simulations and establish the procedure to minimize the fitting errors. In addition, we propose methods for quantifying the statistical variance of the diffusivity and ionic conductivity from the number of diffusion events observed during the AIMD simulation. Since an adequate number of diffusion events must be sampled, AIMD simulations should be sufficiently long and can only be performed on materials with reasonably fast diffusion. We chart the ranges of materials and physical conditions that can be accessible by AIMD simulations in studying diffusional properties. Our work provides the foundation for quantifying the statistical confidence levels of diffusion results from AIMD simulations and for correctly employing this powerful technique.

Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation

NASA Astrophysics Data System (ADS)

Kekenes-Huskey, P. M.; Gillette, A. K.; McCammon, J. A.

2014-05-01

The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute "obstacles" and (2) long-range interactions between those obstacles and the diffuser. Increasing excluded volume reduces transport of the diffuser, while long-range interactions can either increase or decrease diffusivity, depending on the nature of the potential. We previously demonstrated [P. M. Kekenes-Huskey et al., Biophys. J. 105, 2130 (2013)] using homogenization theory that the configuration of molecular-scale obstacles can both hinder diffusion and induce diffusional anisotropy for small ions. As the density of molecular obstacles increases, van der Waals (vdW) and electrostatic interactions between obstacle and a diffuser become significant and can strongly influence the latter's diffusivity, which was neglected in our original model. Here, we extend this methodology to include a fixed (time-independent) potential of mean force, through homogenization of the Smoluchowski equation. We consider the diffusion of ions in crowded, hydrophilic environments at physiological ionic strengths and find that electrostatic and vdW interactions can enhance or depress effective diffusion rates for attractive or repulsive forces, respectively. Additionally, we show that the observed diffusion rate may be reduced independent of non-specific electrostatic and vdW interactions by treating obstacles that exhibit specific binding interactions as "buffers" that absorb free diffusers. Finally, we demonstrate that effective diffusion rates are sensitive to distribution of surface charge on a globular protein, Troponin C, suggesting that the use of molecular structures with atomistic-scale resolution can account for electrostatic influences on substrate transport. This approach offers new insight into the influence of molecular-scale, long-range interactions on transport of charged species, particularly for diffusion-influenced signaling events occurring in crowded cellular environments.

Soot Volume Fraction Maps for Normal and Reduced Gravity Laminar Acetylene Jet Diffusion Flames

NASA Technical Reports Server (NTRS)

Greenberg, Paul S.; Ku, Jerry C.

1997-01-01

The study of soot particulate distribution inside gas jet diffusion flames is important to the understanding of fundamental soot particle and thermal radiative transport processes, as well as providing findings relevant to spacecraft fire safety, soot emissions, and radiant heat loads for combustors used in air-breathing propulsion systems. Compared to those under normal gravity (1-g) conditions, the elimination of buoyancy-induced flows is expected to significantly change the flow field in microgravity (O g) flames, resulting in taller and wider flames with longer particle residence times. Work by Bahadori and Edelman demonstrate many previously unreported qualitative and semi-quantitative results, including flame shape and radiation, for sooting laminar zas jet diffusion flames. Work by Ku et al. report soot aggregate size and morphology analyses and data and model predictions of soot volume fraction maps for various gas jet diffusion flames. In this study, we present the first 1-g and 0-g comparisons of soot volume fraction maps for laminar acetylene and nitrogen-diluted acetylene jet diffusion flames. Volume fraction is one of the most useful properties in the study of sooting diffusion flames. The amount of radiation heat transfer depends directly on the volume fraction and this parameter can be measured from line-of-sight extinction measurements. Although most Soot aggregates are submicron in size, the primary particles (20 to 50 nm in diameter) are in the Rayleigh limit, so the extinction absorption) cross section of aggregates can be accurately approximated by the Rayleigh solution as a function of incident wavelength, particles' complex refractive index, and particles' volume fraction.

The Limitation of Species Range: A Consequence of Searching Along Resource Gradients

PubMed Central

Rowell, Jonathan T.

2009-01-01

Ecological modelers have long puzzled over the spatial distribution of species. The random walk or diffusive approach to dispersal has yielded important results for biology and mathematics, yet it has been inadequate in explaining all phenomenological features. Ranges can terminate non-smoothly absent a complementary shift in the characteristics of the environment. Also unexplained is the absence of a species from nearby areas of adequate, or even abundant, resources. In this paper, I show how local searching behavior - keyed to a density-dependent fitness - can limit the speed and extent of a species’ spread. In contrast to standard diffusive processes, pseudo-rational movement facilitates the clustering of populations. It also can be used to estimate the speed of an expanding population range, explain expansion stall, and provides a mechanism by which a population can colonize seemingly removed regions - biogeographic islands in a continental framework. Finally, I discuss the effect of resource degradation and different resource impact/utilization curves on the model. PMID:19303032

Modes of Diffusion of Cholera Toxin Bound to GM1 on Live Cell Membrane by Image Mean Square Displacement Analysis

PubMed Central

Moens, Pierre D.J.; Digman, Michelle A.; Gratton, Enrico

2015-01-01

The image-mean square displacement technique applies the calculation of the mean square displacement commonly used in single-molecule tracking to images without resolving single particles. The image-mean square displacement plot obtained is similar to the mean square displacement plot obtained using the single-particle tracking technique. This plot is then used to reconstruct the protein diffusion law and to identify whether the labeled molecules are undergoing pure isotropic, restricted, corralled, transiently confined, or directed diffusion. In our study total internal reflection fluorescence microscopy images were taken of Cholera toxin subunit B (CtxB) membrane-labeled NIH 3T3 mouse fibroblasts and MDA 231 MB cells. We found a population of CTxB undergoing purely isotropic diffusion and one displaying restricted diffusion with corral sizes ranging from 150 to ∼1800 nm. We show that the diffusion rate of CTxB bound to GM1 is independent of the size of the confinement, suggesting that the mechanism of confinement is different from the mechanism controlling the diffusion rate of CtxB. We highlight the potential effect of continuous illumination on the diffusion mode of CTxB. We also show that aggregation of CTxB/GM1 in large complexes occurs and that these aggregates tend to have slower diffusion rates. PMID:25809257

Modes of diffusion of cholera toxin bound to GM1 on live cell membrane by image mean square displacement analysis.

PubMed

Moens, Pierre D J; Digman, Michelle A; Gratton, Enrico

2015-03-24

The image-mean square displacement technique applies the calculation of the mean square displacement commonly used in single-molecule tracking to images without resolving single particles. The image-mean square displacement plot obtained is similar to the mean square displacement plot obtained using the single-particle tracking technique. This plot is then used to reconstruct the protein diffusion law and to identify whether the labeled molecules are undergoing pure isotropic, restricted, corralled, transiently confined, or directed diffusion. In our study total internal reflection fluorescence microscopy images were taken of Cholera toxin subunit B (CtxB) membrane-labeled NIH 3T3 mouse fibroblasts and MDA 231 MB cells. We found a population of CTxB undergoing purely isotropic diffusion and one displaying restricted diffusion with corral sizes ranging from 150 to ∼1800 nm. We show that the diffusion rate of CTxB bound to GM1 is independent of the size of the confinement, suggesting that the mechanism of confinement is different from the mechanism controlling the diffusion rate of CtxB. We highlight the potential effect of continuous illumination on the diffusion mode of CTxB. We also show that aggregation of CTxB/GM1 in large complexes occurs and that these aggregates tend to have slower diffusion rates. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Differential Microscopic Mobility of Components within a Deep Eutectic Solvent

DOE PAGES

Wagle, Durgesh V.; Baker, Gary A.; Mamontov, Eugene

2015-07-13

From macroscopic measurements of deep eutectic solvents such as glyceline (1:2 molar ratio of choline chloride to glycerol), the long-range translational diffusion of the larger cation (choline) is known to be slower compared to that of the smaller hydrogen bond donor (glycerol). However, when the diffusion dynamics are analyzed on the subnanometer length scale, we discover that the displacements associated with the localized diffusive motions are actually larger for choline. This counterintuitive diffusive behavior can be understood as follows. The localized diffusive motions confined in the transient cage of neighbor particles, which precede the cage-breaking long-range diffusion jumps, are moremore » spatially constrained for glycerol than for choline because of the stronger hydrogen bonds the former makes with chloride anions. The implications of differential localized mobility of the constituents should be especially important for applications where deep eutectic solvents are confined on the nanometer length scale and their long-range translational diffusion is strongly inhibited (e.g., within microporous media).« less

31P and 1H NMR Studies of the Molecular Organization of Lipids in the Parallel Artificial Membrane Permeability Assay.

PubMed

Assmus, Frauke; Ross, Alfred; Fischer, Holger; Seelig, Joachim; Seelig, Anna

2017-01-03

The parallel artificial membrane permeability assay (PAMPA) has emerged as a widely used primary in vitro screen for passive permeability of potential drug candidates. However, the molecular structure of the permeation barrier (consisting of a filter-supported dodecane-egg lecithin mixture) has never been characterized. Here, we investigated the long-range order of phospholipids in the PAMPA barrier by means of 31 P static solid-state NMR. Diffusion constants of PAMPA membrane components were derived from liquid state NMR and, in addition, drug distribution between the PAMPA lipid phase and buffer (log D PAMPA at pH 7.4) was systematically investigated. Increasing concentration of n-dodecane to the system egg lecithin-water (lamellar phase, L α ) induces formation of inverted hexagonal (H ii ) and isotropic phases. At n-dodecane concentrations matching those used in PAMPA (9%, w/v) a purely "isotropic" phase was observed corresponding to lipid aggregates with a diameter in the range 4-7 nm. Drug distribution studies indicate that these reverse micelles facilitate the binding to, and in turn the permeation across, the PAMPA dodecane barrier, in particular for amphiphilic solutes. The proposed model for the molecular architecture and function of the PAMPA barrier provides a fundamental, hitherto missing framework to evaluate the scope but also limitations of PAMPA for the prediction of in vivo membrane permeability.

Aggregation, sedimentation, dissolution and bioavailability of ...

EPA Pesticide Factsheets

Due to increasing use in flat screen applications, solar cells, ink–jet printing, and medical devices, cadmium-based quantum dots (QDs) are among the fastest growing classes of engineered nanomaterial. These wide-ranging consumer product applications and end of use disposal issues assure that QDs will eventually enter the marine environment. In an effort to understand the fate and transport of CdSe QDs in estuarine systems, the aggregation, sedimentation, dissolution, and bioavailability of CdSe QDs in seawater was investigated. The size of CdSe QDs increased from 40-60 nm to >1 mm within one hour once introduced to seawater, and the diffusion-limited aggregation led to highly polydispersed aggregates with loose structures. As a result, the sedimentation rate of CdSe QD aggregates in seawater was measured to be 4-10 mm/day, which was slow considering their relatively large size. Humic acid (HA), as a model natural organic matter, further increased the size and polydispersity of CdSe QDs, and slowed their sedimentation accordingly. Given the effect of light on CdSe QDs, natural sunlight and light filters were employed to simulate the photic conditions at different water depths in an estuarine system. It was observed that light played a vital role in promoting the dissolution of CdSe QDs and the release of dissolved Cd. The ZnS shell surrounding the CdSe core also significantly hindered the degradation of CdSe QDs into their ionic components. With sufficient

Stacking and Branching in Self-Aggregation of Caffeine in Aqueous Solution: From the Supramolecular to Atomic Scale Clustering.

PubMed

Tavagnacco, Letizia; Gerelli, Yuri; Cesàro, Attilio; Brady, John W

2016-09-22

The dynamical and structural properties of caffeine solutions at the solubility limit have been investigated as a function of temperature by means of MD simulations, static and dynamic light scattering, and small angle neutron scattering experiments. A clear picture unambiguously supported by both experiment and simulation emerges: caffeine self-aggregation promotes the formation of two distinct types of clusters: linear aggregates of stacked molecules, formed by 2-14 caffeine molecules depending on the thermodynamic conditions and disordered branched aggregates with a size in the range 1000-3000 Å. While the first type of association is well-known to occur under room temperature conditions for both caffeine and other purine systems, such as nucleotides, the presence of the supramolecular aggregates has not been reported previously. MD simulations indicate that branched structures are formed by caffeine molecules in a T-shaped arrangement. An increase of the solubility limit (higher temperature but also higher concentration) broadens the distribution of cluster sizes, promoting the formation of stacked aggregates composed by a larger number of caffeine molecules. Surprisingly, the effect on the branched aggregates is rather limited. Their internal structure and size do not change considerably in the range of solubility limits investigated.

Effect of film multi-scale structure on the water vapor permeability in hydroxypropyl starch (HPS)/Na-MMT nanocomposites.

PubMed

Liu, Siyuan; Cai, Panfu; Li, Xiaoxi; Chen, Ling; Li, Lin; Li, Bing

2016-12-10

To improve the water vapor resistance of starch-based films, Na-MMT (Na-montmorillonite) as nanofillers were fabricated into hydroxypropyl starch and the multi-scale structural changes (including intermolecular interaction, short-range conformation, long-range ordered structure and the aggregated structure of the film) were revealed. The elongation of the water vapor molecule pathway by tortuous path is generally recognized as the main reason for the improvement of water resistance. However this study observed the lowest water vapor permeability (WVP) was at the 3% Na-MMT/hydroxypropyl starch (HPS) ratio instead of 5% even nanofillers were partially exfoliated at both ratio. Except for the "tortuous path" caused by nanofillers, this observation proposed that the short-range conformation of HPS chains, long-range ordered structure and the aggregated structure likely influenced the water barrier property. The relationship between WVP and multi-scale structure of the film was investigated. The results suggested that a good balance of short-range conformationin the amorphous region, long-range ordered structure and the aggregated structure of the film was required for the improvement of water vapor barrier property. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecules in motion: influences of diffusion on metabolic structure and function in skeletal muscle.

PubMed

Kinsey, Stephen T; Locke, Bruce R; Dillaman, Richard M

2011-01-15

Metabolic processes are often represented as a group of metabolites that interact through enzymatic reactions, thus forming a network of linked biochemical pathways. Implicit in this view is that diffusion of metabolites to and from enzymes is very fast compared with reaction rates, and metabolic fluxes are therefore almost exclusively dictated by catalytic properties. However, diffusion may exert greater control over the rates of reactions through: (1) an increase in reaction rates; (2) an increase in diffusion distances; or (3) a decrease in the relevant diffusion coefficients. It is therefore not surprising that skeletal muscle fibers have long been the focus of reaction-diffusion analyses because they have high and variable rates of ATP turnover, long diffusion distances, and hindered metabolite diffusion due to an abundance of intracellular barriers. Examination of the diversity of skeletal muscle fiber designs found in animals provides insights into the role that diffusion plays in governing both rates of metabolic fluxes and cellular organization. Experimental measurements of metabolic fluxes, diffusion distances and diffusion coefficients, coupled with reaction-diffusion mathematical models in a range of muscle types has started to reveal some general principles guiding muscle structure and metabolic function. Foremost among these is that metabolic processes in muscles do, in fact, appear to be largely reaction controlled and are not greatly limited by diffusion. However, the influence of diffusion is apparent in patterns of fiber growth and metabolic organization that appear to result from selective pressure to maintain reaction control of metabolism in muscle.

Analysis of aggregated tick returns: Evidence for anomalous diffusion

NASA Astrophysics Data System (ADS)

Weber, Philipp

2007-01-01

In order to investigate the origin of large price fluctuations, we analyze stock price changes of ten frequently traded NASDAQ stocks in the year 2002. Though the influence of the trading frequency on the aggregate return in a certain time interval is important, it cannot alone explain the heavy-tailed distribution of stock price changes. For this reason, we analyze intervals with a fixed number of trades in order to eliminate the influence of the trading frequency and investigate the relevance of other factors for the aggregate return. We show that in tick time the price follows a discrete diffusion process with a variable step width while the difference between the number of steps in positive and negative direction in an interval is Gaussian distributed. The step width is given by the return due to a single trade and is long-term correlated in tick time. Hence, its mean value can well characterize an interval of many trades and turns out to be an important determinant for large aggregate returns. We also present a statistical model reproducing the cumulative distribution of aggregate returns. For an accurate agreement with the empirical distribution, we also take into account asymmetries of the step widths in different directions together with cross correlations between these asymmetries and the mean step width as well as the signs of the steps.

Approaching conversion limit with all-dielectric solar cell reflectors.

PubMed

Fu, Sze Ming; Lai, Yi-Chun; Tseng, Chi Wei; Yan, Sheng Lun; Zhong, Yan Kai; Shen, Chang-Hong; Shieh, Jia-Min; Li, Yu-Ren; Cheng, Huang-Chung; Chi, Gou-chung; Yu, Peichen; Lin, Albert

2015-02-09

Metallic back reflectors has been used for thin-film and wafer-based solar cells for very long time. Nonetheless, the metallic mirrors might not be the best choices for photovoltaics. In this work, we show that solar cells with all-dielectric reflectors can surpass the best-configured metal-backed devices. Theoretical and experimental results all show that superior large-angle light scattering capability can be achieved by the diffuse medium reflectors, and the solar cell J-V enhancement is higher for solar cells using all-dielectric reflectors. Specifically, the measured diffused scattering efficiency (D.S.E.) of a diffuse medium reflector is >0.8 for the light trapping spectral range (600nm-1000nm), and the measured reflectance of a diffuse medium can be as high as silver if the geometry of embedded titanium oxide(TiO(2)) nanoparticles is optimized. Moreover, the diffuse medium reflectors have the additional advantage of room-temperature processing, low cost, and very high throughput. We believe that using all-dielectric solar cell reflectors is a way to approach the thermodynamic conversion limit by completely excluding metallic dissipation.

Surface chemistry of ferrihydrite: Part 2. Kinetics of arsenate adsorption and coprecipitation

USGS Publications Warehouse

Fuller, C.C.; Dadis, J.A.; Waychunas, G.A.

1993-01-01

The kinetics of As(V) adsorption by ferrihydrite was investigated in coprecipitation and postsynthesis adsorption experiments conducted in the pH range 7.5-9.0. In coprecipitation experiments, As(V) was present in solution during the hydrolysis and precipitation of iron. In adsorption experiments, a period of rapid (<5 min) As(V) uptake from solution was followed by continued uptake for at least eight days, as As(V) diffused to adsorption sites on ferrihydrite surfaces within aggregates of colloidal particles. The time dependence of As(V) adsorption is well described by a general model for diffusion into a sphere if a subset of surface sites located near the exterior of aggregates is assumed to attain adsorptive equilibrium rapidly. The kinetics of As(V) desorption after an increase in pH were also consistent with diffusion as a rate-limiting process. Aging of pure ferrihydrite prior to As(V) adsorption caused a decrease in adsorption sites on the precipitate owing to crystallite growth. In coprecipitation experiments, the initial As(V) uptake was significantly greater than in post-synthesis adsorption experiments, and the rate of uptake was not diffusion limited because As(V) was coordinated by surface sites before crystallite growth and coagulation processes could proceed. After the initial adsorption, As(V) was slowly released from coprecipitates for at least one month, as crystallite growth caused desorption of As(V). Adsorption densities as high as 0.7 mole As(V) per mole of Fe were measured in coprecipitates, in comparison to 0.25 mole As(V) per mole of Fe in post-synthesis adsorption experiments. Despite the high Concentration of As(V) in the precipitates, EXAFS spectroscopy (Waychunas et al., 1993) showed that neither ferric arsenate nor any other As-bearing surface precipitate or solid solution was formed. The high adsorption densities are possible because the ferrihydrite particles are extremely small, approaching the size of small dioctahedral chains at the highest As(V) adsorption density. The results suggest that the solid solution model proposed by Fox (1989, 1992) for control of arsenate and phosphate concentrations in natural waters may be invalid. ?? 1993.

Impact of short range hydrophobic interactions and long range electrostatic forces on the aggregation kinetics of a monoclonal antibody and a dual-variable domain immunoglobulin at low and high concentrations.

PubMed

Kumar, Vineet; Dixit, Nitin; Zhou, Liqiang Lisa; Fraunhofer, Wolfgang

2011-12-12

The purpose of this work was to determine the nature of long and short-range forces governing protein aggregation kinetics at low and high concentrations for a monoclonal antibody (IgG1) and a dual-variable-domain immunoglobulin (DVD-Ig). Protein-protein interactions (PPI) were studied under dilute conditions by utilizing the methods of static (B(22)) and dynamic light scattering (k(D)). PPI in solutions containing minimal ionic strengths were characterized to get detailed insights into the impact of ionic strength on aggregation. Microcalorimetry and susceptibility to denature at air-liquid interface were used to assess the tertiary structure and quiescent stability studies were conducted to study aggregation characteristics. Results for IgG1 showed that electrostatic interactions governed protein aggregation kinetics both under dilute and concentrated conditions (i.e., 5 mg/mL and 150 mg/mL). For DVD-Ig molecules, on the other hand, although electrostatic interactions governed protein aggregation under dilute conditions, hydrophobic forces clearly determined the kinetics at high concentrations. This manuscript shows for the first time that short-range hydrophobic interactions can outweigh electrostatic forces and play an important role in determining protein aggregation at high concentrations. Additionally, results show that although higher-order virial coefficients become significant under low ionic strength conditions, removal of added charges may be used to enhance the aggregation stability of dilute protein formulations. Copyright © 2011 Elsevier B.V. All rights reserved.

Porosity and Organic Carbon Controls on Naturally Reduced Zone (NRZ) Formation Creating Microbial ';Hotspots' for Fe, S, and U Cycling in Subsurface Sediments

NASA Astrophysics Data System (ADS)

Jones, M. E.; Janot, N.; Bargar, J.; Fendorf, S. E.

2013-12-01

Previous studies have illustrated the importance of Naturally Reduced Zones (NRZs) within saturated sediments for the cycling of metals and redox sensitive contaminants. NRZs can provide a source of reducing equivalents such as reduced organic compounds or hydrogen to stimulate subsurface microbial communities. These NRZ's are typically characterized by low permeability and elevated concentrations of organic carbon and trace metals. However, both the formation of NRZs and their importance to the overall aquifer carbon remineralization is not fully understood. Within NRZs the hydrolysis of particulate organic carbon (POC) and subsequent fermentation of dissolved organic carbon (DOC) to form low molecular weight dissolved organic carbon (LMW-DOC) provides electron donors necessary for the respiration of Fe, S, and in the case of the Rifle aquifer, U. Rates of POC hydrolysis and subsequent fermentation have been poorly constrained and rates in excess and deficit to the rates of subsurface anaerobic respiratory processes have been suggested. In this study, we simulate the development of NRZ sediments in diffusion-limited aggregates to investigate the physical and chemical conditions required for NRZ formation. Effects of sediment porosity and POC loading on Fe, S, and U cycling on molecular and nanoscale are investigated with synchrotron-based Near Edge X-ray Absorption Fine Structure Spectroscopy (NEXAFS). Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) and Fourier Transform Infrared spectroscopy (FTIR) are used to characterize the transformations in POC and DOC. Sediment aggregates are inoculated with the natural microbial biota from the Rifle aquifer and population dynamics are monitored by 16S RNA analysis. Overall, establishment of low permeability NRZs within the aquifer stimulate microbial respiration beyond the diffusion-limited zones and can limit the transport of U through a contaminated aquifer. However, the long-term stability of NRZs and the co-located U is unknown and requires further study.

Neurocomputation by Reaction Diffusion

NASA Astrophysics Data System (ADS)

Liang, Ping

1995-08-01

This Letter demonstrates the possible role nonsynaptic diffusion neurotransmission may play in neurocomputation using an artificial neural network model. A reaction-diffusion neural network model with field-based information-processing mechanisms is proposed. The advantages of nonsynaptic field neurotransmission from a computational viewpoint demonstrated in this Letter include long-range inhibition using only local interaction, nonhardwired and changeable (target specific) long-range communication pathways, and multiple simultaneous spatiotemporal organization processes in the same medium.

Fractal Measure and Microscopic Modeling of Osseointegration.

PubMed

Santos, Leonardo Cavalcanti Bezerra; Carvalho, Alessandra Albuquerque; Leão, Jair Carneiro; Neto, Paulo Jose; Stosic, Tatijana; Stosic, Borko

2015-01-01

In this study, the process of osseointegration on titanium implant surfaces with different physicochemical treatments subjected to a simulated corporal fluid submersion was evaluated using the concept of fractal dimension. It was found that different treatments led to rather different calcium phosphate crystal growth patterns, with fractal dimension ranging from 1.68 to 1.93. The observed crystal patterns may be explained by a general deposition, diffusion, and aggregation growth mechanism, where diffusing particle sticking probability plays a fundamental role.

Engineering cell aggregates through incorporated polymeric microparticles.

PubMed

Ahrens, Caroline C; Dong, Ziye; Li, Wei

2017-10-15

Ex vivo cell aggregates must overcome significant limitations in the transport of nutrients, drugs, and signaling proteins compared to vascularized native tissue. Further, engineered extracellular environments often fail to sufficiently replicate tethered signaling cues and the complex architecture of native tissue. Co-cultures of cells with microparticles (MPs) is a growing field directed towards overcoming many of these challenges by providing local and controlled presentation of both soluble and tethered proteins and small molecules. Further, co-cultured MPs offer a mechanism to better control aggregate architecture and even to report key characteristics of the local microenvironment such as pH or oxygen levels. Herein, we provide a brief introduction to established and developing strategies for MP production including the choice of MP materials, fabrication techniques, and techniques for incorporating additional functionality. In all cases, we emphasize the specific utility of each approach to form MPs useful for applications in cell aggregate co-culture. We review established techniques to integrate cells and MPs. We highlight those strategies that promote targeted heterogeneity or homogeneity, and we describe approaches to engineer cell-particle and particle-particle interactions that enhance aggregate stability and biological response. Finally, we review advances in key application areas of MP aggregates and future areas of development. Cell-scaled polymer microparticles (MPs) integrated into cellular aggregates have been shown to be a powerful tool to direct cell response. MPs have supported the development of healthy cartilage, islets, nerves, and vasculature by the maintenance of soluble gradients as well as by the local presentation of tethered cues and diffusing proteins and small molecules. MPs integrated with pluripotent stem cells have directed in vivo expansion and differentiation. Looking forward, MPs are expected to support both the characterization and development of in vitro tissue systems for applications such as drug testing platforms. However, useful co-cultures must be designed keeping in mind the limitations and attributes of each material strategy within the context of the overall tissue biology. The present review integrates prospectives from materials development, drug delivery, and tissue engineering to provide a toolbox for the development and application of MPs useful for long-term co-culture within cell aggregates. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Stochastic Analysis of Reaction–Diffusion Processes

PubMed Central

Hu, Jifeng; Kang, Hye-Won

2013-01-01

Reaction and diffusion processes are used to model chemical and biological processes over a wide range of spatial and temporal scales. Several routes to the diffusion process at various levels of description in time and space are discussed and the master equation for spatially discretized systems involving reaction and diffusion is developed. We discuss an estimator for the appropriate compartment size for simulating reaction–diffusion systems and introduce a measure of fluctuations in a discretized system. We then describe a new computational algorithm for implementing a modified Gillespie method for compartmental systems in which reactions are aggregated into equivalence classes and computational cells are searched via an optimized tree structure. Finally, we discuss several examples that illustrate the issues that have to be addressed in general systems. PMID:23719732

A physical description of the adhesion and aggregation of platelets

NASA Astrophysics Data System (ADS)

Chopard, Bastien; de Sousa, Daniel Ribeiro; Lätt, Jonas; Mountrakis, Lampros; Dubois, Frank; Yourassowsky, Catherine; Van Antwerpen, Pierre; Eker, Omer; Vanhamme, Luc; Perez-Morga, David; Courbebaisse, Guy; Lorenz, Eric; Hoekstra, Alfons G.; Boudjeltia, Karim Zouaoui

2017-04-01

The early stages of clot formation in blood vessels involve platelet adhesion-aggregation. Although these mechanisms have been extensively studied, gaps in their understanding still persist. We have performed detailed in vitro experiments, using the well-known Impact-R device, and developed a numerical model to better describe and understand this phenomenon. Unlike previous studies, we took into account the differential role of pre-activated and non-activated platelets, as well as the three-dimensional nature of the aggregation process. Our investigation reveals that blood albumin is a major parameter limiting platelet aggregate formation in our experiment. Simulations are in very good agreement with observations and provide quantitative estimates of the adhesion and aggregation rates that are hard to measure experimentally. They also provide a value of the effective diffusion of platelets in blood subject to the shear rate produced by the Impact-R.

Molecules in motion: influences of diffusion on metabolic structure and function in skeletal muscle

PubMed Central

Kinsey, Stephen T.; Locke, Bruce R.; Dillaman, Richard M.

2011-01-01

Metabolic processes are often represented as a group of metabolites that interact through enzymatic reactions, thus forming a network of linked biochemical pathways. Implicit in this view is that diffusion of metabolites to and from enzymes is very fast compared with reaction rates, and metabolic fluxes are therefore almost exclusively dictated by catalytic properties. However, diffusion may exert greater control over the rates of reactions through: (1) an increase in reaction rates; (2) an increase in diffusion distances; or (3) a decrease in the relevant diffusion coefficients. It is therefore not surprising that skeletal muscle fibers have long been the focus of reaction–diffusion analyses because they have high and variable rates of ATP turnover, long diffusion distances, and hindered metabolite diffusion due to an abundance of intracellular barriers. Examination of the diversity of skeletal muscle fiber designs found in animals provides insights into the role that diffusion plays in governing both rates of metabolic fluxes and cellular organization. Experimental measurements of metabolic fluxes, diffusion distances and diffusion coefficients, coupled with reaction–diffusion mathematical models in a range of muscle types has started to reveal some general principles guiding muscle structure and metabolic function. Foremost among these is that metabolic processes in muscles do, in fact, appear to be largely reaction controlled and are not greatly limited by diffusion. However, the influence of diffusion is apparent in patterns of fiber growth and metabolic organization that appear to result from selective pressure to maintain reaction control of metabolism in muscle. PMID:21177946

Aggregate-mediated charge transport in ionomeric electrolytes

NASA Astrophysics Data System (ADS)

Lu, Keran; Maranas, Janna; Milner, Scott

Polymers such PEO can conduct ions, and have been studied as possible replacements for organic liquid electrolytes in rechargeable metal-ion batteries. More generally, fast room-temperature ionic conduction has been reported for a variety of materials, from liquids to crystalline solids. Unfortunately, polymer electrolytes generally have limited conductivity; these polymers are too viscous to have fast ion diffusion like liquids, and too unstructured to promote cooperative transport like crystalline solids. Ionomers are polymer electrolytes in which ionic groups are covalently bound to the polymer backbone, neutralized by free counterions. These materials also conduct ions, and can exhibit strong ionic aggregation. Using coarse-grained molecular dynamics, we explore the forces driving ionic aggregation, and describe the role ion aggregates have in mediating charge transport. The aggregates are string-like such that ions typically have two neighbors. We find ion aggregates self-assemble like worm-like micelles. Excess charge, or free ions, occasionally coordinate with aggregates and are transported along the chain in a Grotthuss-like mechanism. We propose that controlling ionomer aggregate structure through materials design can enhance cooperative ion transport.

FPGA implementation of advanced FEC schemes for intelligent aggregation networks

NASA Astrophysics Data System (ADS)

Zou, Ding; Djordjevic, Ivan B.

2016-02-01

In state-of-the-art fiber-optics communication systems the fixed forward error correction (FEC) and constellation size are employed. While it is important to closely approach the Shannon limit by using turbo product codes (TPC) and low-density parity-check (LDPC) codes with soft-decision decoding (SDD) algorithm; rate-adaptive techniques, which enable increased information rates over short links and reliable transmission over long links, are likely to become more important with ever-increasing network traffic demands. In this invited paper, we describe a rate adaptive non-binary LDPC coding technique, and demonstrate its flexibility and good performance exhibiting no error floor at BER down to 10-15 in entire code rate range, by FPGA-based emulation, making it a viable solution in the next-generation high-speed intelligent aggregation networks.

Dynamic characterization of external and internal mass transport in heterotrophic biofilms from microsensors measurements.

PubMed

Guimerà, Xavier; Dorado, Antonio David; Bonsfills, Anna; Gabriel, Gemma; Gabriel, David; Gamisans, Xavier

2016-10-01

Knowledge of mass transport mechanisms in biofilm-based technologies such as biofilters is essential to improve bioreactors performance by preventing mass transport limitation. External and internal mass transport in biofilms was characterized in heterotrophic biofilms grown on a flat plate bioreactor. Mass transport resistance through the liquid-biofilm interphase and diffusion within biofilms were quantified by in situ measurements using microsensors with a high spatial resolution (<50 μm). Experimental conditions were selected using a mathematical procedure based on the Fisher Information Matrix to increase the reliability of experimental data and minimize confidence intervals of estimated mass transport coefficients. The sensitivity of external and internal mass transport resistances to flow conditions within the range of typical fluid velocities over biofilms (Reynolds numbers between 0.5 and 7) was assessed. Estimated external mass transfer coefficients at different liquid phase flow velocities showed discrepancies with studies considering laminar conditions in the diffusive boundary layer near the liquid-biofilm interphase. The correlation of effective diffusivity with flow velocities showed that the heterogeneous structure of biofilms defines the transport mechanisms inside biofilms. Internal mass transport was driven by diffusion through cell clusters and aggregates at Re below 2.8. Conversely, mass transport was driven by advection within pores, voids and water channels at Re above 5.6. Between both flow velocities, mass transport occurred by a combination of advection and diffusion. Effective diffusivities estimated at different biofilm densities showed a linear increase of mass transport resistance due to a porosity decrease up to biofilm densities of 50 g VSS·L(-1). Mass transport was strongly limited at higher biofilm densities. Internal mass transport results were used to propose an empirical correlation to assess the effective diffusivity within biofilms considering the influence of hydrodynamics and biofilm density. Copyright © 2016 Elsevier Ltd. All rights reserved.

Diffusivity measurements of volatile organics in levitated viscous aerosol particles

NASA Astrophysics Data System (ADS)

Bastelberger, Sandra; Krieger, Ulrich K.; Luo, Beiping; Peter, Thomas

2017-07-01

Field measurements indicating that atmospheric secondary organic aerosol (SOA) particles can be present in a highly viscous, glassy state have spurred numerous studies addressing low diffusivities of water in glassy aerosols. The focus of these studies is on kinetic limitations of hygroscopic growth and the plasticizing effect of water. In contrast, much less is known about diffusion limitations of organic molecules and oxidants in viscous matrices. These may affect atmospheric chemistry and gas-particle partitioning of complex mixtures with constituents of different volatility. In this study, we quantify the diffusivity of a volatile organic in a viscous matrix. Evaporation of single particles generated from an aqueous solution of sucrose and small amounts of volatile tetraethylene glycol (PEG-4) is investigated in an electrodynamic balance at controlled relative humidity (RH) and temperature. The evaporative loss of PEG-4 as determined by Mie resonance spectroscopy is used in conjunction with a radially resolved diffusion model to retrieve translational diffusion coefficients of PEG-4. Comparison of the experimentally derived diffusivities with viscosity estimates for the ternary system reveals a breakdown of the Stokes-Einstein relationship, which has often been invoked to infer diffusivity from viscosity. The evaporation of PEG-4 shows pronounced RH and temperature dependencies and is severely depressed for RH ≲ 30 %, corresponding to diffusivities < 10-14 cm2 s-1 at temperatures < 15 °C. The temperature dependence is strong, suggesting a diffusion activation energy of about 300 kJ mol-1. We conclude that atmospheric volatile organic compounds can be subject to severe diffusion limitations in viscous organic aerosol particles. This may enable an important long-range transport mechanism for organic material, including pollutant molecules such as polycyclic aromatic hydrocarbons (PAHs).

Stability of aggregates in the environment: role of solid bridging

NASA Astrophysics Data System (ADS)

Seiphoori, A.; Jerolmack, D. J.; Arratia, P. E.

2017-12-01

Colloids in suspension may form larger flocs under favorable conditions, via diffusion- or reaction-limited aggregation. In addition, the process of drying colloidal suspensions drives colloids together via hydrodynamic forces to form aggregates, that may be stable or unstable when subject to re-wetting and transport. Channel banks, shorelines and hillslopes are examples where the periodic wetting and drying results in the aggregation of muds. If aggregates disperse, the mud structure is unstable to subsequent wetting or fluid shear and can easily be detached and transported to rivers and coasts. The effective friction that governs hillslope and channel-bank soil creep rates also depends on the stability of the soil aggregates. Yet, few studies probe the particle-scale assembly or stability of aggregates subject to environmental loads, and the effects of shape or size heterogeneity have not been examined in detail. Here we investigate the formation and stability of aggregates subject to passive re-wetting (by misting) and shearing using a simple Poiseuille flow in a microfluidic device. We study the kinetics of a wide range of silicate colloids of different size and surface charge properties using in situ microscopy and particle tracking. We find that negatively charged silica microspheres are dragged by the retreating edge of an evaporating drop and are resuspended easily on re-wetting, showing that aggregates are unstable. In contrast, a bi-disperse suspension created by the addition of silica nanoparticles forms stable deposits, where nanoparticles bind larger particles by bridging the interparticle space, a mechanism similar to capillary bridging that we refer to as "solid bridging." Although aggregate structure and dynamics of the bi-disperse system changes quantitatively with surface-charge of the nanoparticles, smaller particles always conferred stability on the aggregates. Investigation of other colloids, including asbestos fibers and various clays, reveals that this solid bridging effect is robust across variations in particle shape and material composition. These experiments suggest that natural mud and soil may form more stable aggregates than would naively be expected by considering the charge effects alone, because their inherent size heterogeneity is conducive to solid bridging.

Simulations of sheared dense noncolloidal suspensions: Evaluation of the role of long-range hydrodynamics

NASA Astrophysics Data System (ADS)

Gallier, Stany; Peters, François; Lobry, Laurent

2018-04-01

This work intends to evaluate the role of many-body long-range hydrodynamics by simulations of sheared neutrally buoyant non-Brownian, noncolloidal suspensions. Three-dimensional simulations of sheared suspensions are conducted with and without long-range hydrodynamics, for a volume fraction range between 0.1-0.62 (frictionless) and 0.1-0.56 (frictional). Discarding long-range hydrodynamics has only a moderate effect on viscosity for the range of volume fractions investigated and viscosities diverge with similar scaling laws; the critical fraction is found to be approximately 0.64 (frictionless) and 0.58 (frictional). Conversely, many-body hydrodynamics are found to affect diffusion and particle velocities, which are correlated on a longer range when long-range interactions are included, even in dense suspensions. This means that long-range hydrodynamics may not be significantly screened by crowding. Assuming only short-range lubrication interactions is therefore suitable for predicting viscosity in noncolloidal suspensions but becomes questionable when flow details (e.g., diffusion or velocity correlations) are needed.

Separation and quantification of monoclonal-antibody aggregates by hollow-fiber-flow field-flow fractionation.

PubMed

Fukuda, Jun; Iwura, Takafumi; Yanagihara, Shigehiro; Kano, Kenji

2014-10-01

Hollow-fiber-flow field-flow fractionation (HF5) separates protein molecules on the basis of the difference in the diffusion coefficient, and can evaluate the aggregation ratio of proteins. However, HF5 is still a minor technique because information on the separation conditions is limited. We examined in detail the effect of different settings, including the main-flow rate, the cross-flow rate, the focus point, the injection amount, and the ionic strength of the mobile phase, on fractographic characteristics. On the basis of the results, we proposed optimized conditions of the HF5 method for quantification of monoclonal antibody in sample solutions. The HF5 method was qualified regarding the precision, accuracy, linearity of the main peak, and quantitation limit. In addition, the HF5 method was applied to non-heated Mab A and heat-induced-antibody-aggregate-containing samples to evaluate the aggregation ratio and the distribution extent. The separation performance was comparable with or better than that of conventional methods including analytical ultracentrifugation-sedimentation velocity and asymmetric-flow field-flow fractionation.

Long-range two-dimensional superstructure in the superconducting electron-doped cuprate Pr 0.88 LaCe 0.12 CuO 4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campbell, B. J.; Rosenkranz, S.; Kang, H. J.

2015-07-01

Utilizing single-crystal synchrotron x-ray scattering, we observe distorted CuO 2 planes in the electron- doped superconductor Pr 1-xLaCe xCuO 4+δ , x =0.12. Resolution-limited rods of scattering are indicative of a long-range two-dimensional 2√2 × 2√2 superstructure in the a-b plane, adhering to planar space-group symmetry p4gm, which is subject to stacking disorder perpendicular to the planes. This superstructure is present only in annealed, superconducting samples, but not in the as-grown, nonsuperconducting samples. These long-range distortions of the CuO 2 planes, which are generally considered to be detrimental to superconductivity, have avoided detection to date due to the challenges ofmore » observing and interpreting subtle diffuse-scattering features.« less

Water Use in the US Electric Power Sector: Energy Systems Level Perspectives

EPA Science Inventory

This presentation reviews the water demands of long-range electricity scenarios. It addresses questions such as: What are the aggregate water requirements of the U.S. electric power sector? How could water requirements evolve under different long-range regional generation mixes? ...

What is the alternative to the Alexander-Orbach relation?

NASA Astrophysics Data System (ADS)

Sokolov, Igor M.

2016-03-01

The Alexander-Orbach (AO) relation d w = 2d f /d s connecting the fractal dimension of a random walk’s (RW) trajectory d w or the exponent of anomalous diffusion α = 2/d w on a fractal structure with the fractal and spectral dimension of the structure itself plays a key role in discussion of dynamical properties of complex systems including living cells and single biomolecules. This relation however does not hold universally and breaks down for some structures like diffusion limited aggregates and Eden trees. We show that the alternative to the AO relation is the explicit dependence of the coefficient of the anomalous diffusion on the system’s size, i.e. the absence of its thermodynamical limit. The prerequisite for its breakdown is the dependence of the local structure of possible steps of the RW on the system’s size. The discussion is illustrated by the examples of diffusion on a Koch curve (AO-conform) and on a Cantor dust (violating AO relation).

Fragmentation, rings and coarsening: structure and transformations of nanocrystal aggregate networks on a liquid surface

NASA Astrophysics Data System (ADS)

Yang, Bo; Scheidtmann, Jens; Mayer, Joachim; Wuttig, Matthias; Michely, Thomas

2002-01-01

Deposition of Ag on a silicon oil surface leads to the formation of nm-sized Ag crystals floating on the oil surface. These nanocrystals mutually attract each other, forming strongly branched nanocrystal aggregates and continuous aggregate networks. Transformation processes of such nanocrystal aggregate networks are imaged in situ by optical microscopy. The observations are explained on the basis of a simple model involving diffusion of nanocrystals along aggregate edges and the rupture of branches resulting from branch width fluctuations due to edge diffusion.

Three essays in energy consumption: Time series analyses

NASA Astrophysics Data System (ADS)

Ahn, Hee Bai

1997-10-01

Firstly, this dissertation investigates that which demand specification is an appropriate model for long-run energy demand between the conventional demand specification and the limited demand specification. In order to determine the components of a stable long-run demand for different sectors of the energy industry, I perform cointegration tests by using the Johansen test procedure. First, I test the conventional demand specification including prices and income as components. Second, I test a limited demand specification only income as a component. The reason for performing these tests is that we can determine that which demand specification is a good long-run predictor of energy consumption between the two demand specifications by using the cointegration tests. Secondly, for the purpose of planning and forecasting energy demand in case of cointegrated system, long-run elasticities are of particular interest. To retrieve the optimal level of energy demand in case of price shock, we need long-run elasticities rather than short-run elasticities. The energy demand study provides valuable information to the energy policy makers who are concerned about the long-run impact of taxes and tariffs. A long-run price elasticity is a primary barometer of the substitution effect between energy and non-energy inputs and long-run income elasticity is an important factor since we can measure the energy demand growing slowly or fast than in the past depending on the magnitude of long-run elasticity. The one other problem in estimating the total energy demand is that there exists an aggregation bias stemming from the process of summation in four different energy types for the total aggregation prices and total aggregation energy consumption. In order to measure the aggregation bias between the Btu aggregation method and the Divisia Index method, i.e., which methodology has less aggregation bias in the long-run, I compare the two estimation results with calculated results estimated on a disaggregated basis. Thus, we can confirm whether or not the theoretically superior methodology has less aggregation bias in empirical estimation. Thirdly, I investigate the causal relationships between energy use and GDP. In order to detect causal relationships both in the long-run and in the short-run, the VECM (Vector Error Correction Model) can be used if there exists cointegration relationships among the variables. I detect the causal effects between energy use and GDP by estimating the VECM based on the multivariate production function including the labor and capital variables.

Long-Range Correlations in Sentence Series from A Story of the Stone

PubMed Central

Yang, Tianguang; Gu, Changgui; Yang, Huijie

2016-01-01

A sentence is the natural unit of language. Patterns embedded in series of sentences can be used to model the formation and evolution of languages, and to solve practical problems such as evaluating linguistic ability. In this paper, we apply de-trended fluctuation analysis to detect long-range correlations embedded in sentence series from A Story of the Stone, one of the greatest masterpieces of Chinese literature. We identified a weak long-range correlation, with a Hurst exponent of 0.575±0.002 up to a scale of 104. We used the structural stability to confirm the behavior of the long-range correlation, and found that different parts of the series had almost identical Hurst exponents. We found that noisy records can lead to false results and conclusions, even if the noise covers a limited proportion of the total records (e.g., less than 1%). Thus, the structural stability test is an essential procedure for confirming the existence of long-range correlations, which has been widely neglected in previous studies. Furthermore, a combination of de-trended fluctuation analysis and diffusion entropy analysis demonstrated that the sentence series was generated by a fractional Brownian motion. PMID:27648941

Long-Range Correlations in Sentence Series from A Story of the Stone.

PubMed

Yang, Tianguang; Gu, Changgui; Yang, Huijie

2016-01-01

A sentence is the natural unit of language. Patterns embedded in series of sentences can be used to model the formation and evolution of languages, and to solve practical problems such as evaluating linguistic ability. In this paper, we apply de-trended fluctuation analysis to detect long-range correlations embedded in sentence series from A Story of the Stone, one of the greatest masterpieces of Chinese literature. We identified a weak long-range correlation, with a Hurst exponent of 0.575±0.002 up to a scale of 104. We used the structural stability to confirm the behavior of the long-range correlation, and found that different parts of the series had almost identical Hurst exponents. We found that noisy records can lead to false results and conclusions, even if the noise covers a limited proportion of the total records (e.g., less than 1%). Thus, the structural stability test is an essential procedure for confirming the existence of long-range correlations, which has been widely neglected in previous studies. Furthermore, a combination of de-trended fluctuation analysis and diffusion entropy analysis demonstrated that the sentence series was generated by a fractional Brownian motion.

Information diffusion, Facebook clusters, and the simplicial model of social aggregation: a computational simulation of simplicial diffusers for community health interventions.

PubMed

Kee, Kerk F; Sparks, Lisa; Struppa, Daniele C; Mannucci, Mirco A; Damiano, Alberto

2016-01-01

By integrating the simplicial model of social aggregation with existing research on opinion leadership and diffusion networks, this article introduces the constructs of simplicial diffusers (mathematically defined as nodes embedded in simplexes; a simplex is a socially bonded cluster) and simplicial diffusing sets (mathematically defined as minimal covers of a simplicial complex; a simplicial complex is a social aggregation in which socially bonded clusters are embedded) to propose a strategic approach for information diffusion of cancer screenings as a health intervention on Facebook for community cancer prevention and control. This approach is novel in its incorporation of interpersonally bonded clusters, culturally distinct subgroups, and different united social entities that coexist within a larger community into a computational simulation to select sets of simplicial diffusers with the highest degree of information diffusion for health intervention dissemination. The unique contributions of the article also include seven propositions and five algorithmic steps for computationally modeling the simplicial model with Facebook data.

Interactions between drought and soil biogeochemistry: scaling from molecules to meters

NASA Astrophysics Data System (ADS)

Schimel, J.; Schaeffer, S. M.

2011-12-01

Water is the perhaps the single most critical resource for life, yet most terrestrial ecosystems experience regular drought. Reduced water potential causes physiological stress; reduced diffusion limits resource availability when microbes may need resources to acclimate. Most biogeochemical models, however, have assumed that soil processes either slow down or stop during drought. But organisms survive and enzymes remain viable. In California, as soils stay dry through the long summer drought, microbial biomass actually increases and pools of extractable organic C increase, probably because extracellular enzymes continue to break down plant detritus (notably roots). Yet 14C suggests that in deeper soils, the pulse of C released on rewetting comes from pools with turnover times of as long as 800 years. What are the mechanisms that regulate these complex dynamics? They appear to involve differential moisture sensitivity for the activity of extracellular enzymes, substrate diffusion, and microbial metabolism. Rewetting not only redistributes materials made available during the drought, but it also disrupts aggregates and may make previously-protected substrates available as well. We have used several methods to simply capture these linkages between water and carbon in models that are applicable at the ecosystem scale and that could improve our ability to model biogeochemical cycles in arid and semi-arid ecosystems. One is a simple empirical modification to the DAYCENT model while the other is a mechanistic model that incorporates microbial dry-season processes.

Bioturbation, advection, and diffusion of a conserved tracer in a laboratory flume

NASA Astrophysics Data System (ADS)

Work, P. A.; Moore, P. R.; Reible, D. D.

2002-06-01

Laboratory experiments indicating the relative influences of advection, diffusion, and bioturbation on transport of NaCl tracer between a stream and streambed are described. Data were collected in a recirculating flume housing a box filled with test sediments. Peclet numbers ranged from 0 to 1.5. Sediment components included a medium sand (d50 = 0.31 mm), kaolinite, and topsoil. Lumbriculus variegatus were introduced as bioturbators. Conductivity probes were employed to document the flux of the tracer solution out of the bed. Measurements are compared to one-dimensional effective diffusion models assuming one or two horizontal sediment layers. These simple models provide a good indication of tracer half-life in the bed if a suitable effective diffusion coefficient is chosen but underpredict initial flux and overpredict flux at long times. Organism activity was limited to the upper reaches of the sediment test box but eventually exerts a secondary influence on flux from deeper regions.

Predicting the weathering of fuel and oil spills: A diffusion-limited evaporation model.

PubMed

Kotzakoulakis, Konstantinos; George, Simon C

2018-01-01

The majority of the evaporation models currently available in the literature for the prediction of oil spill weathering do not take into account diffusion-limited mass transport and the formation of a concentration gradient in the oil phase. The altered surface concentration of the spill caused by diffusion-limited transport leads to a slower evaporation rate compared to the predictions of diffusion-agnostic evaporation models. The model presented in this study incorporates a diffusive layer in the oil phase and predicts the diffusion-limited evaporation rate. The information required is the composition of the fluid from gas chromatography or alternatively the distillation data. If the density or a single viscosity measurement is available the accuracy of the predictions is higher. Environmental conditions such as water temperature, air pressure and wind velocity are taken into account. The model was tested with synthetic mixtures, petroleum fuels and crude oils with initial viscosities ranging from 2 to 13,000 cSt. The tested temperatures varied from 0 °C to 23.4 °C and wind velocities from 0.3 to 3.8 m/s. The average absolute deviation (AAD) of the diffusion-limited model ranged between 1.62% and 24.87%. In comparison, the AAD of a diffusion-agnostic model ranged between 2.34% and 136.62% against the same tested fluids. Copyright © 2017 Elsevier Ltd. All rights reserved.

Anomalous diffusion and long-range correlations in the score evolution of the game of cricket

NASA Astrophysics Data System (ADS)

Ribeiro, Haroldo V.; Mukherjee, Satyam; Zeng, Xiao Han T.

2012-08-01

We investigate the time evolution of the scores of the second most popular sport in the world: the game of cricket. By analyzing, event by event, the scores of more than 2000 matches, we point out that the score dynamics is an anomalous diffusive process. Our analysis reveals that the variance of the process is described by a power-law dependence with a superdiffusive exponent, that the scores are statistically self-similar following a universal Gaussian distribution, and that there are long-range correlations in the score evolution. We employ a generalized Langevin equation with a power-law correlated noise that describes all the empirical findings very well. These observations suggest that competition among agents may be a mechanism leading to anomalous diffusion and long-range correlation.

Trehalose limits BSA aggregation in spray-dried formulations at high temperatures: implications in preparing polymer implants for long-term protein delivery.

PubMed

Rajagopal, Karthikan; Wood, Joseph; Tran, Benjamin; Patapoff, Thomas W; Nivaggioli, Thierry

2013-08-01

Polymer implants are promising systems for sustained release applications but their utility for protein delivery has been hindered because of concerns over drug stability at elevated temperatures required for processing. Using bovine serum albumin (BSA) as a model, we have assessed whether proteins can be formulated for processing at elevated temperatures. Specifically, the effect of trehalose and histidine-HCl buffer on BSA stability in a spray-dried formulation has been investigated at temperatures ranging from 80°C to 110°C. When both the sugar and buffer are present, aggregation is suppressed even when exposed to 100°C, the extrusion temperature of poly(lactide-co-glycolide) (PLGA), a bioresorbable polymer. Estimation of aggregation rate constants (k) indicate that though both trehalose and histidine-HCl buffer contribute to BSA stability, the effect because of trehalose alone is more pronounced. BSA-loaded PLGA implants were prepared using hot-melt extrusion process and in vitro release was conducted in phosphate buffered saline at 37°C. Comparison of drug released from implants prepared using four different formulations confirmed that maximal release was achieved from the formulation in which BSA was least aggregated. These studies demonstrate that when trehalose and histidine-HCl buffer are included in spray-dried formulations, BSA stability is maintained both during processing at 100°C and long-term residence within implants. Copyright © 2013 Wiley Periodicals, Inc.

Long-range hot-carrier transport in hybrid perovskites visualized by ultrafast microscopy

NASA Astrophysics Data System (ADS)

Guo, Zhi; Wan, Yan; Yang, Mengjin; Snaider, Jordan; Zhu, Kai; Huang, Libai

2017-04-01

The Shockley-Queisser limit for solar cell efficiency can be overcome if hot carriers can be harvested before they thermalize. Recently, carrier cooling time up to 100 picoseconds was observed in hybrid perovskites, but it is unclear whether these long-lived hot carriers can migrate long distance for efficient collection. We report direct visualization of hot-carrier migration in methylammonium lead iodide (CH3NH3PbI3) thin films by ultrafast transient absorption microscopy, demonstrating three distinct transport regimes. Quasiballistic transport was observed to correlate with excess kinetic energy, resulting in up to 230 nanometers transport distance that could overcome grain boundaries. The nonequilibrium transport persisted over tens of picoseconds and ~600 nanometers before reaching the diffusive transport limit. These results suggest potential applications of hot-carrier devices based on hybrid perovskites.

Breakdown and Limit of Continuum Diffusion Velocity for Binary Gas Mixtures from Direct Simulation

NASA Astrophysics Data System (ADS)

Martin, Robert Scott; Najmabadi, Farrokh

2011-05-01

This work investigates the breakdown of the continuum relations for diffusion velocity in inert binary gas mixtures. Values of the relative diffusion velocities for components of a gas mixture may be calculated using of Chapman-Enskog theory and occur not only due to concentration gradients, but also pressure and temperature gradients in the flow as described by Hirschfelder. Because Chapman-Enskog theory employs a linear perturbation around equilibrium, it is expected to break down when the velocity distribution deviates significantly from equilibrium. This breakdown of the overall flow has long been an area of interest in rarefied gas dynamics. By comparing the continuum values to results from Bird's DS2V Monte Carlo code, we propose a new limit on the continuum approach specific to binary gases. To remove the confounding influence of an inconsistent molecular model, we also present the application of the variable hard sphere (VSS) model used in DS2V to the continuum diffusion velocity calculation. Fitting sample asymptotic curves to the breakdown, a limit, Vmax, that is a fraction of an analytically derived limit resulting from the kinetic temperature of the mixture is proposed. With an expected deviation of only 2% between the physical values and continuum calculations within ±Vmax/4, we suggest this as a conservative estimate on the range of applicability for the continuum theory.

Influence of external factors on the self-assembly of two structurally related antidepressant drugs: a thermodynamic study

NASA Astrophysics Data System (ADS)

Gutiérrez-Pichel, Manuel; Attwood, David; Taboada, Pablo; Mosquera, Víctor

Apparent molal volumes and adiabatic compressibilities of aqueous solutions of the amphiphilic antidepressant drugs imipramine and desipramine hydrochlorides have been determined from density and ultrasound velocity measurements in the temperature range 288.15-313.15 K in buffered solution of pH 3.0 and 5.5. Critical concentrations for aggregation of these drugs were obtained from inflections on the plots of the sound velocity against drug concentration. Positive deviation from the Debye-Hückel limiting law of the apparent molal volume of imipramine provides evidence of limited association at concentrations below the critical concentration over the temperature range studied. Apparent molal adiabatic compressibilities of the aggregates formed by the drugs, calculated by combining the ultrasound velocity and density data, were typical of those for a stacked aggregate. The critical concentration and energy involved in the aggregation process of these drugs have been evaluated using isothermal titration calorimetry. The solvent-aggregate interactions have been discussed from compressibility and calorimetry data.

How Hot Precursor Modify Island Nucleation: A Rate-Equation Model

NASA Astrophysics Data System (ADS)

Morales-Cifuentes, Josue; Einstein, T. L.; Pimpinelli, Alberto

2015-03-01

We describe the analysis, based on rate equations, of the hot precursor model mentioned in the previous talk. Two key parameters are the competing times of ballistic monomers decaying into thermalized monomers vs. being captured by an island, which naturally define a ``thermalization'' scale for the system. We interpret the energies and dimmensionless parameters used in the model, and provide both an implicit analytic solution and a convenient asymptotic approximation. Further analysis reveals novel scaling regimes and nonmonotonic crossovers between them. To test our model, we applied it to experiments on parahexaphenyl (6P) on sputtered mica. With the resulting parameters, the curves derived from our analytic treatment account very well for the data at the 4 different temperatures. The fit shows that the high-flux regime corresponds not to ALA (attachment-limited aggregation) or HMA (hot monomer aggregation) but rather to an intermediate scaling regime related to DLA (diffusion-limited aggregation). We hope this work stimulates further experimental investigations. Work at UMD supported by NSF CHE 13-05892.

A novel approach to a fine particle coating using porous spherical silica as core particles.

PubMed

Ishida, Makoto; Uchiyama, Jumpei; Isaji, Keiko; Suzuki, Yuta; Ikematsu, Yasuyuki; Aoki, Shigeru

2014-08-01

Abstract The applicability of porous spherical silica (PSS) was evaluated as core particles for pharmaceutical products by comparing it with commercial core particles such as mannitol (NP-108), sucrose and microcrystalline cellulose spheres. We investigated the physical properties of core particles, such as particle size distribution, flow properties, crushing strength, plastic limit, drying rate, hygroscopic property and aggregation degree. It was found that PSS was a core particle of small particle size, low friability, high water adsorption capacity, rapid drying rate and lower occurrence of particle aggregation, although wettability is a factor to be carefully considered. The aggregation and taste-masking ability using PSS and NP-108 as core particles were evaluated at a fluidized-bed coating process. The functional coating under the excess spray rate shows different aggregation trends and dissolution profiles between PSS and NP-108; thereby, exhibiting the formation of uniform coating under the excess spray rate in the case of PSS. This expands the range of the acceptable spray feed rates to coat fine particles, and indicates the possibility of decreasing the coating time. The results obtained in this study suggested that the core particle, which has a property like that of PSS, was useful in overcoming such disadvantages as large particle size, which feels gritty in oral cavity; particle aggregation; and the long coating time of the particle coating process. These results will enable the practical fine particle coating method by increasing the range of optimum coating conditions and decreasing the coating time in fluidized bed technology.

Thermodynamic criteria analysis for the use of taro starch spherical aggregates as microencapsulant matrix.

PubMed

Hoyos-Leyva, Javier D; Bello-Pérez, Luis A; Alvarez-Ramirez, J

2018-09-01

Spherical aggregates can be obtained from taro starch by spray-drying without using bonding agents. Accurate information about thermal issues of spherical aggregates can provide valuable information for assessing the application as encapsulant. Spherical aggregates of taro starch were obtained by spray-drying and analyzed using dynamic vapour sorption. The use of the Guggenheim, Anderson and de Boer (GAB) model indicated a Type II isotherm pattern with weaker interactions in the multilayer region. Differential enthalpy and entropy estimates reflected a mesoporous microstructure, implying that energetic mechanisms dominate over transport mechanisms in the sorption process. The limitation by energetic mechanisms was corroborated with enthalpy-entropy compensation estimates. The diffusivity coefficient was of the order of 10 -8  m 2 ·s -1 , which is in line with results obtained for common materials used for encapsulation purposes. The thermodynamic properties and the lack of a bonding agent indicated the viability of spherical aggregates of taro starch for encapsulation of biocompounds. Copyright © 2018 Elsevier Ltd. All rights reserved.

Electrohydrodynamic properties of succinoglycan as probed by fluorescence correlation spectroscopy, potentiometric titration and capillary electrophoresis.

PubMed

Duval, Jérôme F L; Slaveykova, Vera I; Hosse, Monika; Buffle, Jacques; Wilkinson, Kevin J

2006-10-01

The electrostatic, hydrodynamic and conformational properties of aqueous solutions of succinoglycan have been analyzed by fluorescence correlation spectroscopy (FCS), proton titration, and capillary electrophoresis (CE) over a large range of pH values and electrolyte (NaCl) concentrations. Using the theoretical formalism developed previously for the electrokinetic properties of soft, permeable particles, a quantitative analysis for the electro-hydrodynamics of succinoglycan is performed by taking into account, in a self-consistent manner, the measured values of the diffusion coefficients, electric charge densities, and electrophoretic mobilities. For that purpose, two limiting conformations for the polysaccharide in solution are tested, i.e. succinoglycan behaves as (i) a spherical, random coil polymer or (ii) a rodlike particle with charged lateral chains. The results show that satisfactory modeling of the titration data for ionic strengths larger than 50 mM can be accomplished using both geometries over the entire range of pH values. Electrophoretic mobilities measured for sufficiently large pH values (pH > 5-6) are in line with predictions based on either model. The best manner to discriminate between these two conceptual models is briefly discussed. For low pH values (pH < 5), both models indicate aggregation, resulting in an increase of the hydrodynamic permeability and a decrease of the diffusion coefficient.

Controlled Aggregation of Ferritin to Modulate MRI Relaxivity

PubMed Central

Bennett, Kevin M.; Shapiro, Erik M.; Sotak, Christopher H.; Koretsky, Alan P.

2008-01-01

Ferritin is an iron storage protein expressed in varying concentrations in mammalian cells. The deposition of ferric iron in the core of ferritin makes it a magnetic resonance imaging contrast agent, and ferritin has recently been proposed as a gene expression reporter protein for magnetic resonance imaging. To date, ferritin has been overexpressed in vivo and has been coexpressed with transferrin receptor to increase iron loading in cells. However, ferritin has a relatively low T2 relaxivity (R2 ≈ 1 mM−1s−1) at typical magnetic field strengths and so requires high levels of expression to be detected. One way to modulate the transverse relaxivity of a superparamagnetic agent is to cause it to aggregate, thereby manipulating the magnetic field gradients through which water diffuses. In this work, it is demonstrated by computer simulation and in vitro that aggregation of ferritin can alter relaxivity. The effects of aggregate size and intraaggregate perturber spacing on R2 are studied. Computer modeling indicates that the optimal spacing of the ferritin molecules in aggregate for increasing R2 is 100–200 nm for a typical range of water diffusion rates. Chemical cross-linking of ferritin at 12 Å spacing led to a 70% increase in R2 compared to uncross-linked ferritin controls. To modulate ferritin aggregation in a potentially biologically relevant manner, ferritin was attached to actin and polymerized in vitro. The polymerization of ferritin-F-actin caused a 20% increase in R2 compared to unpolymerized ferritin-G-actin. The R2-value was increased by another 10% by spacing the ferritin farther apart on the actin filaments. The modulation of ferritin aggregation by binding to cytoskeletal elements may be a useful strategy to make a functional reporter gene for magnetic resonance imaging. PMID:18326661

NMR study on the network structure of a mixed gel of kappa and iota carrageenans.

PubMed

Hu, Bingjie; Du, Lei; Matsukawa, Shingo

2016-10-05

The temperature dependencies of the (1)H T2 and diffusion coefficient (D) of a mixed solution of kappa-carrageenan and iota-carrageenan were measured by NMR. Rheological and NMR measurements suggested an exponential formation of rigid aggregates of kappa-carrageenan and a gradual formation of fine aggregates of iota-carrageenan during two step increases of G'. The results also suggested that longer carrageenan chains are preferentially involved in aggregation, thus resulting in a decrease in the average Mw of solute carrageenans. The results of diffusion measurements for poly(ethylene oxide) (PEO) suggested that kappa-carrageenan formed thick aggregates that decreased hindrance to PEO diffusion by decreasing the solute kappa-carrageenan concentration in the voids of the aggregated chains, and that iota-carrageenan formed fine aggregates that decreased the solute iota-carrageenan concentration less. DPEO in a mixed solution of kappa-carrageenan and iota-carrageenan suggested two possibilities for the microscopic network structure: an interpenetrating network structure, or micro-phase separation. Copyright © 2016. Published by Elsevier Ltd.

UV-visible light-activated Ag-decorated, monodisperse TiO2 aggregates for treatment of the pharmaceutical oxytetracycline.

PubMed

Han, Changseok; Likodimos, Vlassis; Khan, Javed Ali; Nadagouda, Mallikarjuna N; Andersen, Joel; Falaras, Polycarpos; Rosales-Lombardi, Pablo; Dionysiou, Dionysios D

2014-10-01

Noble metal Ag-decorated, monodisperse TiO2 aggregates were successfully synthesized by an ionic strength-assisted, simple sol-gel method and were used for the photocatalytic degradation of the antibiotic oxytetracycline (OTC) under both UV and visible light (UV-visible light) irradiation. The synthesized samples were characterized by X-ray diffraction analysis (XRD); UV-vis diffuse reflectance spectroscopy; environmental scanning electron microscopy (ESEM); transmission electron microscopy (TEM); high-resolution TEM (HR-TEM); micro-Raman, energy-dispersive X-ray spectroscopy (EDS); and inductively coupled plasma optical emission spectrometry (ICP-OES). The results showed that the uniformity of TiO2 aggregates was finely tuned by the sol-gel method, and Ag was well decorated on the monodisperse TiO2 aggregates. The absorption of the samples in the visible light region increased with increasing Ag loading that was proportional to the amount of Ag precursor added in the solution over the tested concentration range. The Brunauer, Emmett, and Teller (The BET) surface area slightly decreased with increasing Ag loading on the TiO2 aggregates. Ag-decorated TiO2 samples demonstrated enhanced photocatalytic activity for the degradation of OTC under UV-visible light illumination compared to that of pure TiO2. The sample containing 1.9 wt% Ag showed the highest photocatalytic activity for the degradation of OTC under both UV-visible light and visible light illumination. During the experiments, the detected Ag leaching for the best TiO2-Ag photocatalyst was much lower than the National Secondary Drinking Water Regulation for Ag limit (0.1 mg L(-1)) issued by the US Environmental Protection Agency.

Impact of Spatial Soil and Climate Input Data Aggregation on Regional Yield Simulations

PubMed Central

Hoffmann, Holger; Zhao, Gang; Asseng, Senthold; Bindi, Marco; Biernath, Christian; Constantin, Julie; Coucheney, Elsa; Dechow, Rene; Doro, Luca; Eckersten, Henrik; Gaiser, Thomas; Grosz, Balázs; Heinlein, Florian; Kassie, Belay T.; Kersebaum, Kurt-Christian; Klein, Christian; Kuhnert, Matthias; Lewan, Elisabet; Moriondo, Marco; Nendel, Claas; Priesack, Eckart; Raynal, Helene; Roggero, Pier P.; Rötter, Reimund P.; Siebert, Stefan; Specka, Xenia; Tao, Fulu; Teixeira, Edmar; Trombi, Giacomo; Wallach, Daniel; Weihermüller, Lutz; Yeluripati, Jagadeesh; Ewert, Frank

2016-01-01

We show the error in water-limited yields simulated by crop models which is associated with spatially aggregated soil and climate input data. Crop simulations at large scales (regional, national, continental) frequently use input data of low resolution. Therefore, climate and soil data are often generated via averaging and sampling by area majority. This may bias simulated yields at large scales, varying largely across models. Thus, we evaluated the error associated with spatially aggregated soil and climate data for 14 crop models. Yields of winter wheat and silage maize were simulated under water-limited production conditions. We calculated this error from crop yields simulated at spatial resolutions from 1 to 100 km for the state of North Rhine-Westphalia, Germany. Most models showed yields biased by <15% when aggregating only soil data. The relative mean absolute error (rMAE) of most models using aggregated soil data was in the range or larger than the inter-annual or inter-model variability in yields. This error increased further when both climate and soil data were aggregated. Distinct error patterns indicate that the rMAE may be estimated from few soil variables. Illustrating the range of these aggregation effects across models, this study is a first step towards an ex-ante assessment of aggregation errors in large-scale simulations. PMID:27055028

Impact of Spatial Soil and Climate Input Data Aggregation on Regional Yield Simulations.

PubMed

Hoffmann, Holger; Zhao, Gang; Asseng, Senthold; Bindi, Marco; Biernath, Christian; Constantin, Julie; Coucheney, Elsa; Dechow, Rene; Doro, Luca; Eckersten, Henrik; Gaiser, Thomas; Grosz, Balázs; Heinlein, Florian; Kassie, Belay T; Kersebaum, Kurt-Christian; Klein, Christian; Kuhnert, Matthias; Lewan, Elisabet; Moriondo, Marco; Nendel, Claas; Priesack, Eckart; Raynal, Helene; Roggero, Pier P; Rötter, Reimund P; Siebert, Stefan; Specka, Xenia; Tao, Fulu; Teixeira, Edmar; Trombi, Giacomo; Wallach, Daniel; Weihermüller, Lutz; Yeluripati, Jagadeesh; Ewert, Frank

2016-01-01

We show the error in water-limited yields simulated by crop models which is associated with spatially aggregated soil and climate input data. Crop simulations at large scales (regional, national, continental) frequently use input data of low resolution. Therefore, climate and soil data are often generated via averaging and sampling by area majority. This may bias simulated yields at large scales, varying largely across models. Thus, we evaluated the error associated with spatially aggregated soil and climate data for 14 crop models. Yields of winter wheat and silage maize were simulated under water-limited production conditions. We calculated this error from crop yields simulated at spatial resolutions from 1 to 100 km for the state of North Rhine-Westphalia, Germany. Most models showed yields biased by <15% when aggregating only soil data. The relative mean absolute error (rMAE) of most models using aggregated soil data was in the range or larger than the inter-annual or inter-model variability in yields. This error increased further when both climate and soil data were aggregated. Distinct error patterns indicate that the rMAE may be estimated from few soil variables. Illustrating the range of these aggregation effects across models, this study is a first step towards an ex-ante assessment of aggregation errors in large-scale simulations.

New product forecasting with limited or no data

NASA Astrophysics Data System (ADS)

Ismai, Zuhaimy; Abu, Noratikah; Sufahani, Suliadi

2016-10-01

In the real world, forecasts would always be based on historical data with the assumption that the behaviour be the same for the future. But how do we forecast when there is no such data available? New product or new technologies normally has limited amount of data available. Knowing that forecasting is valuable for decision making, this paper presents forecasting of new product or new technologies using aggregate diffusion models and modified Bass Model. A newly launched Proton car and its penetration was chosen to demonstrate the possibility of forecasting sales demand where there is limited or no data available. The model was developed to forecast diffusion of new vehicle or an innovation in the Malaysian society. It is to represent the level of spread on the new vehicle among a given set of the society in terms of a simple mathematical function that elapsed since the introduction of the new product. This model will forecast the car sales volume. A procedure of the proposed diffusion model was designed and the parameters were estimated. Results obtained by applying the proposed diffusion model and numerical calculation shows that the model is robust and effective for forecasting demand of the new vehicle. The results reveal that newly developed modified Bass diffusion of demand function has significantly contributed for forecasting the diffusion of new Proton car or new product.

Diffusion-limited mixing by incompressible flows

NASA Astrophysics Data System (ADS)

Miles, Christopher J.; Doering, Charles R.

2018-05-01

Incompressible flows can be effective mixers by appropriately advecting a passive tracer to produce small filamentation length scales. In addition, diffusion is generally perceived as beneficial to mixing due to its ability to homogenize a passive tracer. However we provide numerical evidence that, in cases where advection and diffusion are both actively present, diffusion may produce negative effects by limiting the mixing effectiveness of incompressible optimal flows. This limitation appears to be due to the presence of a limiting length scale given by a generalised Batchelor length (Batchelor 1959 J. Fluid Mech. 5 113–33). This length scale limitation may in turn affect long-term mixing rates. More specifically, we consider local-in-time flow optimisation under energy and enstrophy flow constraints with the objective of maximising the mixing rate. We observe that, for enstrophy-bounded optimal flows, the strength of diffusion may not impact the long-term mixing rate. For energy-constrained optimal flows, however, an increase in the strength of diffusion can decrease the mixing rate. We provide analytical lower bounds on mixing rates and length scales achievable under related constraints (point-wise bounded speed and rate-of-strain) by extending the work of Lin et al (2011 J. Fluid Mech. 675 465–76) and Poon (1996 Commun. PDE 21 521–39).

Multiscale modelling of dual-porosity porous media; a computational pore-scale study for flow and solute transport

NASA Astrophysics Data System (ADS)

de Vries, Enno T.; Raoof, Amir; van Genuchten, Martinus Th.

2017-07-01

Many environmental and agricultural applications involve the transport of water and dissolved constituents through aggregated soil profiles, or porous media that are structured, fractured or macroporous in other ways. During the past several decades, various process-based macroscopic models have been used to simulate contaminant transport in such media. Many of these models consider advective-dispersive transport through relatively large inter-aggregate pore domains, while exchange with the smaller intra-aggregate pores is assumed to be controlled by diffusion. Exchange of solute between the two domains is often represented using a first-order mass transfer coefficient, which is commonly obtained by fitting to observed data. This study aims to understand and quantify the solute exchange term by applying a dual-porosity pore-scale network model to relatively large domains, and analysing the pore-scale results in terms of the classical dual-porosity (mobile-immobile) transport formulation. We examined the effects of key parameters (notably aggregate porosity and aggregate permeability) on the main dual-porosity model parameters, i.e., the mobile water fraction (ϕm) and the mass transfer coefficient (α). Results were obtained for a wide range of aggregate porosities (between 0.082 and 0.700). The effect of aggregate permeability was explored by varying pore throat sizes within the aggregates. Solute breakthrough curves (BTCs) obtained with the pore-scale network model at several locations along the domain were analysed using analytical solutions of the dual-porosity model to obtain estimates of ϕm and α. An increase in aggregate porosity was found to decrease ϕm and increase α, leading to considerable tailing in the BTCs. Changes in the aggregate pore throat size affected the relative flow velocity between the intra- and inter-aggregate domains. Higher flow velocities within the aggregates caused a change in the transport regime from diffusion dominated to more advection dominated. This change increased the exchange rate of solutes between the mobile and immobile domains, with a related increase in the value of the mass transfer coefficient and less tailing in the BTCs.

Investigation of Aggregates as a Model for Titan's Aerosols Using Microwave Analog Experiments and Radiative Transfer Theory

NASA Astrophysics Data System (ADS)

Thomas-Osip, J. E.; Gustafson, B. Å. S.

1996-09-01

It has been suggested that the aerosols in the atmosphere of Titan have an aggregate morphology (Bar-Nun et al., 1988: West and Smith, 1991). Previous studies were based on formulations of the Discrete Dipole Approximation to calculate the single scattering properties of such aggregates. These studies were limited in the size of the individual spheres and total size of the aggregate. We present microwave to light analog scattering measurements and radiative transfer calculations for aggregates of 250-500 individual spheres near the Raleigh size limit in a plane parallel atmosphere. The advantages of using microwave analog experiments include the possibility of investigating a broad range of particle sizes and morphologies.

Photothermal Beam Deflection Spectroscopy for the Determination of Thermal Diffusivity of Soils and Soil Aggregates

NASA Astrophysics Data System (ADS)

Proskurnin, M. A.; Korte, D.; Rogova, O. B.; Volkov, D. S.; Franko, M.

2018-07-01

Photothermal beam deflection spectroscopy (BDS) with a red He-Ne laser (632.8 nm, 35 mW) as an excitation beam source and a green He-Ne laser (543.1 nm, 2 mW) as a probe was used for estimating thermal diffusivity of several types of soil samples and individual soil aggregates with small surfaces (2 × 2 mm). It is shown that BDS can be used on demand for studies of changes in properties of soil entities of different hierarchical levels under the action of agrogenesis. It is presented that BDS clearly distinguishes between thermal diffusivities of different soil types: Sod-podzolic [Umbric Albeluvisols, Abruptic], 29 ± 3; Chernozem typical [Voronic Chernozems, Pachic], 9.9 ± 0.9; and Light Chestnut [Haplic Kastanozems, Chromic], 9.7 ± 0.9 cm2·h-1. Aggregates of chernozem soil show a significantly higher thermal diffusivity compared to the bulk soil. Thermal diffusivities of aggregates of Chernozem for virgin and bare fallow samples differ, 53 ± 4 cm2·h-1 and 45 ± 4 cm2·h-1, respectively. Micromonoliths of different Sod-podzolic soil horizons within the same profile (topsoil, depth 10-14 cm, and a parent rock with Fe illuviation, depth 180-185 cm) also show a significant difference, thermal diffusivities are 9.5 ± 0.8 cm2·h-1 and 27 ± 2 cm2·h-1, respectively. For soil micromonoliths, BDS is capable to distinguish the difference in thermal diffusivity resulting from the changes in the structure of aggregates.

Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation

PubMed Central

2012-01-01

Background Fluorescence loss in photobleaching (FLIP) is a widely used imaging technique, which provides information about protein dynamics in various cellular regions. In FLIP, a small cellular region is repeatedly illuminated by an intense laser pulse, while images are taken with reduced laser power with a time lag between the bleaches. Despite its popularity, tools are lacking for quantitative analysis of FLIP experiments. Typically, the user defines regions of interest (ROIs) for further analysis which is subjective and does not allow for comparing different cells and experimental settings. Results We present two complementary methods to detect and quantify protein transport and aggregation in living cells from FLIP image series. In the first approach, a stretched exponential (StrExp) function is fitted to fluorescence loss (FL) inside and outside the bleached region. We show by reaction–diffusion simulations, that the StrExp function can describe both, binding/barrier–limited and diffusion-limited FL kinetics. By pixel-wise regression of that function to FL kinetics of enhanced green fluorescent protein (eGFP), we determined in a user-unbiased manner from which cellular regions eGFP can be replenished in the bleached area. Spatial variation in the parameters calculated from the StrExp function allow for detecting diffusion barriers for eGFP in the nucleus and cytoplasm of living cells. Polyglutamine (polyQ) disease proteins like mutant huntingtin (mtHtt) can form large aggregates called inclusion bodies (IB’s). The second method combines single particle tracking with multi-compartment modelling of FL kinetics in moving IB’s to determine exchange rates of eGFP-tagged mtHtt protein (eGFP-mtHtt) between aggregates and the cytoplasm. This method is self-calibrating since it relates the FL inside and outside the bleached regions. It makes it therefore possible to compare release kinetics of eGFP-mtHtt between different cells and experiments. Conclusions We present two complementary methods for quantitative analysis of FLIP experiments in living cells. They provide spatial maps of exchange dynamics and absolute binding parameters of fluorescent molecules to moving intracellular entities, respectively. Our methods should be of great value for quantitative studies of intracellular transport. PMID:23148417

Molecular dynamics simulations of the electrical double layer on smectite surfaces contacting concentrated mixed electrolyte (NaCl-CaCl2) solutions.

PubMed

Bourg, Ian C; Sposito, Garrison

2011-08-15

We report new molecular dynamics results elucidating the structure of the electrical double layer (EDL) on smectite surfaces contacting mixed NaCl-CaCl(2) electrolyte solutions in the range of concentrations relevant to pore waters in geologic repositories for CO(2) or high-level radioactive waste (0.34-1.83 mol(c) dm(-3)). Our results confirm the existence of three distinct ion adsorption planes (0-, β-, and d-planes), often assumed in EDL models, but with two important qualifications: (1) the location of the β- and d-planes are independent of ionic strength or ion type and (2) "indifferent electrolyte" ions can occupy all three planes. Charge inversion occurred in the diffuse ion swarm because of the affinity of the clay surface for CaCl(+) ion pairs. Therefore, at concentrations ≥0.34 mol(c) dm(-3), properties arising from long-range electrostatics at interfaces (electrophoresis, electro-osmosis, co-ion exclusion, colloidal aggregation) will not be correctly predicted by most EDL models. Co-ion exclusion, typically neglected by surface speciation models, balanced a large part of the clay mineral structural charge in the more concentrated solutions. Water molecules and ions diffused relatively rapidly even in the first statistical water monolayer, contradicting reports of rigid "ice-like" structures for water on clay mineral surfaces. Published by Elsevier Inc.

Development of Coarse Grained Models for Long Chain Alkanes

NASA Astrophysics Data System (ADS)

Gyawali, Gaurav; Sternfield, Samuel; Hwang, In Chul; Rick, Steven; Kumar, Revati; Rick Group Team; Kumar Group Team

Modeling aggregation in aqueous solution is a challenge for molecular simulations as it involves long time scales, a range of length scales, and the correct balance of hydrophobic and hydrophilic interactions. We have developed a coarse-grained model fast enough for the rapid testing of molecular structures for their aggregation properties. This model, using the Stillinger-Weber potential, achieves efficiency through a reduction in the number of interaction sites and the use of short-ranged interactions. The model can be two to three orders of magnitude more efficient than conventional all atom simulations, yet through a careful parameterization process and the use of many-body interactions can be remarkably accurate. We have developed models for long chain alkanes in water that reproduce the thermodynamics and structure of water-alkane and liquid alkane systems.

Mercury porosimetry for comparing piece-wise hydraulic properties with full range pore characteristics of soil aggregates and porous rocks

NASA Astrophysics Data System (ADS)

Turturro, Antonietta Celeste; Caputo, Maria C.; Gerke, Horst H.

2017-04-01

Unsaturated hydraulic properties are essential in the modeling of water and solute movement in the vadose zone. Since standard hydraulic techniques are limited to specific moisture ranges, maybe affected by air entrapment, wettability problems, limitations due to water vapor pressure, and are depending on the initial saturation, the continuous maximal drying curves of the complete hydraulic functions can mostly not reflect the basic pore size distribution. The aim of this work was to compare the water retention curves of soil aggregates and porous rocks with their porosity characteristics. Soil aggregates of Haplic Luvisols from Loess L (Hneveceves, Czech Republic) and glacial Till T (Holzendorf, Germany) and two lithotypes of porous rock C (Canosa) and M (Massafra), Italy, were analyzed using, suction table, evaporation, psychrometry methods, and the adopted Quasi-Steady Centrifuge method for determination of unsaturated hydraulic conductivity. These various water-based techniques were applied to determine the piece-wise retention and the unsaturated hydraulic conductivity functions in the range of pore water saturations. The pore-size distribution was determined with the mercury intrusion porosimetry (MIP). MIP results allowed assessing the volumetric mercury content at applied pressures up to 420000 kPa. Greater intrusion and porosity values were found for the porous rocks than for the soil aggregates. Except for the aggregate samples from glacial till, maximum liquid contents were always smaller than porosity. Multimodal porosities and retention curves were observed for both porous rocks and aggregate soils. Two pore-size peaks with pore diameters of 0.135 and 27.5 µm, 1.847 and 19.7 µm, and 0.75 and 232 µm were found for C, M and T, respectively, while three peaks of 0.005, 0.392 and 222 µm were identified for L. The MIP data allowed describing the retention curve in the entire mercury saturation range as compared to water retention curves that required combining several methods for limited suction ranges. Although the soil aggregates and porous rocks differed in pore geometries and pore size distributions, MIP provided additional information for characterizing the relation between pore structure and hydraulic properties for both.

Slow Lévy flights

NASA Astrophysics Data System (ADS)

Boyer, Denis; Pineda, Inti

2016-02-01

Among Markovian processes, the hallmark of Lévy flights is superdiffusion, or faster-than-Brownian dynamics. Here we show that Lévy laws, as well as Gaussian distributions, can also be the limit distributions of processes with long-range memory that exhibit very slow diffusion, logarithmic in time. These processes are path dependent and anomalous motion emerges from frequent relocations to already visited sites. We show how the central limit theorem is modified in this context, keeping the usual distinction between analytic and nonanalytic characteristic functions. A fluctuation-dissipation relation is also derived. Our results may have important applications in the study of animal and human displacements.

Are Long-Range Structural Correlations Behind the Aggregration Phenomena of Polyglutamine Diseases?

PubMed Central

Moradi, Mahmoud; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

2012-01-01

We have characterized the conformational ensembles of polyglutamine peptides of various lengths (ranging from to ), both with and without the presence of a C-terminal polyproline hexapeptide. For this, we used state-of-the-art molecular dynamics simulations combined with a novel statistical analysis to characterize the various properties of the backbone dihedral angles and secondary structural motifs of the glutamine residues. For (i.e., just above the pathological length for Huntington's disease), the equilibrium conformations of the monomer consist primarily of disordered, compact structures with non-negligible -helical and turn content. We also observed a relatively small population of extended structures suitable for forming aggregates including - and -strands, and - and -hairpins. Most importantly, for we find that there exists a long-range correlation (ranging for at least residues) among the backbone dihedral angles of the Q residues. For polyglutamine peptides below the pathological length, the population of the extended strands and hairpins is considerably smaller, and the correlations are short-range (at most residues apart). Adding a C-terminal hexaproline to suppresses both the population of these rare motifs and the long-range correlation of the dihedral angles. We argue that the long-range correlation of the polyglutamine homopeptide, along with the presence of these rare motifs, could be responsible for its aggregation phenomena. PMID:22577357

Enhancing energy transport in conjugated polymers

NASA Astrophysics Data System (ADS)

Holmes, Russell J.

2018-05-01

The conversion of light into usable chemical energy by plants is enabled by the precise spatial arrangement of light-absorbing photosynthetic systems and associated molecular complexes (1). In organic solar cells, there is also the need to control intermolecular spacing and molecular orientation, as well as thin-film crystallinity and morphology, so as to enable efficient energy migration and photoconversion (2). In an organic solar cell, light absorption creates excitons, tightly bound electron-hole pairs that must be efficiently dissociated into their component charge carriers in order to create an electrical current. Thus, long-range exciton migration must occur from the point of photogeneration to a dissociating site. On page 897 of this issue, Jin et al. (3) report on a conjugated polymer nanofiber system that yields exciton diffusion lengths greater than 200 nm. In comparison, organic solar cells are typically constructed with materials having exciton diffusion lengths one order of magnitude smaller than this value, which limits device thickness and optical absorption. Their approach exploits a sequential synthesis method that enables measurement of this long exciton diffusion length (see the figure).

Reaction limited aggregation in surfactant-mediated epitaxy

NASA Astrophysics Data System (ADS)

Wu, Jing; Liu, Bang-Gui; Zhang, Zhenyu; Wang, E. G.

2000-05-01

A theoretical model for reaction limited aggregation (RLA) is introduced to study the effect of a monolayer of surfactant on the formation of two-dimensional islands in heteroepitaxial and homoepitaxial growth. In this model the basic atomic processes are considered as follows. A stable island consists of the adatoms that have exchanged positions with the surfactant atoms beneath them. Movable active adatoms may (a) diffuse on the surfactant terrace, (b) exchange positions with the surfactant atoms beneath them and become island seeds (seed exchange), or (c) stick to stable islands and become stuck but still active adatoms. The rate-limiting step for the formation of a stable island is the seed exchange. Furthermore, a stuck but still active adatom must overcome a sizable potential-energy barrier to exchange positions with the surfactant atom beneath it and become a member of the stable island (aided exchange). The seed exchange process can occur with an adatom or collectively with an addimer. In the case of dimer exchange, the diffusing adatoms on the surfactant terrace can meet and (after exchanging) form stable dimers, which can then become island seeds. Systematic kinetic Monte Carlo simulations and rate-equation analysis of the model are carried out. The key finding of these simulations is that a counterintuitive fractal-to-compact island shape transition can be induced either by increasing deposition flux or by decreasing growth temperature. This major qualitative conclusion is valid for both the monomer and the dimer seed exchanges and for two different substrate lattices (square and triangular, respectively), although there are some quantitative differences in the flux and temperature dependence of the island density. The shape transition observed is contrary to the prediction of the classic diffusion-limited aggregation (DLA) theory, but in excellent qualitative agreement with recent experiments. In rationalizing the main finding, it is crucial to realize that the adatoms stuck to a stable island edge are still active and are surrounded by the surfactant atoms. Therefore, these stuck atoms cannot capture incoming adatoms before they join the island through aided exchange. As a result, an incoming adatom must on average hit the island many times before it finally finds a free edge site to stick to. This search is effectively equivalent to edge diffusion in DLA theory. The stuck adatoms thus act as shields which prevent other mobile adatoms from sticking to the stable islands. This shielding effect, determined by the aided exchange barrier and the density of the mobile adatoms, plays an essential role in inducing the above shape transition in surfactant-mediated epitaxial growth.

Effects of C/O Ratio and Temperature on Sooting Limits of Spherical Diffusion Flames

NASA Technical Reports Server (NTRS)

Lecoustre, V. R.; Sunderland, P. B.; Chao, B. H.; Urban, D. L.; Stocker, D. P.; Axelbaum, R. L.

2008-01-01

Limiting conditions for soot particle inception in spherical diffusion flames were investigated numerically. The flames were modeled using a one-dimensional, time accurate diffusion flame code with detailed chemistry and transport and an optically thick radiation model. Seventeen normal and inverse flames were considered, covering a wide range of stoichiometric mixture fraction, adiabatic flame temperature, residence time and scalar dissipation rate. These flames were previously observed to reach their sooting limits after 2 s of microgravity. Sooting-limit diffusion flames with scalar dissipation rate lower than 2/s were found to have temperatures near 1400 K where C/O = 0.51, whereas flames with greater scalar dissipation rate required increased temperatures. This finding was valid across a broad range of fuel and oxidizer compositions and convection directions.

Pepsin diffusion in dairy gels depends on casein concentration and microstructure.

PubMed

Thévenot, J; Cauty, C; Legland, D; Dupont, D; Floury, J

2017-05-15

Fundamental knowledge of gastric digestion had only focused on acid diffusion from the gastric fluid, but no data are available for pepsin diffusion. Using fluorescence recovery after photobleaching technique, diffusion coefficients D of fluorescein isothiocyanate (FITC)-pepsin were measured in rennet gels across a range of casein concentrations allowing to form networks of protein aggregates with different structures. To investigate the microstructural parameters of native gels, electron microscopy image analysis were performed and qualitatively related to diffusion behavior of FITC-pepsin in these dairy gels. This study is the first report on quantification of pepsin diffusion in dairy product. Pepsin diffusion in rennet gels depends on casein concentration and microstructure. Models of polymer science can be used to assess D in dairy gel. Such data should be confronted with pepsin activity in acidic environment, and will be very useful as input parameters in mathematical models of food degradation in the human stomach. Copyright © 2016 Elsevier Ltd. All rights reserved.

Spatial Modeling of Iron Transformations Within Artificial Soil Aggregates

NASA Astrophysics Data System (ADS)

Kausch, M.; Meile, C.; Pallud, C.

2008-12-01

Structured soils exhibit significant variations in transport characteristics at the aggregate scale. Preferential flow occurs through macropores while predominantly diffusive exchange takes place in intra-aggregate micropores. Such environments characterized by mass transfer limitations are conducive to the formation of small-scale chemical gradients and promote strong spatial variation in processes controlling the fate of redox-sensitive elements such as Fe. In this study, we present a reactive transport model used to spatially resolve iron bioreductive processes occurring within a spherical aggregate at the interface between advective and diffusive domains. The model is derived from current conceptual models of iron(hydr)oxide (HFO) transformations and constrained by literature and experimental data. Data were obtained from flow-through experiments on artificial soil aggregates inoculated with Shewanella putrefaciens strain CN32, and include the temporal evolution of the bulk solution composition, as well as spatial information on the final solid phase distribution within aggregates. With all iron initially in the form of ferrihydrite, spatially heterogeneous formation of goethite/lepidocrocite, magnetite and siderite was observed during the course of the experiments. These transformations were reproduced by the model, which ascribes a central role to divalent iron as a driver of HFO transformations and master variable in the rate laws of the considered reaction network. The predicted dissolved iron breakthrough curves also match the experimental ones closely. Thus, the computed chemical concentration fields help identify factors governing the observed trends in the solid phase distribution patterns inside the aggregate. Building on a mechanistic description of transformation reactions, fluid flow and solute transport, the model was able to describe the observations and hence illustrates the importance of small-scale gradients and dynamics of bioreductive processes for assessing bulk iron cycling. As HFOs are ubiquitous in soils, such process-level understanding of aggregate-scale iron dynamics has broad implications for the prediction of the subsurface fate of nutrients and contaminants that interact strongly with HFO surfaces.

Dynamics of proteins aggregation. I. Universal scaling in unbounded media

NASA Astrophysics Data System (ADS)

Zheng, Size; Javidpour, Leili; Shing, Katherine S.; Sahimi, Muhammad

2016-10-01

It is well understood that in some cases proteins do not fold correctly and, depending on their environment, even properly-folded proteins change their conformation spontaneously, taking on a misfolded state that leads to protein aggregation and formation of large aggregates. An important factor that contributes to the aggregation is the interactions between the misfolded proteins. Depending on the aggregation environment, the aggregates may take on various shapes forming larger structures, such as protein plaques that are often toxic. Their deposition in tissues is a major contributing factor to many neuro-degenerative diseases, such as Alzheimer's, Parkinson's, amyotrophic lateral sclerosis, and prion. This paper represents the first part in a series devoted to molecular simulation of protein aggregation. We use the PRIME, a meso-scale model of proteins, together with extensive discontinuous molecular dynamics simulation to study the aggregation process in an unbounded fluid system, as the first step toward MD simulation of the same phenomenon in crowded cellular environments. Various properties of the aggregates have been computed, including dynamic evolution of aggregate-size distribution, mean aggregate size, number of peptides that contribute to the formation of β sheets, number of various types of hydrogen bonds formed in the system, radius of gyration of the aggregates, and the aggregates' diffusivity. We show that many of such quantities follow dynamic scaling, similar to those for aggregation of colloidal clusters. In particular, at long times the mean aggregate size S(t) grows with time as, S(t) ˜ tz, where z is the dynamic exponent. To our knowledge, this is the first time that the qualitative similarity between aggregation of proteins and colloidal aggregates has been pointed out.

Anomalous diffusion with linear reaction dynamics: from continuous time random walks to fractional reaction-diffusion equations.

PubMed

Henry, B I; Langlands, T A M; Wearne, S L

2006-09-01

We have revisited the problem of anomalously diffusing species, modeled at the mesoscopic level using continuous time random walks, to include linear reaction dynamics. If a constant proportion of walkers are added or removed instantaneously at the start of each step then the long time asymptotic limit yields a fractional reaction-diffusion equation with a fractional order temporal derivative operating on both the standard diffusion term and a linear reaction kinetics term. If the walkers are added or removed at a constant per capita rate during the waiting time between steps then the long time asymptotic limit has a standard linear reaction kinetics term but a fractional order temporal derivative operating on a nonstandard diffusion term. Results from the above two models are compared with a phenomenological model with standard linear reaction kinetics and a fractional order temporal derivative operating on a standard diffusion term. We have also developed further extensions of the CTRW model to include more general reaction dynamics.

Long-range hot-carrier transport in hybrid perovskites visualized by ultrafast microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Zhi; Wan, Yan; Yang, Mengjin

The Shockley-Queisser limit for solar cell efficiency can be overcome if hot carriers can be harvested before they thermalize. Recently, carrier cooling time up to 100 picoseconds was observed in hybrid perovskites, but it is unclear whether these long-lived hot carriers can migrate long distance for efficient collection. Here, we report direct visualization of hot-carrier migration in methylammonium lead iodide (CH 3NH 3PbI 3) thin films by ultrafast transient absorption microscopy, demonstrating three distinct transport regimes. Quasiballistic transport was observed to correlate with excess kinetic energy, resulting in up to 230 nanometers transport distance that could overcome grain boundaries. Themore » nonequilibrium transport persisted over tens of picoseconds and ~600 nanometers before reaching the diffusive transport limit. Lastly, these results suggest potential applications of hot-carrier devices based on hybrid perovskites.« less

Long-range hot-carrier transport in hybrid perovskites visualized by ultrafast microscopy

DOE PAGES

Guo, Zhi; Wan, Yan; Yang, Mengjin; ...

2017-04-07

The Shockley-Queisser limit for solar cell efficiency can be overcome if hot carriers can be harvested before they thermalize. Recently, carrier cooling time up to 100 picoseconds was observed in hybrid perovskites, but it is unclear whether these long-lived hot carriers can migrate long distance for efficient collection. Here, we report direct visualization of hot-carrier migration in methylammonium lead iodide (CH 3NH 3PbI 3) thin films by ultrafast transient absorption microscopy, demonstrating three distinct transport regimes. Quasiballistic transport was observed to correlate with excess kinetic energy, resulting in up to 230 nanometers transport distance that could overcome grain boundaries. Themore » nonequilibrium transport persisted over tens of picoseconds and ~600 nanometers before reaching the diffusive transport limit. Lastly, these results suggest potential applications of hot-carrier devices based on hybrid perovskites.« less

Relative distance between tracers as a measure of diffusivity within moving aggregates

NASA Astrophysics Data System (ADS)

Pönisch, Wolfram; Zaburdaev, Vasily

2018-02-01

Tracking of particles, be it a passive tracer or an actively moving bacterium in the growing bacterial colony, is a powerful technique to probe the physical properties of the environment of the particles. One of the most common measures of particle motion driven by fluctuations and random forces is its diffusivity, which is routinely obtained by measuring the mean squared displacement of the particles. However, often the tracer particles may be moving in a domain or an aggregate which itself experiences some regular or random motion and thus masks the diffusivity of tracers. Here we provide a method for assessing the diffusivity of tracer particles within mobile aggregates by measuring the so-called mean squared relative distance (MSRD) between two tracers. We provide analytical expressions for both the ensemble and time averaged MSRD allowing for direct identification of diffusivities from experimental data.

Refractive indices at visible wavelengths of soot emitted from buoyant turbulent diffusion flames

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, J.S.; Krishnan, S.K.; Faeth, G.M.

1996-11-01

Measurements of the optical properties of soot, emphasizing refractive indices, are reported for visible wavelengths. The experiments considered soot in the fuel-lean (overfire) region of buoyant turbulent diffusion flames in the long residence time regime where soot properties are independent of position in the overfire region and residence time. Flames fueled with acetylene, propylene, ethylene and propane burning in still air provided a range of soot physical and structure properties. Measurements included soot composition, density, structure, gravimetric volume fraction, scattering properties and absorption properties. These data were analyzed to find soot fractal dimensions, refractive indices and dimensionless extinction coefficients, assumingmore » Rayleigh-Debye-Gans scattering for polydisperse mass fractal aggregates (RDG-PFA theory). RDG-PFA theory was successfully evaluated, based on measured scattering patterns. Soot fractal dimensions were independent of both fuel type and wavelength, yielding a mean value of 1.77 with a standard deviation of 0.04. Refractive indices were independent of fuel type within experimental uncertainties and were in reasonably good agreement with earlier measurements for soot in the fuel-lean region of diffusion flames due to Dalzell and Sarofim (1969). Dimensionless extinction coefficients were independent of both fuel type and wavelength, yielding a mean value of 5.1 with a standard deviation of 0.5, which is lower than earlier measurements for reasons that still must be explained.« less

Diffusion limit of Lévy-Lorentz gas is Brownian motion

NASA Astrophysics Data System (ADS)

Magdziarz, Marcin; Szczotka, Wladyslaw

2018-07-01

In this paper we analyze asymptotic behaviour of a stochastic process called Lévy-Lorentz gas. This process is aspecial kind of continuous-time random walk in which walker moves in the fixed environment composed of scattering points. Upon each collision the walker performs a flight to the nearest scattering point. This type of dynamics is observed in Lévy glasses or long quenched polymers. We show that the diffusion limit of Lévy-Lorentz gas with finite mean distance between scattering centers is the standard Brownian motion. Thus, for long times the behaviour of the Lévy-Lorentz gas is close to the diffusive regime.

Tempered fractional calculus

NASA Astrophysics Data System (ADS)

Sabzikar, Farzad; Meerschaert, Mark M.; Chen, Jinghua

2015-07-01

Fractional derivatives and integrals are convolutions with a power law. Multiplying by an exponential factor leads to tempered fractional derivatives and integrals. Tempered fractional diffusion equations, where the usual second derivative in space is replaced by a tempered fractional derivative, govern the limits of random walk models with an exponentially tempered power law jump distribution. The limiting tempered stable probability densities exhibit semi-heavy tails, which are commonly observed in finance. Tempered power law waiting times lead to tempered fractional time derivatives, which have proven useful in geophysics. The tempered fractional derivative or integral of a Brownian motion, called a tempered fractional Brownian motion, can exhibit semi-long range dependence. The increments of this process, called tempered fractional Gaussian noise, provide a useful new stochastic model for wind speed data. A tempered fractional difference forms the basis for numerical methods to solve tempered fractional diffusion equations, and it also provides a useful new correlation model in time series.

TEMPERED FRACTIONAL CALCULUS.

PubMed

Meerschaert, Mark M; Sabzikar, Farzad; Chen, Jinghua

2015-07-15

Fractional derivatives and integrals are convolutions with a power law. Multiplying by an exponential factor leads to tempered fractional derivatives and integrals. Tempered fractional diffusion equations, where the usual second derivative in space is replaced by a tempered fractional derivative, govern the limits of random walk models with an exponentially tempered power law jump distribution. The limiting tempered stable probability densities exhibit semi-heavy tails, which are commonly observed in finance. Tempered power law waiting times lead to tempered fractional time derivatives, which have proven useful in geophysics. The tempered fractional derivative or integral of a Brownian motion, called a tempered fractional Brownian motion, can exhibit semi-long range dependence. The increments of this process, called tempered fractional Gaussian noise, provide a useful new stochastic model for wind speed data. A tempered difference forms the basis for numerical methods to solve tempered fractional diffusion equations, and it also provides a useful new correlation model in time series.

TEMPERED FRACTIONAL CALCULUS

PubMed Central

MEERSCHAERT, MARK M.; SABZIKAR, FARZAD; CHEN, JINGHUA

2014-01-01

Fractional derivatives and integrals are convolutions with a power law. Multiplying by an exponential factor leads to tempered fractional derivatives and integrals. Tempered fractional diffusion equations, where the usual second derivative in space is replaced by a tempered fractional derivative, govern the limits of random walk models with an exponentially tempered power law jump distribution. The limiting tempered stable probability densities exhibit semi-heavy tails, which are commonly observed in finance. Tempered power law waiting times lead to tempered fractional time derivatives, which have proven useful in geophysics. The tempered fractional derivative or integral of a Brownian motion, called a tempered fractional Brownian motion, can exhibit semi-long range dependence. The increments of this process, called tempered fractional Gaussian noise, provide a useful new stochastic model for wind speed data. A tempered difference forms the basis for numerical methods to solve tempered fractional diffusion equations, and it also provides a useful new correlation model in time series. PMID:26085690

Tempered fractional calculus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sabzikar, Farzad, E-mail: sabzika2@stt.msu.edu; Meerschaert, Mark M., E-mail: mcubed@stt.msu.edu; Chen, Jinghua, E-mail: cjhdzdz@163.com

2015-07-15

Fractional derivatives and integrals are convolutions with a power law. Multiplying by an exponential factor leads to tempered fractional derivatives and integrals. Tempered fractional diffusion equations, where the usual second derivative in space is replaced by a tempered fractional derivative, govern the limits of random walk models with an exponentially tempered power law jump distribution. The limiting tempered stable probability densities exhibit semi-heavy tails, which are commonly observed in finance. Tempered power law waiting times lead to tempered fractional time derivatives, which have proven useful in geophysics. The tempered fractional derivative or integral of a Brownian motion, called a temperedmore » fractional Brownian motion, can exhibit semi-long range dependence. The increments of this process, called tempered fractional Gaussian noise, provide a useful new stochastic model for wind speed data. A tempered fractional difference forms the basis for numerical methods to solve tempered fractional diffusion equations, and it also provides a useful new correlation model in time series.« less

Simulation of Bacillus subtilis biofilm growth on agar plate by diffusion-reaction based continuum model

NASA Astrophysics Data System (ADS)

Zhang, Xianlong; Wang, Xiaoling; Nie, Kai; Li, Mingpeng; Sun, Qingping

2016-08-01

Various species of bacteria form highly organized spatially-structured aggregates known as biofilms. To understand how microenvironments impact biofilm growth dynamics, we propose a diffusion-reaction continuum model to simulate the formation of Bacillus subtilis biofilm on an agar plate. The extended finite element method combined with level set method are employed to perform the simulation, numerical results show the quantitative relationship between colony morphologies and nutrient depletion over time. Considering that the production of polysaccharide in wild-type cells may enhance biofilm spreading on the agar plate, we inoculate mutant colony incapable of producing polysaccharide to verify our results. Predictions of the glutamate source biofilm’s shape parameters agree with the experimental mutant colony better than that of glycerol source biofilm, suggesting that glutamate is rate limiting nutrient for Bacillus subtilis biofilm growth on agar plate, and the diffusion-limited is a better description to the experiment. In addition, we find that the diffusion time scale is of the same magnitude as growth process, and the common-employed quasi-steady approximation is not applicable here.

Simulation of Bacillus subtilis biofilm growth on agar plate by diffusion-reaction based continuum model.

PubMed

Zhang, Xianlong; Wang, Xiaoling; Nie, Kai; Li, Mingpeng; Sun, Qingping

2016-07-19

Various species of bacteria form highly organized spatially-structured aggregates known as biofilms. To understand how microenvironments impact biofilm growth dynamics, we propose a diffusion-reaction continuum model to simulate the formation of Bacillus subtilis biofilm on an agar plate. The extended finite element method combined with level set method are employed to perform the simulation, numerical results show the quantitative relationship between colony morphologies and nutrient depletion over time. Considering that the production of polysaccharide in wild-type cells may enhance biofilm spreading on the agar plate, we inoculate mutant colony incapable of producing polysaccharide to verify our results. Predictions of the glutamate source biofilm's shape parameters agree with the experimental mutant colony better than that of glycerol source biofilm, suggesting that glutamate is rate limiting nutrient for Bacillus subtilis biofilm growth on agar plate, and the diffusion-limited is a better description to the experiment. In addition, we find that the diffusion time scale is of the same magnitude as growth process, and the common-employed quasi-steady approximation is not applicable here.

Computer Simulation of Fracture in Aerogels

NASA Technical Reports Server (NTRS)

Good, Brian S.

2006-01-01

Aerogels are of interest to the aerospace community primarily for their thermal properties, notably their low thermal conductivities. While the gels are typically fragile, recent advances in the application of conformal polymer layers to these gels has made them potentially useful as lightweight structural materials as well. In this work, we investigate the strength and fracture behavior of silica aerogels using a molecular statics-based computer simulation technique. The gels' structure is simulated via a Diffusion Limited Cluster Aggregation (DLCA) algorithm, which produces fractal structures representing experimentally observed aggregates of so-called secondary particles, themselves composed of amorphous silica primary particles an order of magnitude smaller. We have performed multi-length-scale simulations of fracture in silica aerogels, in which the interaction b e e n two secondary particles is assumed to be described by a Morse pair potential parameterized such that the potential range is much smaller than the secondary particle size. These Morse parameters are obtained by atomistic simulation of models of the experimentally-observed amorphous silica "bridges," with the fracture behavior of these bridges modeled via molecular statics using a Morse/Coulomb potential for silica. We consider the energetics of the fracture, and compare qualitative features of low-and high-density gel fracture.

Hot particles attract in a cold bath

NASA Astrophysics Data System (ADS)

Tanaka, Hidenori; Lee, Alpha A.; Brenner, Michael P.

2017-04-01

Controlling interactions out of thermodynamic equilibrium is crucial for designing addressable and functional self-organizing structures. These active interactions also underpin collective behavior in biological systems. Here we study a general setting of active particles in a bath of passive particles and demonstrate a mechanism for long-range attraction between active particles. The mechanism operates when the translational persistence length of the active particle motion is smaller than the particle diameter. In this limit, the system reduces to particles of higher diffusivity ("hot" particles) in a bath of particles with lower diffusivity ("cold" particles). This attractive interaction arises as a hot particle pushes cold particles away to create a large hole around itself, and the holes interact via a depletion-like attraction. Strikingly, the interaction range is more than an order of magnitude larger than the particle radius, well beyond the range of the conventional depletion force. Although the mechanism occurs outside the parameter regime of typical biological swimmers, the mechanism could be realized in the laboratory.

Mechanobiological induction of long-range contractility by diffusing biomolecules and size scaling in cell assemblies

NASA Astrophysics Data System (ADS)

Dasbiswas, K.; Alster, E.; Safran, S. A.

2016-06-01

Mechanobiological studies of cell assemblies have generally focused on cells that are, in principle, identical. Here we predict theoretically the effect on cells in culture of locally introduced biochemical signals that diffuse and locally induce cytoskeletal contractility which is initially small. In steady-state, both the concentration profile of the signaling molecule as well as the contractility profile of the cell assembly are inhomogeneous, with a characteristic length that can be of the order of the system size. The long-range nature of this state originates in the elastic interactions of contractile cells (similar to long-range “macroscopic modes” in non-living elastic inclusions) and the non-linear diffusion of the signaling molecules, here termed mechanogens. We suggest model experiments on cell assemblies on substrates that can test the theory as a prelude to its applicability in embryo development where spatial gradients of morphogens initiate cellular development.

New sensitive micro-measurements of dynamic surface tension and diffusion coefficients: Validated and tested for the adsorption of 1-Octanol at a microscopic air-water interface and its dissolution into water.

PubMed

Kinoshita, Koji; Parra, Elisa; Needham, David

2017-02-15

Currently available dynamic surface tension (DST) measurement methods, such as Wilhelmy plate, droplet- or bubble-based methods, still have various experimental limitations such as the large size of the interface, convection in the solution, or a certain "dead time" at initial measurement. These limitations create inconsistencies for the kinetic analysis of surfactant adsorption/desorption, especially significant for ionic surfactants. Here, the "micropipette interfacial area-expansion method" was introduced and validated as a new DST measurement having a high enough sensitivity to detect diffusion controlled molecular adsorption at the air-water interfaces. To validate the new technique, the diffusion coefficient of 1-Octanol in water was investigated with existing models: the Ward Tordai model for the long time adsorption regime (1-100s), and the Langmuir and Frumkin adsorption isotherm models for surface excess concentration. We found that the measured diffusion coefficient of 1-Octanol, 7.2±0.8×10 -6 cm 2 /s, showed excellent agreement with the result from an alternative method, "single microdroplet catching method", to measure the diffusion coefficient from diffusion-controlled microdroplet dissolution, 7.3±0.1×10 -6 cm 2 /s. These new techniques for determining adsorption and diffusion coefficients can apply for a range of surface active molecules, especially the less-characterized ionic surfactants, and biological compounds such as lipids, peptides, and proteins. Copyright © 2016 Elsevier Inc. All rights reserved.

Fractal patterns formed by growth of radial viscous fingers*

NASA Astrophysics Data System (ADS)

Praud, Olivier

2004-03-01

We examine fractal patterns formed by the injection of air into oil in a thin (0.13 mm) layer contained between two cylindrical glass plates of 288 mm diameter (a Hele-Shaw cell) [1]. The resultant radially grown patterns are similar to those formed in Diffusion Limited Aggregation (DLA), but the relation between the continuum limit of DLA and continuum (Laplacian) growth remains an open question. Our viscous fingering patterns in the limit of very high pressure difference reach an asymptotic state in which they exhibit a fractal dimension of 1.70± 0.02, in good agreement with a calculation of the fractal dimension of a DLA cluster, 1.713± 0.003 [2]. The generalized dimensions are also computed and show that the observed pattern is self-similar with Dq = 1.70 for all q. Further, the probability density function of shielding angles suggests the existence of a critical angle close to 75 degrees. This result is in accord with numerical and analytical evidence of a critical angle in DLA [3]. Thus fractal viscous fingering patterns and Diffusion Limited Aggregation clusters have a similar geometrical structure. *Work conducted in collaboration with H.L. Swinney, M.G. Moore and Eran Sharon [1] E. Sharon, M. G. Moore, W. D. McCormick, and H. L. Swinney, Phys. Rev. Lett. 91, 205504 (2003). [2] B.Davidovitch et A. Levermann and I. Procaccia, Phys. Rev. E 62, 5919 (2000). [3] D. A. Kessler et al., Phys. Rev. E 57, 6913 (1998).

Utilisation of steel furnace slag coarse aggregate in a low calcium fly ash geopolymer concrete

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khan, M. S.H.,; Castel, Arnaud; Akbarnezhad, A.

This paper evaluates the performance of steel furnace slag (SFS) coarse aggregate in blended slag and low calcium fly ash geopolymer concrete (GPC). The geopolymer binder is composed of 90% of low calcium fly ash and 10% of ground granulated blast furnace slag (GGBFS). Mechanical and physical properties, shrinkage, and detailed microstructure analysis were carried out. The results showed that geopolymer concrete with SFS aggregate offered higher compressive strength, surface resistivity and pulse velocity than that of GPC with traditional aggregate. The shrinkage results showed no expansion or swelling due to delayed calcium oxide (CaO) hydration after 320 days. Nomore » traditional porous interfacial transition zone (ITZ) was detected using scanning electron microscopy, indicating a better bond between SFS aggregate and geopolymer matrix. Energy dispersive spectroscopy results further revealed calcium (Ca) diffusion at the vicinity of ITZ. Raman spectroscopy results showed no new crystalline phase formed due to Ca diffusion. X-ray fluorescence result showed Mg diffusion from SFS aggregate towards geopolymer matrix. The incorporation of Ca and Mg into the geopolymer structure and better bond between SFS aggregate and geopolymer matrix are the most likely reasons for the higher compressive strength observed in GPC with SFS aggregate.« less

Influence of cell shape, inhomogeneities and diffusion barriers in cell polarization models

NASA Astrophysics Data System (ADS)

Giese, Wolfgang; Eigel, Martin; Westerheide, Sebastian; Engwer, Christian; Klipp, Edda

2015-12-01

In silico experiments bear the potential for further understanding of biological transport processes by allowing a systematic modification of any spatial property and providing immediate simulation results. Cell polarization and spatial reorganization of membrane proteins are fundamental for cell division, chemotaxis and morphogenesis. We chose the yeast Saccharomyces cerevisiae as an exemplary model system which entails the shuttling of small Rho GTPases such as Cdc42 and Rho, between an active membrane-bound form and an inactive cytosolic form. We used partial differential equations to describe the membrane-cytosol shuttling of proteins. In this study, a consistent extension of a class of 1D reaction-diffusion systems into higher space dimensions is suggested. The membrane is modeled as a thin layer to allow for lateral diffusion and the cytosol is modeled as an enclosed volume. Two well-known polarization mechanisms were considered. One shows the classical Turing-instability patterns, the other exhibits wave-pinning dynamics. For both models, we investigated how cell shape and diffusion barriers like septin structures or bud scars influence the formation of signaling molecule clusters and subsequent polarization. An extensive set of in silico experiments with different modeling hypotheses illustrated the dependence of cell polarization models on local membrane curvature, cell size and inhomogeneities on the membrane and in the cytosol. In particular, the results of our computer simulations suggested that for both mechanisms, local diffusion barriers on the membrane facilitate Rho GTPase aggregation, while diffusion barriers in the cytosol and cell protrusions limit spontaneous molecule aggregations of active Rho GTPase locally.

Aggregation Kinetics of Diesel Soot Nanoparticles in Wet Environments.

PubMed

Chen, Chengyu; Huang, Weilin

2017-02-21

Soot produced during incomplete combustion consists mainly of carbonaceous nanoparticles (NPs) with severe adverse environmental and health effects, and its environmental fate and transport are largely controlled by aggregation. In this study, we examined the aggregation behavior for diesel soot NPs under aqueous condition in an effort to elucidate the fundamental processes that govern soot particle-particle interactions in wet environments such as rain droplets or surface aquatic systems. The influence of electrolytes and aqueous pH on colloidal stability of these NPs was investigated by measuring their aggregation kinetics in different aqueous solution chemistries. The results showed that the NPs had negatively charged surfaces and exhibited both reaction- and diffusion-limited aggregation regimes with rates depended upon solution chemistry. The aggregation kinetics data were in good agreement with the classic Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. The critical coagulation concentrations (CCC) were quantified and the Hamaker constant was derived for the soot (1.4 × 10 -20 J) using the colloidal chemistry approach. The study indicated that, depending upon local aqueous chemistry, single soot NPs could remain stable against self-aggregation in typical freshwater environments and in neutral cloud droplets but are likely to aggregate under salty (e.g., estuaries) or acidic (e.g., acid rain droplets) aquatic conditions or both.

Numerical insights into the early stages of nanoscale electrodeposition: nanocluster surface diffusion and aggregative growth.

PubMed

Mamme, Mesfin Haile; Köhn, Christoph; Deconinck, Johan; Ustarroz, Jon

2018-04-19

Fundamental understanding of the early stages of electrodeposition at the nanoscale is key to address the challenges in a wide range of applications. Despite having been studied for decades, a comprehensive understanding of the whole process is still out of reach. In this work, we introduce a novel modelling approach that couples a finite element method (FEM) with a random walk algorithm, to study the early stages of nanocluster formation, aggregation and growth, during electrochemical deposition. This approach takes into account not only electrochemical kinetics and transport of active species, but also the surface diffusion and aggregation of adatoms and small nanoclusters. The simulation results reveal that the relative surface mobility of the nanoclusters compared to that of the adatoms plays a crucial role in the early growth stages. The number of clusters, their size and their size dispersion are influenced more significantly by nanocluster mobility than by the applied overpotential itself. Increasing the overpotential results in shorter induction times and leads to aggregation prevalence at shorter times. A higher mobility results in longer induction times, a delayed transition from nucleation to aggregation prevalence, and as a consequence, a larger surface coverage of smaller clusters with a smaller size dispersion. As a consequence, it is shown that a classical first-order nucleation kinetics equation cannot describe the evolution of the number of clusters with time, N(t), in potentiostatic electrodeposition. Instead, a more accurate representation of N(t) is provided. We show that an evaluation of N(t), which neglects the effect of nanocluster mobility and aggregation, can induce errors of several orders of magnitude in the determination of nucleation rate constants. These findings are extremely important towards evaluating the elementary electrodeposition processes, considering not only adatoms, but also nanoclusters as building blocks.

Single-Grain (U-Th)/He Ages of Phosphates from St. Severin Chondrite

NASA Astrophysics Data System (ADS)

Min, K. K.; Reiners, P. W.; Shuster, D. L.

2010-12-01

Thermal evolution of chondrites provides valuable information on the heat budget, internal structure and dimensions of their parent bodies once existed before disruption. St. Severin LL6 ordinary chondrite is known to have experienced relatively slow cooling compared to H chondrites. The timings of primary cooling and subsequent thermal metamorphism were constrained by U/Pb (4.55 Ga), Sm/Nd (4.55 Ga), Rb/Sr (4.51 Ga) and K/Ar (4.4 Ga) systems. However, cooling history after the thermal metamorphism in a low temperature range (<200 °C) is poorly understood. In order to constrain the low-T thermal history of this meteorite, we performed (1) single-grain (U-Th)/He dating for five chlorapatite and fourteen merrillite aggregates from St. Severin, (2) examination of textural and chemical features of the phosphate aggregates using a scanning electron microscope (SEM), and (3) proton-irradiation followed by 4He and 3He diffusion experiments for single grains of chlorapatite and merrillite from Guarena meteorite, for general characterization of He diffusivity in these major U-Th reservoirs in meteorites. The α-recoil-uncorrected ages from St. Severin are distributed in a wide range of 333 ± 6 Ma and 4620 ± 1307 Ma. The probability density plot of these data shows a typical younging-skewed age distribution with a prominent peak at ~ 4.3 Ga. The weighted mean of the nine oldest samples is 4.284 ± 0.130 Ga, which is consistent with the peak of the probability plot. The linear dimensions of the phosphates are generally in the range of ~50 µm to 200 µm. The α recoil correction factor (FT) based on the morphology of the phosphate yields improbably old ages (>4.6 Ga), suggesting that within the sample aggregates, significant amounts of the α particles ejected from phosphates were implanted into the adjacent phases and therefore that this correction may not be appropriate in this case. The minimum FT value of 0.95 is calculated based on the peak (U-Th)/He age and 40Ar/39Ar data which provide the upper limit of the α-recoil-corrected (U-Th)/He ages. From these data, we conclude that the St. Severin cooled through the closure temperatures of chlorapatite and merrillite during ~4.3 - 4.4 Ga. The radiogenic 4He and proton-induced 3He diffusion experiments yield two well-defined linear trends in Arrhenius plot for chlorapatite (r = 43 µm) and merrillite (r = 59 µm) grains. The linear regression of 3He data for chlorapatite yields Ea = 128.1 ± 2.4 kJ/mol, and ln(Do/a2) = 11.6 ± 0.5 ln(s-1) which are generally consistent with the terrestrial Durango apatite and meteoritic Acapulco apatite. Linear regression to the merrillite data corresponds to Ea = 135.1 ± 2.5 kJ/mol, and ln(Do/a2) = 5.73 ± 0.37 ln(s-1). The new data indicate that diffusive retentivity of He within merrillite is significantly higher than that of chlorapatite, which has implications for quantitative interpretation of He ages measured in meteoritic phosphates.

Hydrodynamic effects and receptor interactions of platelets and their aggregates in linear shear flow.

PubMed Central

Tandon, P; Diamond, S L

1997-01-01

We have modeled platelet aggregation in a linear shear flow by accounting for two body collision hydrodynamics, platelet activation and receptor biology. Considering platelets and their aggregates as unequal-sized spheres with DLVO interactions (psi(platelet) = -15 mV, Hamaker constant = 10(-19) J), detailed hydrodynamics provided the flow field around the colliding platelets. Trajectory calculations were performed to obtain the far upstream cross-sectional area and the particle flux through this area provided the collision frequency. Only a fraction of platelets brought together by a shearing fluid flow were held together if successfully bound by fibrinogen cross-bridging GPIIb/IIIa receptors on the platelet surfaces. This fraction was calculated by modeling receptor-mediated aggregation using the formalism of Bell (Bell, G. I. 1979. A theoretical model for adhesion between cells mediated by multivalent ligands. Cell Biophys. 1:133-147) where the forward rate of bond formation dictated aggregation during collision and was estimated from the diffusional limited rate of lateral association of receptors multiplied by an effectiveness factor, eta, to give an apparent rate. For a value of eta = 0.0178, we calculated the overall efficiency (including both receptor binding and hydrodynamics effects) for equal-sized platelets with 50,000 receptors/platelet to be 0.206 for G = 41.9 s(-1), 0.05 for G = 335 s(-1), and 0.0086 for G = 1920 s(-1), values which are in agreement with efficiencies determined from initial platelet singlet consumption rates in flow through a tube. From our analysis, we predict that bond formation proceeds at a rate of approximately 0.1925 bonds/microm2 per ms, which is approximately 50-fold slower than the diffusion limited rate of association. This value of eta is also consistent with a colloidal stability of unactivated platelets at low shear rates. Fibrinogen was calculated to mediate aggregation quite efficiently at low shear rates but not at high shear rates. Although secondary collisions (an orbitlike trajectory) form only a small fraction of the total number of collisions, they become important at high shear rates (>750 s(-1)), as these are the only collisions that provide enough time to result in successful aggregate formation mediated by fibrinogen. The overall method provides a hydrodynamic and receptor correction of the Smoluchowski collision kernel and gives a first estimate of eta for the fibrinogen-GPIIb/IIIa cross-bridging of platelets. We also predict that secondary collisions extend the shear rate range at which fibrinogen can mediate successful aggregation. Images FIGURE 2 PMID:9370476

Aggregation kinetics of microplastics in aquatic environment: Complex roles of electrolytes, pH, and natural organic matter.

PubMed

Li, Shuocong; Liu, Hong; Gao, Rui; Abdurahman, Abliz; Dai, Juan; Zeng, Feng

2018-06-01

Microplastics are an emerging contaminants of concern in aquatic environments. The aggregation behaviors of microplastics governing their fate and ecological risks in aquatic environments is in need of evaluation. In this study, the aggregation behavior of polystyrene microspheres (micro-PS) in aquatic environments was systematically investigated over a range of monovalent and divalent electrolytes with and without natural organic matter (i.e., Suwannee River humic acid (HA)), at pH 6.0, respectively. The zeta potentials and hydrodynamic diameters of micro-PS were measured and the subsequent aggregation kinetics and attachment efficiencies (α) were calculated. The aggregation kinetics of micro-PS exhibited reaction- and diffusion-limited regimes in the presence of monovalent or divalent electrolytes with distinct critical coagulation concentration (CCC) values, followed the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. The CCC values of micro-PS were14.9, 13.7, 14.8, 2.95 and 3.20 mM for NaCl, NaNO 3 , KNO 3 , CaCl 2 and BaCl 2 , respectively. As expected, divalent electrolytes (i.e., CaCl 2 and BaCl 2 ) had stronger influence on the aggregation behaviors of micro-PS as compared to monovalent electrolytes (i.e., NaCl, NaNO 3 and KNO 3 ). HA enhanced micro-PS stability and shifted the CCC values to higher electrolyte concentrations for all types of electrolytes. The CCC values of micro-PS were lower than reported carbonaceous nanoparticles CCC values. The CCC[Ca 2+ ]/CCC [Na + ] ratios in the absence and presence of HA at pH 6.0 were proportional to Z -2.34 and Z -2.30 , respectively. These ratios were in accordance with the theoretical Schulze-Hardy rule, which considers that the CCC is proportional to z -6 -z -2 . These results indicate that the stability of micro-PS in the natural aquatic environment and the possibility of significant aqueous transport of micro-PS. Copyright © 2018 Elsevier Ltd. All rights reserved.

Intra-aggregate CO2 enrichment: a modelling approach for aerobic soils

NASA Astrophysics Data System (ADS)

Schlotter, D.; Schack-Kirchner, H.

2013-02-01

CO2 concentration gradients inside soil aggregates, caused by the respiration of soil microorganisms and fungal hyphae, might lead to variations in the soil solution chemistry on a mm-scale, and to an underestimation of the CO2 storage. But, up to now, there seems to be no feasible method for measuring CO2 inside natural aggregates with sufficient spatial resolution. We combined a one-dimensional model for gas diffusion in the inter-aggregate pore space with a cylinder diffusion model, simulating the consumption/production and diffusion of O2 and CO2 inside soil aggregates with air- and water-filled pores. Our model predicts that for aerobic respiration (respiratory quotient = 1) the intra-aggregate increase in the CO2 partial pressure can never be higher than 0.9 kPa for siliceous, and 0.1 kPa for calcaric aggregates, independent of the level of water-saturation. This suggests that only for siliceous aggregates CO2 produced by aerobic respiration might cause a high small-scale spatial variability in the soil solution chemistry. In calcaric aggregates, however, the contribution of carbonate species to the CO2 transport should lead to secondary carbonates on the aggregate surfaces. As regards the total CO2 storage in aerobic soils, both siliceous and calcaric, the effect of intra-aggregate CO2 gradients seems to be negligible. To assess the effect of anaerobic respiration on the intra-aggregate CO2 gradients, the development of a device for measuring CO2 on a mm-scale in soils is indispensable.

Long-range sclerotome induction by sonic hedgehog: direct role of the amino-terminal cleavage product and modulation by the cyclic AMP signaling pathway.

PubMed

Fan, C M; Porter, J A; Chiang, C; Chang, D T; Beachy, P A; Tessier-Lavigne, M

1995-05-05

A long-range signal encoded by the Sonic hedgehog (Shh) gene has been implicated as the ventral patterning influence from the notochord that induces sclerotome and represses dermomyotome in somite differentiation. Long-range effects of hedgehog (hh) signaling have been suggested to result either from local induction of a secondary diffusible signal or from the direct action of the highly diffusible carboxy-terminal product of HH autoproteolytic cleavage. Here we provide evidence that the long-range somite patterning effects of SHH are instead mediated by a direct action of the amino-terminal cleavage product. We also show that pharmacological manipulations to increase the activity of cyclic AMP-dependent protein kinase A can selectively antagonize the effects of the amino-terminal cleavage product. Our results support the operation of a single evolutionarily conserved signaling pathway for both local and direct long-range inductive actions of HH family members.

Stemming the Diffusion of Responsibility: A Longitudinal Case Study of America's Chemistry Teachers

ERIC Educational Resources Information Center

Rushton, Gregory T.; Ray, Herman E.; Criswell, Brett A.; Polizzi, Samuel J.; Bearss, Clyde J.; Levelsmier, Nicholas; Chhita, Himanshu; Kirchhoff, Mary

2014-01-01

National initiatives to expand the aggregate science, technology, engineering, and math (STEM) workforce reflect America's goals to increase global competitiveness. However, the aggregation of STEM stakeholders may elicit a "diffusion of responsibility" because individuals assume others are already acting. Here, we perform a longitudinal…

Fragmentation approach to the point-island model with hindered aggregation: Accessing the barrier energy

NASA Astrophysics Data System (ADS)

González, Diego Luis; Pimpinelli, Alberto; Einstein, T. L.

2017-07-01

We study the effect of hindered aggregation on the island formation process in a one- (1D) and two-dimensional (2D) point-island model for epitaxial growth with arbitrary critical nucleus size i . In our model, the attachment of monomers to preexisting islands is hindered by an additional attachment barrier, characterized by length la. For la=0 the islands behave as perfect sinks while for la→∞ they behave as reflecting boundaries. For intermediate values of la, the system exhibits a crossover between two different kinds of processes, diffusion-limited aggregation and attachment-limited aggregation. We calculate the growth exponents of the density of islands and monomers for the low coverage and aggregation regimes. The capture-zone (CZ) distributions are also calculated for different values of i and la. In order to obtain a good spatial description of the nucleation process, we propose a fragmentation model, which is based on an approximate description of nucleation inside of the gaps for 1D and the CZs for 2D. In both cases, the nucleation is described by using two different physically rooted probabilities, which are related with the microscopic parameters of the model (i and la). We test our analytical model with extensive numerical simulations and previously established results. The proposed model describes excellently the statistical behavior of the system for arbitrary values of la and i =1 , 2, and 3.

Determination of kinetic data for soot oxidation: Modeling of competition between oxygen diffusion and reaction during thermogravimetric analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gilot, P.; Bonnefoy, F.; Marcuccilli, F.

1993-10-01

Kinetic data concerning carbon black oxidation in the temperature range between 600 and 900 C have been obtained using thermogravimetric analysis. Modeling of diffusion in a boundary layer above the pan and inside the porous medium coupled to oxygen reaction with carbon black is necessary to obtain kinetic constants as a function of temperature. These calculations require the knowledge of the oxidation rate at a given constant temperature as a function of the initial mass loading m[sub o]. This oxidation rate, expressed in milligrams of soot consumed per second and per milligram of initial soot loading, decreases when m[sub o]more » increases, in agreement with a reaction in an intermediary regime where the kinetics and the oxygen diffusion operate. The equivalent diffusivity of oxygen inside the porous medium is evaluated assuming two degrees of porosity: between soot aggregates and inside each aggregate. Below 700 C an activation energy of about 103 kJ/mol can be related to a combustion reaction probably kinetically controlled. Beyond 700 C the activation energy of about 20 kJ/ mol corresponds to a reaction essentially controlled by oxygen diffusion leading to a constant density oxidation with oxygen consumption at or near the particle surface. To validate these data, they are used in the modeling of a Diesel particulate trap regeneration. In this particular case, the oxidizing flux is forced across the carbon black deposit, oxygen diffusion being insignificant. A good agreement between experimental results and model predictions is obtained, proving the rate constants validity.« less

Scaling in the aggregation dynamics of a magnetorheological fluid.

PubMed

Domínguez-García, P; Melle, Sonia; Pastor, J M; Rubio, M A

2007-11-01

We present experimental results on the aggregation dynamics of a magnetorheological fluid, namely, an aqueous suspension of micrometer-sized superparamagnetic particles, under the action of a constant uniaxial magnetic field using video microscopy and image analysis. We find a scaling behavior in several variables describing the aggregation kinetics. The data agree well with the Family-Vicsek scaling ansatz for diffusion-limited cluster-cluster aggregation. The kinetic exponents z and z' are obtained from the temporal evolution of the mean cluster size S(t) and the number of clusters N(t), respectively. The crossover exponent Delta is calculated in two ways: first, from the initial slope of the scaling function; second, from the evolution of the nonaggregated particles, n1(t). We report on results of Brownian two-dimensional dynamics simulations and compare the results with the experiments. Finally, we discuss the differences obtained between the kinetic exponents in terms of the variation in the crossover exponent and relate this behavior to the physical interpretation of the crossover exponent.

A modulation wave approach to the order hidden in disorder

PubMed Central

Withers, Ray

2015-01-01

The usefulness of a modulation wave approach to understanding and interpreting the highly structured continuous diffuse intensity distributions characteristic of the reciprocal spaces of the very large family of inherently flexible materials which exhibit ordered ‘disorder’ is pointed out. It is shown that both longer range order and truly short-range order are simultaneously encoded in highly structured diffuse intensity distributions. The long-range ordered crystal chemical rules giving rise to such diffuse distributions are highlighted, along with the existence and usefulness of systematic extinction conditions in these types of structured diffuse distributions. PMID:25610629

Adsorption and dynamics of Si atoms at the monolayer Pb/Si(111) surface

NASA Astrophysics Data System (ADS)

Kumar, Rakesh; Fang, Chuang-Kai; Lee, Chih-Hao; Hwang, Ing-Shouh

2017-06-01

In this work, we studied the adsorption behavior of deposited Si atoms along with their diffusion and other dynamic processes on a Pb monolayer-covered Si(111) surface from 125 to 230 K using a variable-temperature scanning tunneling microscope. The Pb-covered Si(111) surface forms a low-symmetry rowlike (√{7 }×√{3 } ) structure in this temperature range and the Si atoms bind favorably to two specific on-top sites (T1 A and T1 B) on the trimer row after deposition at the sample temperature of ˜125 K . The Si atoms were immobile at low temperatures and started to switch between the two neighboring T1 A and T1 B sites within the same trimer when the temperature was raised to ˜150 K . When the temperature was raised above ˜160 K , the adsorbed Si atoms could hop to other trimers along the same trimer row. Below ˜170 K , short hops to adjacent trimers dominated, but long hops dominated at temperatures above ˜170 K . The activation energy and prefactor for the Si atoms diffusion were derived through analysis of continuous-time imaging at temperatures from 160 to 174 K. In addition, irreversible aggregation of single Si atoms into Si clusters started to occur at the phase boundaries or defective sites at temperatures above ˜170 K . At temperature above ˜180 K , nearly all Si atoms aggregated into clusters, which may have important implications for the atomic mechanism of epitaxial growth of Si on the Pb-covered Si(111) surface. In addition, our study provides strong evidence for breaking in the mirror symmetry in the (√{7 }×√{3 } )-Pb structure, which has implications for the atomic model of this controversial structure.

Hydrogen in tungsten as plasma-facing material

NASA Astrophysics Data System (ADS)

Roth, Joachim; Schmid, Klaus

2011-12-01

Materials facing plasmas in fusion experiments and future reactors are loaded with high fluxes (1020-1024 m-2 s-1) of H, D and T fuel particles at energies ranging from a few eV to keV. In this respect, the evolution of the radioactive T inventory in the first wall, the permeation of T through the armour into the coolant and the thermo-mechanical stability after long-term exposure are key parameters determining the applicability of a first wall material. Tungsten exhibits fast hydrogen diffusion, but an extremely low solubility limit. Due to the fast diffusion of hydrogen and the short ion range, most of the incident ions will quickly reach the surface and recycle into the plasma chamber. For steady-state operation the solute hydrogen for the typical fusion reactor geometry and wall conditions can reach an inventory of about 1 kg. However, in short-pulse operation typical of ITER, solute hydrogen will diffuse out after each pulse and the remaining inventory will consist of hydrogen trapped in lattice defects, such as dislocations, grain boundaries and irradiation-induced traps. In high-flux areas the hydrogen energies are too low to create displacement damage. However, under these conditions the solubility limit will be exceeded within the ion range and the formation of gas bubbles and stress-induced damage occurs. In addition, simultaneous neutron fluxes from the nuclear fusion reaction D(T,n)α will lead to damage in the materials and produce trapping sites for diffusing hydrogen atoms throughout the bulk. The formation and diffusive filling of these different traps will determine the evolution of the retained T inventory. This paper will concentrate on experimental evidence for the influence different trapping sites have on the hydrogen inventory in W as studied in ion beam experiments and low-temperature plasmas. Based on the extensive experimental data, models are validated and applied to estimate the contribution of different traps to the tritium inventory in future fusion reactors.

Group living in squamate reptiles: a review of evidence for stable aggregations.

PubMed

Gardner, Michael G; Pearson, Sarah K; Johnston, Gregory R; Schwarz, Michael P

2016-11-01

How sociality evolves and is maintained remains a key question in evolutionary biology. Most studies to date have focused on insects, birds, and mammals but data from a wider range of taxonomic groups are essential to identify general patterns and processes. The extent of social behaviour among squamate reptiles is under-appreciated, yet they are a promising group for further studies. Living in aggregations is posited as an important step in the evolution of more complex sociality. We review data on aggregations among squamates and find evidence for some form of aggregations in 94 species across 22 families. Of these, 18 species across 7 families exhibited 'stable' aggregations that entail overlapping home ranges and stable membership in long-term (years) or seasonal aggregations. Phylogenetic analysis suggests that stable aggregations have evolved multiple times in squamates. We: (i) identify significant gaps in our understanding; (ii) outline key traits which should be the focus of future research; and (iii) outline the potential for utilising reproductive skew theory to provide insights into squamate sociality. © 2015 Cambridge Philosophical Society.

Spreading of nonmotile bacteria on a hard agar plate: Comparison between agent-based and stochastic simulations

NASA Astrophysics Data System (ADS)

Rana, Navdeep; Ghosh, Pushpita; Perlekar, Prasad

2017-11-01

We study spreading of a nonmotile bacteria colony on a hard agar plate by using agent-based and continuum models. We show that the spreading dynamics depends on the initial nutrient concentration, the motility, and the inherent demographic noise. Population fluctuations are inherent in an agent-based model, whereas for the continuum model we model them by using a stochastic Langevin equation. We show that the intrinsic population fluctuations coupled with nonlinear diffusivity lead to a transition from a diffusion limited aggregation type of morphology to an Eden-like morphology on decreasing the initial nutrient concentration.

Unity and diversity in mixing: Stretching, diffusion, breakup, and aggregation in chaotic flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ottino, J.M.

1991-05-01

Experiments and theory have produced a reasonably good qualitative understanding of the evolution of chaotic mixing of passive tracers, especially in two-dimensional time-periodic flow fields. Such an understanding forms a fabric for the evolution of breakup, aggregation, and diffusion-controlled reactions in more complex flows. These systems can be viewed as a population of microstructures'' whose behavior is dictated by iterations of a chaotic flow; microstructures break, diffuse, and aggregate, causing the population to evolve in space and time. This paper presents simple physical models for such processes. Self-similarity is common to all the problems; examples arise in the context ofmore » the distribution of stretchings within chaotic flows, in the asymptotic evolution of diffusion-reaction processes at striation thickness scales, in the equilibrium distribution of drop sizes generated upon mixing of immiscible fluids, in the equations describing mean-field kinetics of coagulation, in the sequence of actions necessary for the destruction of islands in two-dimensional flow, and in the fractal structure of clusters produced upon aggregation in chaotic flows.« less

A passive physical model for DnaK chaperoning

NASA Astrophysics Data System (ADS)

Uhl, Lionel; Dumont, Audrey; Dukan, Sam

2018-03-01

Almost all living organisms use protein chaperones with a view to preventing proteins from misfolding or aggregation either spontaneously or during cellular stress. This work uses a reaction-diffusion stochastic model to describe the dynamic localization of the Hsp70 chaperone DnaK in Escherichia coli cells during transient proteotoxic collapse characterized by the accumulation of insoluble proteins. In the model, misfolded (‘abnormal’) proteins are produced during alcoholic stress and have the propensity to aggregate with a polymerization-like kinetics. When aggregates diffuse more slowly they grow larger. According to Michaelis-Menten-type kinetics, DnaK has the propensity to bind with misfolded proteins or aggregates in order to catalyse refolding. To match experimental fluorescence microscopy data showing clusters of DnaK-GFP localized in multiple foci, the model includes spatial zones with local reduced diffusion rates to generate spontaneous assemblies of DnaK called ‘foci’. Numerical simulations of our model succeed in reproducing the kinetics of DnaK localization experimentally observed. DnaK starts from foci, moves to large aggregates during acute stress, resolves those aggregates during recovery and finally returns to its initial punctate localization pattern. Finally, we compare real biological events with hypothetical repartitions of the protein aggregates or DnaK. We then notice that DnaK action is more efficient on protein aggregates than on protein homogeneously distributed.

Vertical Alignment of Single-Walled Carbon Nanotubes on Nanostructure Fabricated by Atomic Force Microscope

DTIC Science & Technology

2007-03-30

Langmuir - Blodgett and self-assembly methods, WNTs are patterned selectively onto various substrates [3,4]. hou et al. assembled SWNTs into aligned...dispersion usually decreases with increasing ionic concentration, it is suggested that chloride ions are produced by dissociating from acid chloride groups...patterns can be attributed to the Marangoni effect and diffusion-limited aggregation (DLA) in the liquid film during droplet evaporation t different

Field theory and diffusion creep predictions in polycrystalline aggregates

NASA Astrophysics Data System (ADS)

Villani, A.; Busso, E. P.; Forest, S.

2015-07-01

In polycrystals, stress-driven vacancy diffusion at high homologous temperatures leads to inelastic deformation. In this work, a novel continuum mechanics framework is proposed to describe the strain fields resulting from such a diffusion-driven process in a polycrystalline aggregate where grains and grain boundaries are explicitly considered. The choice of an anisotropic eigenstrain in the grain boundary region provides the driving force for the diffusive creep processes. The corresponding inelastic strain rate is shown to be related to the gradient of the vacancy flux. Dislocation driven deformation is then introduced as an additional mechanism, through standard crystal plasticity constitutive equations. The fully coupled diffusion-mechanical model is implemented into the finite element method and then used to describe the biaxial creep behaviour of FCC polycrystalline aggregates. The corresponding results revealed for the first time that such a coupled diffusion-stress approach, involving the gradient of the vacancy flux, can accurately predict the well-known macroscopic strain rate dependency on stress and grain size in the diffusion creep regime. They also predict strongly heterogeneous viscoplastic strain fields, especially close to grain boundaries triple junctions. Finally, a smooth transition from Herring and Coble to dislocation creep behaviour is predicted and compared to experimental results for copper.

The impact of flow focusing on gas hydrate accumulations in overpressured marine sediments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nole, Michael; Daigle, Hugh; Cook, Ann

This study demonstrates the potential for flow focusing due to overpressuring in marine sedimentary environments to act as a significant methane transport mechanism from which methane hydrate can precipitate in large quantities in dipping sandstone bodies. Traditionally, gas hydrate accumulations in nature are discussed as resulting from either short-range diffusive methane migration or from long-range advective fluid transport sourced from depth. However, 3D simulations performed in this study demonstrate that a third migration mechanism, short-range advective transport, can provide a significant methane source that is unencumbered by limitations of the other two end-member mechanisms. Short-range advective sourcing is advantageous overmore » diffusion because it can convey greater amounts of methane to sands over shorter timespans, yet it is not necessarily limited by down-dip pore blocking in sands as is typical of updip advection from a deep source. These results are novel because they integrate pore size impacts on spatial solubility gradients, grid block properties that evolve through time, and methane sourcing through microbial methanogenesis into a holistic characterization of environments exposed to multiple methane hydrate sourcing mechanisms. We show that flow focusing toward sand bodies transports large quantities of methane, the magnitude of which are determined by the sand-clay solubility contrast, and generates larger quantities of hydrate in sands than a solely diffusive system; after depositing methane as hydrate, fluid exiting a sand body is depleted in methane and leaves a hydrate free region in its wake above the sand. Additionally, we demonstrate that in overpressured environments, hydrate growth is initially diffusively dominated before transitioning to an advection-dominated regime. The timescale and depth at which this transition takes place depends primarily on the rate of microbial metabolism and the sedimentation rate but only depends loosely on the degree of overpressuring.« less

In vivo imaging of cancer cell size and cellularity using temporal diffusion spectroscopy.

PubMed

Jiang, Xiaoyu; Li, Hua; Xie, Jingping; McKinley, Eliot T; Zhao, Ping; Gore, John C; Xu, Junzhong

2017-07-01

A temporal diffusion MRI spectroscopy based approach has been developed to quantify cancer cell size and density in vivo. A novel imaging microstructural parameters using limited spectrally edited diffusion (IMPULSED) method selects a specific limited diffusion spectral window for an accurate quantification of cell sizes ranging from 10 to 20 μm in common solid tumors. In practice, it is achieved by a combination of a single long diffusion time pulsed gradient spin echo (PGSE) and three low-frequency oscillating gradient spin echo (OGSE) acquisitions. To validate our approach, hematoxylin and eosin staining and immunostaining of cell membranes, in concert with whole slide imaging, were used to visualize nuclei and cell boundaries, and hence, enabled accurate estimates of cell size and cellularity. Based on a two compartment model (incorporating intra- and extracellular spaces), accurate estimates of cell sizes were obtained in vivo for three types of human colon cancers. The IMPULSED-derived apparent cellularities showed a stronger correlation (r = 0.81; P < 0.0001) with histology-derived cellularities than conventional ADCs (r = -0.69; P < 0.03). The IMPULSED approach samples a specific region of temporal diffusion spectra with enhanced sensitivity to length scales of 10-20 μm, and enables measurements of cell sizes and cellularities in solid tumors in vivo. Magn Reson Med 78:156-164, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Measurement of Average Aggregate Density by Sedimentation and Brownian Motion Analysis.

PubMed

Cavicchi, Richard E; King, Jason; Ripple, Dean C

2018-05-01

The spatially averaged density of protein aggregates is an important parameter that can be used to relate size distributions measured by orthogonal methods, to characterize protein particles, and perhaps to estimate the amount of protein in aggregate form in a sample. We obtained a series of images of protein aggregates exhibiting Brownian diffusion while settling under the influence of gravity in a sealed capillary. The aggregates were formed by stir-stressing a monoclonal antibody (NISTmAb). Image processing yielded particle tracks, which were then examined to determine settling velocity and hydrodynamic diameter down to 1 μm based on mean square displacement analysis. Measurements on polystyrene calibration microspheres ranging in size from 1 to 5 μm showed that the mean square displacement diameter had improved accuracy over the diameter derived from imaged particle area, suggesting a future method for correcting size distributions based on imaging. Stokes' law was used to estimate the density of each particle. It was found that the aggregates were highly porous with density decreasing from 1.080 to 1.028 g/cm 3 as the size increased from 1.37 to 4.9 μm. Published by Elsevier Inc.

Exciton Dynamics in Alternative Solar Cell Materials: Polymers, Nanocrystals, and Small Molecules

NASA Astrophysics Data System (ADS)

Pundsack, Thomas J.

To keep fossil fuel usage in 2040 even with 2010 usage, 50% of global energy will need to come from alternative sources such as solar cells. While the photovoltaic market is currently dominated by crystalline silicon, there are many low-cost solar cell materials such as conjugated polymers, semiconductor nanocrystals, and organic small molecules which could compete with fossil fuels. To create cost-competitive devices, understanding the excited state dynamics of these materials is necessary. The first section of this thesis looks at aggregation in poly(3-hexylthiophene) (P3HT) which is commonly used in organic photovoltaics. The amount of aggregation in P3HT thin films was controlled by using a mixture of regioregular and regiorandom P3HT. Even with few aggregates present, excited states were found to transfer from amorphous to aggregate domains in <50 fs which could indicate efficient long-range energy transfer. To further study P3HT aggregation, a triblock consisting of two P3HT chains with a coil polymer between them was investigated. By changing solvents, aggregation was induced in a stable and reversible manner allowing for spectroscopic studies of P3HT aggregates in solution. The polarity of the solvent was adjusted, and no change in excited state dynamics was observed implying the excited state has little charge-transfer character. Next, the conduction band density of states for copper zinc tin sulfide nanocrystals (CZTS NCs) was measured using pump-probe spectroscopy and found to be in agreement with theoretical results. The density of states shifted and dilated for smaller NCs indicative of quantum confinement. The excited state lifetime was found to be short (<20 ps) and independent of NC size which could limit the efficiency of CZTS photovoltaic devices. Finally, triplet-triplet annihilation (TTA) was studied in platinum octaethylporphyrin (PtOEP) thin films. By analyzing pump-probe spectra, the product of TTA in PtOEP thin films was assigned to a long-lived metal-centered state. To elucidate the mechanism of TTA, the annihilation dynamics were modeled using second order kinetics as well as Forster and Dexter energy transfer. Dexter energy transfer provided the best fits and the most reasonable fitting parameters.

Extension of the dielectric breakdown model for simulation of viscous fingering at finite viscosity ratios.

PubMed

Doorwar, Shashvat; Mohanty, Kishore K

2014-07-01

Immiscible displacement of viscous oil by water in a petroleum reservoir is often hydrodynamically unstable. Due to similarities between the physics of dielectric breakdown and immiscible flow in porous media, we extend the existing dielectric breakdown model to simulate viscous fingering patterns for a wide range of viscosity ratios (μ(r)). At low values of power-law index η, the system behaves like a stable Eden growth model and as the value of η is increased to unity, diffusion limited aggregation-like fractals appear. This model is compared with our two-dimensional (2D) experiments to develop a correlation between the viscosity ratio and the power index, i.e., η = 10(-5)μ(r)(0.8775). The 2D and three-dimensional (3D) simulation data appear scalable. The fingering pattern in 3D simulations at finite viscosity ratios appear qualitatively similar to the few experimental results published in the literature.

NMR investigation of the short-chain ionic surfactant-water systems.

PubMed

Popova, M V; Tchernyshev, Y S; Michel, D

2004-02-03

The structure and dynamics of surfactant molecules [CH3(CH2)7COOK] in heavy water solutions were investigated by 1H and 2H NMR. A double-exponential attenuation of the spin-echo amplitude in a Carr-Purcell-Meiboom-Gill experiment was found. We expect correspondence to both bounded and monomeric states. At high concentrations in the NMR self-diffusion measurements also a double-exponential decay of the spin-echo signal versus the square of the dc magnetic gradient was observed. The slow component of the diffusion process is caused by micellar aggregates, while the fast component is the result of the self-diffusion of the monomers through the micelles. The self-diffusion studies indicate that the form of micelles changes with increasing total surfactant concentration. The critical temperature range for self-association is reflected in the 1H transverse relaxation.

Interpretation of light scattering and turbidity measurements in aggregated systems: effect of intra-cluster multiple-light scattering.

PubMed

Soos, Miroslav; Lattuada, Marco; Sefcik, Jan

2009-11-12

In this work we studied the effect of intracluster multiple-light scattering on the scattering properties of a population of fractal aggregates. To do so, experimental data of diffusion-limited aggregation for three polystyrene latexes with similar surface properties but different primary particle diameters (equal to 118, 420, and 810 nm) were obtained by static light scattering and by means of a spectrophotometer. In parallel, a population balance equation (PBE) model, which takes into account the effect of intracluster multiple-light scattering by solving the T-matrix and the mean-field version of T-matrix, was formulated and validated against time evolution of the root mean radius of gyration, , of the zero angle intensity of scattered light, I(0), and of the turbidity, tau. It was found that the mean-field version of the T-matrix theory is able to correctly predict the time evolution of all measured light scattering quantities for all sizes of primary particles without any adjustable parameter. The structure of the aggregates, characterized by fractal dimension, d(f), was independent of the primary particle size and equal to 1.7, which is in agreement with values found in literature. Since the mean-field version of the T-matrix theory used is rather complicated and requires advanced knowledge of cluster structure (i.e., the particle-particle correlation function), a simplified version of the light scattering model was proposed and tested. It was found that within the range of operating conditions investigated, the simplified version of the light scattering model was able to describe with reasonable accuracy the time evolution of all measured light scattering quantities of the cluster mass distribution (CMD) for all three sizes of primary particles and two values of the laser wavelength.

The influence of mass transfer on solute transport in column experiments with an aggregated soil

NASA Astrophysics Data System (ADS)

Roberts, Paul V.; Goltz, Mark N.; Summers, R. Scott; Crittenden, John C.; Nkedi-Kizza, Peter

1987-06-01

The spreading of concentration fronts in dynamic column experiments conducted with a porous, aggregated soil is analyzed by means of a previously documented transport model (DFPSDM) that accounts for longitudinal dispersion, external mass transfer in the boundary layer surrounding the aggregate particles, and diffusion in the intra-aggregate pores. The data are drawn from a previous report on the transport of tritiated water, chloride, and calcium ion in a column filled with Ione soil having an average aggregate particle diameter of 0.34 cm, at pore water velocities from 3 to 143 cm/h. The parameters for dispersion, external mass transfer, and internal diffusion were predicted for the experimental conditions by means of generalized correlations, independent of the column data. The predicted degree of solute front-spreading agreed well with the experimental observations. Consistent with the aggregate porosity of 45%, the tortuosity factor for internal pore diffusion was approximately equal to 2. Quantitative criteria for the spreading influence of the three mechanisms are evaluated with respect to the column data. Hydrodynamic dispersion is thought to have governed the front shape in the experiments at low velocity, and internal pore diffusion is believed to have dominated at high velocity; the external mass transfer resistance played a minor role under all conditions. A transport model such as DFPSDM is useful for interpreting column data with regard to the mechanisms controlling concentration front dynamics, but care must be exercised to avoid confounding the effects of the relevant processes.

Detection of silver nanoparticles in seawater at ppb levels using UV-visible spectrophotometry with long path cells.

PubMed

Lodeiro, Pablo; Achterberg, Eric P; El-Shahawi, Mohammad S

2017-03-01

Silver nanoparticles (AgNPs) are emerging contaminants that are difficult to detect in natural waters. UV-visible spectrophotometry is a simple technique that allows detection of AgNPs through analysis of their characteristic surface plasmon resonance band. The detection limit for nanoparticles using up to 10cm path length cuvettes with UV-visible spectrophotometry is in the 0.1-10ppm range. This detection limit is insufficiently low to observe AgNPs in natural environments. Here we show how the use of capillary cells with an optical path length up to 200cm, forms an excellent technique for rapid detection and quantification of non-aggregated AgNPs at ppb concentrations in complex natural matrices such as seawater. Copyright © 2016 Elsevier B.V. All rights reserved.

Kinetics of Surface-Mediated Fibrillization of Amyloid-β (12-28) Peptides.

PubMed

Lin, Yi-Chih; Li, Chen; Fakhraai, Zahra

2018-04-17

Surfaces or interfaces are considered to be key factors in facilitating the formation of amyloid fibrils under physiological conditions. In this report, we study the kinetics of the surface-mediated fibrillization (SMF) of an amyloid-β fragment (Aβ 12-28 ) on mica. We employ a spin-coating-based drying procedure to control the exposure time of the substrate to a low-concentration peptide solution and then monitor the fibril growth as a function of time via atomic force microscopy (AFM). The evolution of surface-mediated fibril growth is quantitatively characterized in terms of the length histogram of imaged fibrils and their surface concentration. A two-dimensional (2D) kinetic model is proposed to numerically simulate the length evolution of surface-mediated fibrils by assuming a diffusion-limited aggregation (DLA) process along with size-dependent rate constants. We find that both monomer and fibril diffusion on the surface are required to obtain length histograms as a function of time that resemble those observed in experiments. The best-fit simulated data can accurately describe the key features of experimental length histograms and suggests that the mobility of loosely bound amyloid species is crucial in regulating the kinetics of SMF. We determine that the mobility exponent for the size dependence of the DLA rate constants is α = 0.55 ± 0.05, which suggests that the diffusion of loosely bound surface fibrils roughly depends on the inverse of the square root of their size. These studies elucidate the influence of deposition rate and surface diffusion on the formation of amyloid fibrils through SMF. The method used here can be broadly adopted to study the diffusion and aggregation of peptides or proteins on various surfaces to investigate the role of chemical interactions in two-dimensional fibril formation and diffusion.

Lévy flight with absorption: A model for diffusing diffusivity with long tails

NASA Astrophysics Data System (ADS)

Jain, Rohit; Sebastian, K. L.

2017-03-01

We consider diffusion of a particle in rearranging environment, so that the diffusivity of the particle is a stochastic function of time. In our previous model of "diffusing diffusivity" [Jain and Sebastian, J. Phys. Chem. B 120, 3988 (2016), 10.1021/acs.jpcb.6b01527], it was shown that the mean square displacement of particle remains Fickian, i.e., ∝T at all times, but the probability distribution of particle displacement is not Gaussian at all times. It is exponential at short times and crosses over to become Gaussian only in a large time limit in the case where the distribution of D in that model has a steady state limit which is exponential, i.e., πe(D ) ˜e-D /D0 . In the present study, we model the diffusivity of a particle as a Lévy flight process so that D has a power-law tailed distribution, viz., πe(D ) ˜D-1 -α with 0 <α <1 . We find that in the short time limit, the width of displacement distribution is proportional to √{T }, implying that the diffusion is Fickian. But for long times, the width is proportional to T1 /2 α which is a characteristic of anomalous diffusion. The distribution function for the displacement of the particle is found to be a symmetric stable distribution with a stability index 2 α which preserves its shape at all times.

Sintering of highly porous silica-particle samples: analogues of early Solar-System aggregates

NASA Astrophysics Data System (ADS)

Poppe, T.

2003-07-01

I describe a new method to make particle layers which consist of SiO 2 spheres with 0.78 μm radius. The layers were produced by sedimentation of aggregates which had grown in ballistic particle collisions, and the layers had a porosity of 0.95. They were used for experiments on sintering, i.e., the samples were heated in an oven at varying temperatures and heating durations, and the samples were analyzed by scanning electron microscopy. Based on the change of particle diameter, surface diffusion sintering and viscous flow are identified as important transformation mechanisms. The first effect dominated at the start of restructuring and the latter at higher temperatures. The neck growth of adjacent particles was fitted to a surface diffusion sintering model and predicts neck radii as a heating temperature and duration function. Between the temperature range of neck formation and of melting, further restructuring occurred which lead to dissolution of particulate structure and to densification and which resulted in a porous object consisting of straight elongated substructures which connected kinks of higher material density. The thermal transformation is important for the change of strength, collisional behavior, light-scattering properties, and thermal conductivity with relevance to dust aggregates, planetesimals, comets, interplanetary dust particles, and regolith-covered celestial bodies.

Orogenic inheritance in Death Valley region, western US Basin and Range: implications for Neogene crustal extension.

NASA Astrophysics Data System (ADS)

Lima, R. D.; Hayman, N. W.; Prior, M. G.; Stockli, D. F.; Kelly, E. D.

2016-12-01

Deformation and temperature evolution during orogenic stages may influence later fabric development, thus controlling large-scale extensional processes that can occur millions of years later. Here, we describe pressure-temperature and fabric evolution from the Death Valley (DV) region and show how inherited fabrics, formed in late orogenic stages during Late Cretaceous time, influenced later Neogene age Basin and Range (BR) extension. The DV region is one of the most extended and thinned regions in the western US BR province, and the two of the ranges that bound the eastern valley expose basement rocks exhumed during the Neogene extension. In the Funeral range, it has been established that older (Precambrian) basement underwent Mesozoic age syn-deformational metamorphism during the Sevier-Laramide orogeny. In contrast, the Black Mountains record widespread tectonic stretching and magmatism of Miocene age on Precambrian basement, and have, overall, been lacking previous evidence of Mesozoic metamorphism and fabric development. In the Funeral Range Late Cretaceous migmatitic fabrics were overprinted by zones of high-strain fabrics formed due to melt-consuming reaction that define an overall P-T cooling path likely during late- to post-orogenesis. These fabrics form interconnected layers of quartz + biotite aggregates, in which individual quartz grains lack evidence of intracrystalline plastic deformation and show consistently random [c]-axis microfabrics. This suggests coupled reaction-diffusion processes that favored diffusion-assisted creep. New geochronometric results of melt products in the Black Mountains show evidence of partial melting of Late Cretaceous age. Contrasting with the neighboring Funeral Range, overprinting by extensional fabrics of Miocene age is widespread, and consists of high-strain, anastomosing foliation composed of retrograde products from preexisting, higher-temperature fabrics. These include interconnected fine-grained chlorite + quartz and sericite aggregates showing [c]-axis quartz microfabrics consistent with diffusion-assisted creep. In both ranges, the formation of new-over-old fabric due to the extensional deformation is favored by local heterogeneities in bulk composition due previous melt segregation during late- to post-orogenic stages.

Synthesis and materialization of a reaction-diffusion French flag pattern

NASA Astrophysics Data System (ADS)

Zadorin, Anton S.; Rondelez, Yannick; Gines, Guillaume; Dilhas, Vadim; Urtel, Georg; Zambrano, Adrian; Galas, Jean-Christophe; Estevez-Torres, André

2017-10-01

During embryo development, patterns of protein concentration appear in response to morphogen gradients. These patterns provide spatial and chemical information that directs the fate of the underlying cells. Here, we emulate this process within non-living matter and demonstrate the autonomous structuration of a synthetic material. First, we use DNA-based reaction networks to synthesize a French flag, an archetypal pattern composed of three chemically distinct zones with sharp borders whose synthetic analogue has remained elusive. A bistable network within a shallow concentration gradient creates an immobile, sharp and long-lasting concentration front through a reaction-diffusion mechanism. The combination of two bistable circuits generates a French flag pattern whose 'phenotype' can be reprogrammed by network mutation. Second, these concentration patterns control the macroscopic organization of DNA-decorated particles, inducing a French flag pattern of colloidal aggregation. This experimental framework could be used to test reaction-diffusion models and fabricate soft materials following an autonomous developmental programme.

Diffusion NMR methods applied to xenon gas for materials study

NASA Technical Reports Server (NTRS)

Mair, R. W.; Rosen, M. S.; Wang, R.; Cory, D. G.; Walsworth, R. L.

2002-01-01

We report initial NMR studies of (i) xenon gas diffusion in model heterogeneous porous media and (ii) continuous flow laser-polarized xenon gas. Both areas utilize the pulsed gradient spin-echo (PGSE) techniques in the gas phase, with the aim of obtaining more sophisticated information than just translational self-diffusion coefficients--a brief overview of this area is provided in the Introduction. The heterogeneous or multiple-length scale model porous media consisted of random packs of mixed glass beads of two different sizes. We focus on observing the approach of the time-dependent gas diffusion coefficient, D(t) (an indicator of mean squared displacement), to the long-time asymptote, with the aim of understanding the long-length scale structural information that may be derived from a heterogeneous porous system. We find that D(t) of imbibed xenon gas at short diffusion times is similar for the mixed bead pack and a pack of the smaller sized beads alone, hence reflecting the pore surface area to volume ratio of the smaller bead sample. The approach of D(t) to the long-time limit follows that of a pack of the larger sized beads alone, although the limiting D(t) for the mixed bead pack is lower, reflecting the lower porosity of the sample compared to that of a pack of mono-sized glass beads. The Pade approximation is used to interpolate D(t) data between the short- and long-time limits. Initial studies of continuous flow laser-polarized xenon gas demonstrate velocity-sensitive imaging of much higher flows than can generally be obtained with liquids (20-200 mm s-1). Gas velocity imaging is, however, found to be limited to a resolution of about 1 mm s-1 owing to the high diffusivity of gases compared with liquids. We also present the first gas-phase NMR scattering, or diffusive-diffraction, data, namely flow-enhanced structural features in the echo attenuation data from laser-polarized xenon flowing through a 2 mm glass bead pack. c2002 John Wiley & Sons, Ltd.

Optimizing the durability of the coarse fraction of porous asphalt RAP for effective recycling

NASA Astrophysics Data System (ADS)

Holleran, Irina; Wilson, Douglas J.; Black, Philippa; Holleran, Glynn; Walubita, Lubinda F.

2017-09-01

Porous asphalt (PA) durability depends not only on the binder used to manufacture the mix, but also on the aggregates chosen, particularly the coarse fraction component. Aggregates for PA should be of the highest quality and highly durable to withstand the effects of weather and traffic. To recycle PA into a new PA mix, without compromising the long-term performance, the durability of the recovered aggregates from PA-derived reclaimed asphalt pavement (RAP) should be assessed alongside the aged binder properties. In this study, the Micro-Deval (MD) Abrasion test, combined with water absorption, was found to be a good predictor of asphalt mix performance for PA. Minerology of the aggregates is an important factor when setting limits for MD loss. New Zealand (NZ) aggregates are significantly younger in geological terms, and chemically and physically less stable compared to the aggregates used in many other countries. This is especially true for greywacke, the most used aggregate in NZ for road construction. If the MD limits reported in some literature are applied to NZ PA-derived RAP aggregates, poor performing material can be erroneously incorporated in asphalt mixes. Findings from this study contributes in understanding how PA-derived RAP can be recycled into new value PA mixes.

Fragmentation approach to the point-island model with hindered aggregation: Accessing the barrier energy.

PubMed

González, Diego Luis; Pimpinelli, Alberto; Einstein, T L

2017-07-01

We study the effect of hindered aggregation on the island formation process in a one- (1D) and two-dimensional (2D) point-island model for epitaxial growth with arbitrary critical nucleus size i. In our model, the attachment of monomers to preexisting islands is hindered by an additional attachment barrier, characterized by length l_{a}. For l_{a}=0 the islands behave as perfect sinks while for l_{a}→∞ they behave as reflecting boundaries. For intermediate values of l_{a}, the system exhibits a crossover between two different kinds of processes, diffusion-limited aggregation and attachment-limited aggregation. We calculate the growth exponents of the density of islands and monomers for the low coverage and aggregation regimes. The capture-zone (CZ) distributions are also calculated for different values of i and l_{a}. In order to obtain a good spatial description of the nucleation process, we propose a fragmentation model, which is based on an approximate description of nucleation inside of the gaps for 1D and the CZs for 2D. In both cases, the nucleation is described by using two different physically rooted probabilities, which are related with the microscopic parameters of the model (i and l_{a}). We test our analytical model with extensive numerical simulations and previously established results. The proposed model describes excellently the statistical behavior of the system for arbitrary values of l_{a} and i=1, 2, and 3.

Aggregation Number in Water/n-Hexanol Molecular Clusters Formed in Cyclohexane at Different Water/n-Hexanol/Cyclohexane Compositions Calculated by Titration 1H NMR.

PubMed

Flores, Mario E; Shibue, Toshimichi; Sugimura, Natsuhiko; Nishide, Hiroyuki; Moreno-Villoslada, Ignacio

2017-11-09

Upon titration of n-hexanol/cyclohexane mixtures of different molar compositions with water, water/n-hexanol clusters are formed in cyclohexane. Here, we develop a new method to estimate the water and n-hexanol aggregation numbers in the clusters that combines integration analysis in one-dimensional 1 H NMR spectra, diffusion coefficients calculated by diffusion-ordered NMR spectroscopy, and further application of the Stokes-Einstein equation to calculate the hydrodynamic volume of the clusters. Aggregation numbers of 5-15 molecules of n-hexanol per cluster in the absence of water were observed in the whole range of n-hexanol/cyclohexane molar fractions studied. After saturation with water, aggregation numbers of 6-13 n-hexanol and 0.5-5 water molecules per cluster were found. O-H and O-O atom distances related to hydrogen bonds between donor/acceptor molecules were theoretically calculated using density functional theory. The results show that at low n-hexanol molar fractions, where a robust hydrogen-bond network is held between n-hexanol molecules, addition of water makes the intermolecular O-O atom distance shorter, reinforcing molecular association in the clusters, whereas at high n-hexanol molar fractions, where dipole-dipole interactions dominate, addition of water makes the intermolecular O-O atom distance longer, weakening the cluster structure. This correlates with experimental NMR results, which show an increase in the size and aggregation number in the clusters upon addition of water at low n-hexanol molar fractions, and a decrease of these magnitudes at high n-hexanol molar fractions. In addition, water produces an increase in the proton exchange rate between donor/acceptor molecules at all n-hexanol molar fractions.

Weathering-limited hillslope evolution in carbonate landscapes

NASA Astrophysics Data System (ADS)

Godard, Vincent; Ollivier, Vincent; Bellier, Olivier; Miramont, Cécile; Shabanian, Esmaeil; Fleury, Jules; Benedetti, Lucilla; Guillou, Valéry; Aster Team

2016-07-01

Understanding topographic evolution requires integrating elementary processes acting at the hillslope scale into the long-wavelength framework of landscape dynamics. Recent progress has been made in the quantification of denudation of eroding landscapes and its links with topography. Despite these advances, data is still sparse in carbonate terrain, which covers a significant part of the Earth's surface. In this study, we measured both long-term denudation rates using in situ-produced 36Cl concentrations in bedrock and regolith clasts and surface convexity at 12 sites along ridges of the Luberon carbonate range in Provence, Southeastern France. Starting from ∼30 mm/ka for the lowering of the summit plateau surface, denudation linearly increases with increasing hilltop convexity up to ∼70 mm/ka, as predicted by diffusive mass transport theory. Beyond this point denudation rates appear to be insensitive to the increase in hilltop convexity. We interpret this constant denudation as indicating a transition from a regime where hillslope evolution is primarily controlled by diffusive downslope regolith transport, toward a situation in which denudation is limited by the rate at which physical and chemical weathering processes can produce clasts and lower the hilltop. Such an abrupt transition into a weathering-limited dynamics may prevent hillslope denudation from balancing the rate of base level fall imposed by the river network and could potentially explain the development of high local relief in many Mediterranean carbonate landscapes.

Aggregated filter-feeding consumers alter nutrient limitation: consequences for ecosystem and community dynamics.

PubMed

Atkinson, Carla L; Vaughn, Caryn C; Forshay, Kenneth J; Cooper, Joshua T

2013-06-01

Nutrient cycling is a key process linking organisms in ecosystems. This is especially apparent in stream environments in which nutrients are taken up readily and cycled through the system in a downstream trajectory. Ecological stoichiometry predicts that biogeochemical cycles of different elements are interdependent because the organisms that drive these cycles require fixed ratios of nutrients. There is growing recognition that animals play an important role in biogeochemical cycling across ecosystems. In particular, dense aggregations of consumers can create biogeochemical hotspots in aquatic ecosystems via nutrient translocation. We predicted that filter-feeding freshwater mussels, which occur as speciose, high-biomass aggregates, would create biogeochemical hotspots in streams by altering nutrient limitation and algal dynamics. In a field study, we manipulated nitrogen and phosphorus using nutrient-diffusing substrates in areas with high and low mussel abundance, recorded algal growth and community composition, and determined in situ mussel excretion stoichiometry at 18 sites in three rivers (Kiamichi, Little, and Mountain Fork Rivers, south-central United States). Our results indicate that mussels greatly influence ecosystem processes by modifying the nutrients that limit primary productivity. Sites without mussels were N-limited with -26% higher relative abundances of N-fixing blue-green algae, while sites with high mussel densities were co-limited (N and P) and dominated by diatoms. These results corroborated the results of our excretion experiments; our path analysis indicated that mussel excretion has a strong influence on stream water column N:P. Due to the high N:P of mussel excretion, strict N-limitation was alleviated, and the system switched to being co-limited by both N and P. This shows that translocation of nutrients by mussel aggregations is important to nutrient dynamics and algal species composition in these rivers. Our study highlights the importance of consumers and this imperiled faunal group on nutrient cycling and community dynamics in aquatic ecosystems.

The Spectrum of Wind Power Fluctuations

NASA Astrophysics Data System (ADS)

Bandi, Mahesh

2016-11-01

Wind is a variable energy source whose fluctuations threaten electrical grid stability and complicate dynamical load balancing. The power generated by a wind turbine fluctuates due to the variable wind speed that blows past the turbine. Indeed, the spectrum of wind power fluctuations is widely believed to reflect the Kolmogorov spectrum; both vary with frequency f as f - 5 / 3. This variability decreases when aggregate power fluctuations from geographically distributed wind farms are averaged at the grid via a mechanism known as geographic smoothing. Neither the f - 5 / 3 wind power fluctuation spectrum nor the mechanism of geographic smoothing are understood. In this work, we explain the wind power fluctuation spectrum from the turbine through grid scales. The f - 5 / 3 wind power fluctuation spectrum results from the largest length scales of atmospheric turbulence of order 200 km influencing the small scales where individual turbines operate. This long-range influence spatially couples geographically distributed wind farms and synchronizes farm outputs over a range of frequencies and decreases with increasing inter-farm distance. Consequently, aggregate grid-scale power fluctuations remain correlated, and are smoothed until they reach a limiting f - 7 / 3 spectrum. This work was funded by the Collective Interactions Unit, OIST Graduate University, Japan.

Aggregation of heteropolyanions in aqueous solutions exhibiting short-range attractions and long-range repulsions

DOE PAGES

Bera, Mrinal K.; Qiao, Baofu; Seifert, Soenke; ...

2015-12-15

Charged colloids and proteins in aqueous solutions interact via short-range attractions and long-range repulsions (SALR) and exhibit complex structural phases. These include homogeneously dispersed monomers, percolated monomers, clusters, and percolated clusters. We report the structural architectures of simple charged systems in the form of spherical, Keggin-type heteropolyanions (HPAs) by small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. Structure factors obtained from the SAXS measurements show that the HPAs interact via SALR. Concentration and temperature dependences of the structure factors for HPAs with –3e (e is the charge of an electron) charge are consistent with a mixture of nonassociated monomersmore » and associated randomly percolated monomers, whereas those for HPAs with –4e and –5e charges exhibit only nonassociated monomers in aqueous solutions. Our experiments show that the increase in magnitude of the charge of the HPAs increases their repulsive interactions and inhibits their aggregation in aqueous solutions. MD simulations were done to reveal the atomistic scale origins of SALR between HPAs. As a result, the short-range attractions result from water or proton-mediated hydrogen bonds between neighboring HPAs, whereas the long-range repulsions are due to the distributions of ions surrounding the HPAs.« less

Families in the Army: Looking Ahead

DTIC Science & Technology

1989-06-01

WRi 0ata FEA14-64) This study considers how aggregate demand for Army family services will change in the future and identifies long-range issues posed...although Army actions and policies could potentially modify that future. Four long-range issues deserve closer study and continued monitoring: (1...important issues those changes pose, and explores their implications for force manage- ment and service delivery policies. It is meant to provide RAND and

Dynamics of Single Chains of Suspended Ferrofluid Particles

NASA Technical Reports Server (NTRS)

Cutillas, S.; Liu, J.

1999-01-01

We present an experimental study of the dynamics of isolated chains made of super-paramagnetic particles under the influence of a magnetic field. The motivation of this work is to understand if the chain fluctuations exist and, if it does, how does the fluctuation affect chain aggregation. We find that single chains strongly fluctuate and that the characteristic frequency of their fluctuations is inversely proportional to the magnetic field strength. The higher the field the lower the characteristic frequency of the chain fluctuations. In the high magnetic field limit, chains behave like rigid rods without any internal motions. In this work, we used ferrofluid particles suspended in water. These particles do not have any intrinsic magnetization. Once a magnetic field is applied, a dipole moment is induced in each particle, proportional to the magnetic field. A dipolar magnetic interaction then occurs between particles. If dipole-dipole magnetic energy is higher than the thermal energy, the result is a structure change inside the dipolar fluid. The ratio of these two energies is expressed by a coupling constant lambda as: lambda = (pi(a(exp 3))(chi(exp 2))(mu(sub 0))(H(sub 0))(exp 2))/18kT Where a is the particle radius, mu(sub 0) is the vacuum magnetic permeability, H(sub 0) the applied magnetic field, k the Boltzmann constant and T the absolute temperature. If lambda > 1, magnetic particles form chains along the field direction. The lateral coalescence of several chains may form bigger aggregates especially if the particle volume fraction is high. While many studies and applications deal with the rheological properties and the structural changes of these dipolar fluids, this work focuses on the understanding of the chain dynamics. In order to probe the chain dynamics, we used dynamic light scattering (DLS) in self-beating mode as our experimental technique. The experimental geometry is such that the scattering plane is perpendicular to the magnetic field. Therefore, only motions in this plane are probed. A very dilute sample of a ferrofluid emulsion with a particle volume fraction of 10(exp -5) is used in this experiment. We chose such a low volume fraction to avoid multiple light scattering as well as lateral chain-chain aggregation. DLS measures the dynamic structure factor S(q,t) of the sample (q is the scattering wave vector, t is the time). In the absence of the magnetic field, identical particles of ferrofluid droplets are randomly distributed and S(q,t) reduces to exp(-q(exp 2)2D(sub 0)t). D(sub 0)=(kT/(6(pi)(eta)(a)) is the diffusion coefficient of Brownian particles (where Xi = (6(pi)(eta)(a)) is the Stokes frictional coefficient of a spherical particle in a fluid of viscosity eta). If interactions or polydispersity can not be ignored, an effective diffusion coefficient is introduced. Formally, D(sub eff) is defined as: D(sub eff) = - q(exp -2) partial derivative of (ln(S(q,t)) with respect to time, as t goes to 0. D(sub eff) reduces to D(sub 0) if no interactions and only a few particles size are present. Therefore, we can use DLS to measure particle size. The particle radius was found to be a=0.23 mu m with 7% of polydispersity. In this case, if we vary the scattering angle theta (and so q) we do not have any change in the measured diffusion coefficient: it is q-independent. When a magnetic field is applied, particles aggregate into chains if lambda > 1. We first studied the kinetics of the chain formation when lambda = 406. At a fixed scattering angle, we measured diffusion coefficient D(sub eff) as a function of time. Experimentally, we find that D(sub eff) decreases monotonously with time. Physically, this means that chains are becoming longer and longer. Since we are only sensitive to motions in the scattering plane and since chains have their main axis perpendicular to this plane, the measured diffusion coefficient is the trans-verse diffusion coefficient. We can relate D(sub eff) to the mean number of particles per chain N(t) at a given time and to the diffusion coefficient of an isolated particle D(sub 0) as D(sub eff)=f(N(t))D(sub 0). Since f(N) is known from other recent work, N can be expressed as a function of the time. We found a square root dependency: N(t) proportional to the square root of t. As expected for very low volume fraction, this behavior is characteristic of a diffusion-limited aggregation as suggested by several authors and by our previous work. In this study, we focus on the dependence of the effective diffusion coefficient on the scattering angle and the magnetic field strength. After the magnetic field is applied (lambda = 406) for a long time, typically 6 hours, kinetics of chain formation becomes very slow. Chain size does not vary much over the next hour period. Thus, we can perform different interesting experiments. First, at a fixed magnetic field, we measure the effective diffusion coefficient as a function of the scattering angle (from 5 to 130 deg). Our results show that the measured diffusion coefficient increases linearly with the scattering angle: D(sub eff) proportional to q. If we do the same experiment for different lambda values, D(sub eff) depends on lambda as D(sub eff) proportional to lambda(exp -1/2). We also find for different lambda values that the same asymptotic D(sub eff) value is obtained when q approaches zero. The angle dependency of D(sub eff) suggests that an additional motion exists besides chain drifting. Chain size is constant during experiment, which was verified by measuring the same diffusion coefficient at the beginning and at the end of the angle switching. If chains are rigid, D(sub eff) is independent of q. Therefore, we found that D(sub eff) not only measures the motion of the entire chain but also its internal fluctuations. These internal motions are the fluctuations of the particles in the chain. To understand the q dependency of D(sub eff), let us look at the probing length used. In our study, the characteristic length scale probed is l=2pi/q which is in the range of 0.9

Diffuse x-ray scattering and transmission electron microscopy study of defects in antimony-implanted silicon

NASA Astrophysics Data System (ADS)

Takamura, Y.; Marshall, A. F.; Mehta, A.; Arthur, J.; Griffin, P. B.; Plummer, J. D.; Patel, J. R.

2004-04-01

Ion implantation followed by laser annealing has been used to create supersaturated and electrically active concentrations of antimony in silicon. Upon subsequent thermal annealing, however, these metastable dopants deactivate towards the equilibrium solubility limit. In this work, the formation of inactive antimony structures has been studied with grazing incidence diffuse x-ray scattering, and transmission electron microscopy, and the results are correlated to previous high-resolution x-ray diffraction data. We find that at a concentration of 6.0×1020 cm-3, small, incoherent clusters of radius 3-4 Å form during annealing at 900 °C. At a higher concentration of 2.2×1021 cm-3, deactivation at 600 °C occurs through the formation of small, antimony aggregates and antimony precipitates. The size of these precipitates from diffuse x-ray scattering is roughly 15 Å in radius for anneal times from 15 to 180 seconds. This value is consistent with the features observed in high-resolution and mass contrast transmission electron microscopy images. The coherent nature of the aggregates and precipitates causes the expansion of the surrounding silicon matrix as the deactivation progresses. In addition, the sensitivity of the diffuse x-ray scattering technique has allowed us to detect the presence of small clusters of radius ˜2 Å in unprocessed Czochralski silicon wafers. These defects are not observed in floating zone silicon wafers, and are tentatively attributed to thermal donors.

Fractals and foods.

PubMed

Peleg, M

1993-01-01

Fractal geometry and related concepts have had only a very minor impact on food research. The very few reported food applications deal mainly with the characterization of the contours of agglomerated instant coffee particles, the surface morphology of treated starch particles, the microstructure of casein gels viewed as a product limited diffusion aggregation, and the jagged mechanical signatures of crunchy dry foods. Fractal geometry describes objects having morphological features that are scale invariant. A demonstration of the self-similarity of fractal objects can be found in the familiar morphology of cauliflower and broccoli, both foods. Processes regulated by nonlinear dynamics can exhibit a chaotic behavior that has fractal characteristics. Examples are mixing of viscous fluids, turbulence, crystallization, agglomeration, diffusion, and possibly food spoilage.

Unveiling One-Dimensional Supramolecular Structures Formed through π-π Stacking of Phenothiazines by Differential Pulse Voltammetry.

PubMed

Carvalho, Fernando R; Zampieri, Eduardo H; Caetano, Wilker; Silva, Rafael

2017-05-19

Organic-based nanomaterials can be self-assembled by strong and directional intermolecular forces such as π-π interactions. Experimental information about the stability, size, and geometry of the formed structures is very limited for species that easily aggregate, even at very low concentrations. Differential pulse voltammetry (DPV) can unveil the formation, growth, and also the stability window of ordered, one-dimensional, lamellar self-aggregates formed by supramolecular π stacking of phenothiazines at micromolar (10 -6  mol L -1 ) concentrations. The self-diffusion features of the species at different concentrations are determined by DPV and used to probe the π staking process through the concept of the frictional resistance. It is observed that toluidine blue and methylene blue start to self-aggregate around 9 μmol L -1 , and that the self-aggregation process occurs by one-dimensional growth as the concentration of the phenothiazines is increased up to around 170 μmol L -1 for toluidine blue and 200 μmol L -1 for methylene blue. At higher concentrations, the aggregation process leads to structures with lower anisometry. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides

DOE Office of Scientific and Technical Information (OSTI.GOV)

None, None

Synthetic oligopeptides containing π-conjugated cores self-assemble novel materials with attractive electronic and photophysical properties. All-atom, explicit solvent molecular dynamics simulations of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp peptides were used to parameterize an implicit solvent model to simulate early-stage self-assembly. Under low-pH conditions, peptides assemble into β-sheet-like stacks with strongly favorable monomer association free energies of ΔF ≈ -25kBT. Aggregation at high-pH produces disordered aggregates destabilized by Coulombic repulsion between negatively charged Asp termini (ΔF ≈ -5kBT). In simulations of hundreds of monomers over 70 ns we observe the spontaneous formation of up to undecameric aggregates under low-pH conditions. Modeling assembly as a continuous-time Markovmore » process, we infer transition rates between different aggregate sizes and microsecond relaxation times for early-stage assembly. Our data suggests a hierarchical model of assembly in which peptides coalesce into small clusters over tens of nanoseconds followed by structural ripening and diffusion limited aggregation on longer time scales. This work provides new molecular-level understanding of early-stage assembly, and a means to study the impact of peptide sequence and aromatic core chemistry upon the thermodynamics, assembly kinetics, and morphology of the supramolecular aggregates.« less

Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides

DOE PAGES

None, None

2016-03-22

Synthetic oligopeptides containing π-conjugated cores self-assemble novel materials with attractive electronic and photophysical properties. All-atom, explicit solvent molecular dynamics simulations of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp peptides were used to parameterize an implicit solvent model to simulate early-stage self-assembly. Under low-pH conditions, peptides assemble into β-sheet-like stacks with strongly favorable monomer association free energies of ΔF ≈ -25kBT. Aggregation at high-pH produces disordered aggregates destabilized by Coulombic repulsion between negatively charged Asp termini (ΔF ≈ -5kBT). In simulations of hundreds of monomers over 70 ns we observe the spontaneous formation of up to undecameric aggregates under low-pH conditions. Modeling assembly as a continuous-time Markovmore » process, we infer transition rates between different aggregate sizes and microsecond relaxation times for early-stage assembly. Our data suggests a hierarchical model of assembly in which peptides coalesce into small clusters over tens of nanoseconds followed by structural ripening and diffusion limited aggregation on longer time scales. This work provides new molecular-level understanding of early-stage assembly, and a means to study the impact of peptide sequence and aromatic core chemistry upon the thermodynamics, assembly kinetics, and morphology of the supramolecular aggregates.« less

Modeling anoxic aggregates in the ocean - implications for nitrogen, sulfur and trace metal cycling

NASA Astrophysics Data System (ADS)

Bianchi, D.; Weber, T. S.; Deutsch, C.

2016-02-01

Anoxic conditions are uncommon in the open ocean, and mostly confined to the cores of oxygen minimum zones (OMZs). When oxygen runs out, a suite of alternative electron acceptors are used, leading to denitrification and, rarely in open waters, sulfate reduction. Anoxic conditions have been shown to develop inside millimeter-scale organic particles and aggregates, establishing microscale gradients that could sustain diverse microbial communities along a sequence of redox niches. We develop a model of the biogeochemistry of anoxic aggregates that includes aerobic and anaerobic reactions in a diffusion-limited environment, and present analytical and numerical solutions for the conditions that allow denitrification and sulfate reduction inside aggregates. The model is applied to realistic size spectra of particles sinking through the water column, and used to estimate the potential for particle-bound denitrification and sulfate reduction in the global ocean. We show that anoxia inside aggregates may be common throughout low oxygen waters, extending the niche of denitrifying metabolisms beyond fully anoxic zones. In the OMZ cores, aggregates can sustain pockets of sulfate reduction in otherwise non-sulfidic waters, depending on ambient nitrate concentrations, particle respiration rates, and other factors. We further discuss the implications for nitrogen, sulfur and trace metal cycling in the ocean.

Full three-dimensional morphology evolution of amorphous thin films for atomic layer deposition

NASA Astrophysics Data System (ADS)

Jin, Lingpeng; Li, Yawei; Hu, Zhigao; Chu, Junhao

2018-04-01

We introduce a Monte Carlo model based on random deposition and diffusion limited aggregation in order to study the morphological evolution of deposition of nanofilm, which is difficult to carry out by the experimental methods. The instantaneous evolution of morphology and the corresponding parameters are observed when employing a novel perspective, modeling the aggregation of nanoscale units. Despite simplifying the chemical details, the simulation results qualitatively describe experiments with bulky precursors, and the strong dependence of growth rate on steric hindrance is obtained. Moreover, the well know behavior that the delay before steady growth is accurately predicted and analyzed based solely on modeling. Through this work, the great influence of steric hindrance on the initial stage of ALD is described.

The role of intra-NAPL diffusion on mass transfer from MGP residuals

NASA Astrophysics Data System (ADS)

Shafieiyoun, Saeid; Thomson, Neil R.

2018-06-01

An experimental and computational study was performed to investigate the role of multi-component intra-NAPL diffusion on NAPL-water mass transfer. Molecular weight and the NAPL component concentrations were determined to be the most important parameters affecting intra-NAPL diffusion coefficients. Four NAPLs with different viscosities but the same quantified mass were simulated. For a spherical NAPL body, a combination of NAPL properties and interphase mass transfer rate can result in internal diffusion limitations. When the main intra-NAPL diffusion coefficients are in the range of self-diffusion coefficients (10-5 to 10-6 cm2/s), dissolution is not limited by internal diffusion except for high mass transfer rate coefficients (>180 cm/day). For a complex and relatively high viscous NAPL (>50 g/(cm s)), smaller intra-NAPL diffusion coefficients (<10-8) are expected and even low mass transfer rate coefficients ( 6 cm/day) can result in diffusion-limited dissolution.

Shape characteristics of equilibrium and non-equilibrium fractal clusters.

PubMed

Mansfield, Marc L; Douglas, Jack F

2013-07-28

It is often difficult in practice to discriminate between equilibrium and non-equilibrium nanoparticle or colloidal-particle clusters that form through aggregation in gas or solution phases. Scattering studies often permit the determination of an apparent fractal dimension, but both equilibrium and non-equilibrium clusters in three dimensions frequently have fractal dimensions near 2, so that it is often not possible to discriminate on the basis of this geometrical property. A survey of the anisotropy of a wide variety of polymeric structures (linear and ring random and self-avoiding random walks, percolation clusters, lattice animals, diffusion-limited aggregates, and Eden clusters) based on the principal components of both the radius of gyration and electric polarizability tensor indicates, perhaps counter-intuitively, that self-similar equilibrium clusters tend to be intrinsically anisotropic at all sizes, while non-equilibrium processes such as diffusion-limited aggregation or Eden growth tend to be isotropic in the large-mass limit, providing a potential means of discriminating these clusters experimentally if anisotropy could be determined along with the fractal dimension. Equilibrium polymer structures, such as flexible polymer chains, are normally self-similar due to the existence of only a single relevant length scale, and are thus anisotropic at all length scales, while non-equilibrium polymer structures that grow irreversibly in time eventually become isotropic if there is no difference in the average growth rates in different directions. There is apparently no proof of these general trends and little theoretical insight into what controls the universal anisotropy in equilibrium polymer structures of various kinds. This is an obvious topic of theoretical investigation, as well as a matter of practical interest. To address this general problem, we consider two experimentally accessible ratios, one between the hydrodynamic and gyration radii, the other between the viscosity and hydrodynamic radii, as potential measures of shape anisotropy. We also find a strong correlation between anisotropy and effective fractal dimension. These observations should provide new practical methods for quantifying the nature of particle clustering in diverse contexts.

Optimal approximation of harmonic growth clusters by orthogonal polynomials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Teodorescu, Razvan

2008-01-01

Interface dynamics in two-dimensional systems with a maximal number of conservation laws gives an accurate theoreticaI model for many physical processes, from the hydrodynamics of immiscible, viscous flows (zero surface-tension limit of Hele-Shaw flows), to the granular dynamics of hard spheres, and even diffusion-limited aggregation. Although a complete solution for the continuum case exists, efficient approximations of the boundary evolution are very useful due to their practical applications. In this article, the approximation scheme based on orthogonal polynomials with a deformed Gaussian kernel is discussed, as well as relations to potential theory.

Self-learning kinetic Monte Carlo simulations of diffusion in ferromagnetic α-Fe-Si alloys

NASA Astrophysics Data System (ADS)

Nandipati, Giridhar; Jiang, Xiujuan; Vemuri, Rama S.; Mathaudhu, Suveen; Rohatgi, Aashish

2018-01-01

Diffusion of Si atom and vacancy in the A2-phase of α-Fe-Si alloys in the ferromagnetic state, with and without magnetic order and in various temperature ranges, are studied using AKSOME, an on-lattice self-learning KMC code. Diffusion of the Si atom and the vacancy are studied in the dilute limit and up to 12 at.% Si, respectively, in the temperature range 350-700 K. Local Si neighborhood dependent activation energies for vacancy hops were calculated on-the-fly using a broken-bond model based on pairwise interaction. The migration barrier and prefactor for the Si diffusion in the dilute limit were obtained and found to agree with published data within the limits of uncertainty. Simulations results show that the prefactor and the migration barrier for the Si diffusion are approximately an order of magnitude higher, and a tenth of an electron-volt higher, respectively, in the magnetic disordered state than in the fully ordered state. However, the net result is that magnetic disorder does not have a significant effect on Si diffusivity within the range of parameters studied in this work. Nevertheless, with increasing temperature, the magnetic disorder increases and its effect on the Si diffusivity also increases. In the case of vacancy diffusion, with increasing Si concentration, its diffusion prefactor decreases while the migration barrier more or less remained constant and the effect of magnetic disorder increases with Si concentration. Important vacancy-Si/Fe atom exchange processes and their activation barriers were identified, and the effect of energetics on ordered phase formation in Fe-Si alloys are discussed.

Microfabricated valveless devices for thermal bioreactions based on diffusion-limited evaporation.

PubMed

Wang, Fang; Yang, Ming; Burns, Mark A

2008-01-01

Microfluidic devices that reduce evaporative loss during thermal bioreactions such as PCR without microvalves have been developed by relying on the principle of diffusion-limited evaporation. Both theoretical and experimental results demonstrate that the sample evaporative loss can be reduced by more than 20 times using long narrow diffusion channels on both sides of the reaction region. In order to further suppress the evaporation, the driving force for liquid evaporation is reduced by two additional techniques: decreasing the interfacial temperature using thermal isolation and reducing the vapor concentration gradient by replenishing water vapor in the diffusion channels. Both thermal isolation and vapor replenishment techniques can limit the sample evaporative loss to approximately 1% of the reaction content.

Vertically migrating swimmers generate aggregation-scale eddies in a stratified column.

PubMed

Houghton, Isabel A; Koseff, Jeffrey R; Monismith, Stephen G; Dabiri, John O

2018-04-01

Biologically generated turbulence has been proposed as an important contributor to nutrient transport and ocean mixing 1-3 . However, to produce non-negligible transport and mixing, such turbulence must produce eddies at scales comparable to the length scales of stratification in the ocean. It has previously been argued that biologically generated turbulence is limited to the scale of the individual animals involved 4 , which would make turbulence created by highly abundant centimetre-scale zooplankton such as krill irrelevant to ocean mixing. Their small size notwithstanding, zooplankton form dense aggregations tens of metres in vertical extent as they undergo diurnal vertical migration over hundreds of metres 3,5,6 . This behaviour potentially introduces additional length scales-such as the scale of the aggregation-that are of relevance to animal interactions with the surrounding water column. Here we show that the collective vertical migration of centimetre-scale swimmers-as represented by the brine shrimp Artemia salina-generates aggregation-scale eddies that mix a stable density stratification, resulting in an effective turbulent diffusivity up to three orders of magnitude larger than the molecular diffusivity of salt. These observed large-scale mixing eddies are the result of flow in the wakes of the individual organisms coalescing to form a large-scale downward jet during upward swimming, even in the presence of a strong density stratification relative to typical values observed in the ocean. The results illustrate the potential for marine zooplankton to considerably alter the physical and biogeochemical structure of the water column, with potentially widespread effects owing to their high abundance in climatically important regions of the ocean 7 .

Flux-limited diffusion in a scattering medium. [such as accretion-disk coronae

NASA Technical Reports Server (NTRS)

Melia, Fulvio; Zylstra, Gregory J.

1991-01-01

A diffusion equation (FDT) is presented with a coefficient that reduces to the appropriate limiting form in the streaming and near thermodynamic limits for a moving fluid in which the dominant source of opacity is Thomson scattering. The present results are compared to those obtained with the corresponding equations for an absorptive medium. It is found that FDT for a scattering medium is accurate to better than less than about 17 percent over the range of optical depths of tau in the range of about 0 to 3.

Biexponential characterization of prostate tissue water diffusion decay curves over an extended b-factor range.

PubMed

Mulkern, Robert V; Barnes, Agnieszka Szot; Haker, Steven J; Hung, Yin P; Rybicki, Frank J; Maier, Stephan E; Tempany, Clare M C

2006-06-01

Detailed measurements of water diffusion within the prostate over an extended b-factor range were performed to assess whether the standard assumption of monoexponential signal decay is appropriate in this organ. From nine men undergoing prostate MR staging examinations at 1.5 T, a single 10-mm-thick axial slice was scanned with a line scan diffusion imaging sequence in which 14 equally spaced b factors from 5 to 3,500 s/mm(2) were sampled along three orthogonal diffusion sensitization directions in 6 min. Due to the combination of long scan time and limited volume coverage associated with the multi-b-factor, multidirectional sampling, the slice was chosen online from the available T2-weighted axial images with the specific goal of enabling the sampling of presumed noncancerous regions of interest (ROIs) within the central gland (CG) and peripheral zone (PZ). Histology from prescan biopsy (n=9) and postsurgical resection (n=4) was subsequently employed to help confirm that the ROIs sampled were noncancerous. The CG ROIs were characterized from the T2-weighted images as primarily mixtures of glandular and stromal benign prostatic hyperplasia, which is prevalent in this population. The water signal decays with b factor from all ROIs were clearly non-monoexponential and better served with bi- vs. monoexponential fits, as tested using chi(2)-based F test analyses. Fits to biexponential decay functions yielded intersubject fast diffusion component fractions in the order of 0.73+/-0.08 for both CG and PZ ROIs, fast diffusion coefficients of 2.68+/-0.39 and 2.52+/-0.38 microm(2)/ms and slow diffusion coefficients of 0.44+/-0.16 and 0.23+/-0.16 um(2)/ms for CG and PZ ROIs, respectively. The difference between the slow diffusion coefficients within CG and PZ was statistically significant as assessed with a Mann-Whitney nonparametric test (P<.05). We conclude that a monoexponential model for water diffusion decay in prostate tissue is inadequate when a large range of b factors is sampled and that biexponential analyses are better suited for characterizing prostate diffusion decay curves.

Quantification of Sheet Resistance in Boron-Diffused Silicon Using Micro-Photoluminescence Spectroscopy at Room Temperature

DOE PAGES

Nguyen, Hieu T.; Johnston, Steve; Paduthol, Appu; ...

2017-09-01

A micro-photoluminescence-based technique is presented, to quantify and map sheet resistances of boron-diffused layers in silicon solar cell precursors with micron-scale spatial resolution at room temperature. The technique utilizes bandgap narrowing effects in the heavily-doped layers, yielding a broader photoluminescence spectrum at the long-wavelength side compared to the spectrum emitted from lightly doped silicon. By choosing an appropriate spectral range as a metric to assess the doping density, the impacts of photon reabsorption on the analysis can be avoided; thus, an accurate characterization of the sheet resistance can be made. This metric is demonstrated to be better representative of themore » sheet resistance than the surface doping density or the total dopant concentration of the diffused layer. The technique is applied to quantify sheet resistances of 12-um-wide diffused fingers in interdigitated back-contact solar cell precursors and large diffused areas. The results are confirmed by both 4-point probe and time-of-flight secondary-ion mass spectrometry measurements. Lastly, the practical limitations associated with extending the proposed technique into an imaging mode are presented and explained.« less

Quantification of Sheet Resistance in Boron-Diffused Silicon Using Micro-Photoluminescence Spectroscopy at Room Temperature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, Hieu T.; Johnston, Steve; Paduthol, Appu

A micro-photoluminescence-based technique is presented, to quantify and map sheet resistances of boron-diffused layers in silicon solar cell precursors with micron-scale spatial resolution at room temperature. The technique utilizes bandgap narrowing effects in the heavily-doped layers, yielding a broader photoluminescence spectrum at the long-wavelength side compared to the spectrum emitted from lightly doped silicon. By choosing an appropriate spectral range as a metric to assess the doping density, the impacts of photon reabsorption on the analysis can be avoided; thus, an accurate characterization of the sheet resistance can be made. This metric is demonstrated to be better representative of themore » sheet resistance than the surface doping density or the total dopant concentration of the diffused layer. The technique is applied to quantify sheet resistances of 12-um-wide diffused fingers in interdigitated back-contact solar cell precursors and large diffused areas. The results are confirmed by both 4-point probe and time-of-flight secondary-ion mass spectrometry measurements. Lastly, the practical limitations associated with extending the proposed technique into an imaging mode are presented and explained.« less

Reactive Gas transport in soil: Kinetics versus Local Equilibrium Approach

NASA Astrophysics Data System (ADS)

Geistlinger, Helmut; Jia, Ruijan

2010-05-01

Gas transport through the unsaturated soil zone was studied using an analytical solution of the gas transport model that is mathematically equivalent to the Two-Region model. The gas transport model includes diffusive and convective gas fluxes, interphase mass transfer between the gas and water phase, and biodegradation. The influence of non-equilibrium phenomena, spatially variable initial conditions, and transient boundary conditions are studied. The objective of this paper is to compare the kinetic approach for interphase mass transfer with the standard local equilibrium approach and to find conditions and time-scales under which the local equilibrium approach is justified. The time-scale of investigation was limited to the day-scale, because this is the relevant scale for understanding gas emission from the soil zone with transient water saturation. For the first time a generalized mass transfer coefficient is proposed that justifies the often used steady-state Thin-Film mass transfer coefficient for small and medium water-saturated aggregates of about 10 mm. The main conclusion from this study is that non-equilibrium mass transfer depends strongly on the temporal and small-scale spatial distribution of water within the unsaturated soil zone. For regions with low water saturation and small water-saturated aggregates (radius about 1 mm) the local equilibrium approach can be used as a first approximation for diffusive gas transport. For higher water saturation and medium radii of water-saturated aggregates (radius about 10 mm) and for convective gas transport, the non-equilibrium effect becomes more and more important if the hydraulic residence time and the Damköhler number decrease. Relative errors can range up to 100% and more. While for medium radii the local equilibrium approach describes the main features both of the spatial concentration profile and the time-dependence of the emission rate, it fails completely for larger aggregates (radius about 100 mm). From the comparative study of relevant scenarios with and without biodegradation it can be concluded that, under realistic field conditions, biodegradation within the immobile water phase is often mass-transfer limited and the local equilibrium approach assuming instantaneous mass transfer becomes rather questionable. References Geistlinger, H., Ruiyan Jia, D. Eisermann, and C.-F. Stange (2008): Spatial and temporal variability of dissolved nitrous oxide in near-surface groundwater and bubble-mediated mass transfer to the unsaturated zone, J. Plant Nutrition and Soil Science, in press. Geistlinger, H. (2009) Vapor transport in soil: concepts and mathematical description. In: Eds.: S. Saponari, E. Sezenna, and L. Bonoma, Vapor emission to outdoor air and enclosed spaces for human health risk assessment: Site characterization, monitoring, and modeling. Nova Science Publisher. Milano. Accepted for publication.

On the theory of Lorentz gases with long range interactions

NASA Astrophysics Data System (ADS)

Nota, Alessia; Simonella, Sergio; Velázquez, Juan J. L.

We construct and study the stochastic force field generated by a Poisson distribution of sources at finite density, x1,x2,…, in ℝ3 each of them yielding a long range potential QiΦ(x - xi) with possibly different charges Qi ∈ ℝ. The potential Φ is assumed to behave typically as |x|-s for large |x|, with s > 1/2. We will denote the resulting random field as “generalized Holtsmark field”. We then consider the dynamics of one tagged particle in such random force fields, in several scaling limits where the mean free path is much larger than the average distance between the scatterers. We estimate the diffusive time scale and identify conditions for the vanishing of correlations. These results are used to obtain appropriate kinetic descriptions in terms of a linear Boltzmann or Landau evolution equation depending on the specific choices of the interaction potential.

An unusual slowdown of fast diffusion in a room temperature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chathoth,; Mamontov, Eugene; Fulvio, Pasquale F

2013-01-01

Using quasielastic neutron scattering in the temperature range from 290 to 350 K, we show that the diffusive motions in a room temperature ionic liquid [H2NC(dma)2][BETI] become faster for a fraction of cations when the liquid is confined in a mesoporous carbon. This applies to both the localized and long-range translational diffusive motions of the highly mobile cations, although the former exhibit an unusual trend of slowing-down as the temperature is increased, until the localized diffusivity is reduced to the bulk ionic liquid value at a temperature of 350 K.

Heavy metal removal capacity of individual components of permeable reactive concrete

NASA Astrophysics Data System (ADS)

Holmes, Ryan R.; Hart, Megan L.; Kevern, John T.

2017-01-01

Permeable reactive barriers (PRBs) are a well-known technique for groundwater remediation using industrialized reactive media such as zero-valent iron and activated carbon. Permeable reactive concrete (PRC) is an alternative reactive medium composed of relatively inexpensive materials such as cement and aggregate. A variety of multimodal, simultaneous processes drive remediation of metals from contaminated groundwater within PRC systems due to the complex heterogeneous matrix formed during cement hydration. This research investigated the influence coarse aggregate, portland cement, fly ash, and various combinations had on the removal of lead, cadmium, and zinc in solution. Absorption, adsorption, precipitation, co-precipitation, and internal diffusion of the metals are common mechanisms of removal in the hydrated cement matrix and independent of the aggregate. Local aggregates can be used as the permeable structure also possessing high metal removal capabilities, however calcareous sources of aggregate are preferred due to improved removal with low leachability. Individual adsorption isotherms were linear or curvilinear up, indicating a preferred removal process. For PRC samples, metal saturation was not reached over the range of concentrations tested. Results were then used to compare removal against activated carbon and aggregate-based PRBs by estimating material costs for the remediation of an example heavy metal contaminated Superfund site located in the Midwestern United States, Joplin, Missouri.

Preparation and SERS performance of Au NP/paper strips based on inkjet printing and seed mediated growth: The effect of silver ions

NASA Astrophysics Data System (ADS)

Weng, Guojun; Yang, Yue; Zhao, Jing; Zhu, Jian; Li, Jianjun; Zhao, Junwu

2018-04-01

Surface-enhanced Raman scattering (SERS) has been widely used in biomedical sensing with the advantages of high sensitivity and label-free. However, the fabrication of SERS substrates with good Raman activity, reproducibility, and low cost is still under development in practical applications. This paper presents a practicable method for fabricating Au NP/paper strips by using inkjet printing and seed mediated growth. Small gold seed synthesized by borohydride reduction was used as ink and printed on the filter paper. The printed gold seed grew in situ in the growth solution and formed the gold nanoparticle (Au NP)/paper strips. The fabricated paper strip was characterized by diffuse reflectance spectroscopy and scanning electron microscopy (SEM). The diffuse reflectance spectra indicated that the Au NP/paper strips had two local surface plasmon resonance (LSPR) peaks: the short one at around 540 nm and the long one located in the range of 640-840 nm. And the long LSPR peak firstly shifted to red then to blue with the increased concentrations of silver ions in growth solution. From the SEM images, the shape of grown Au NPs was diverse, including sphere, rod, ellipsoid, dimer, trimer, and big aggregates. We thought the short peak came from the LSPR of nanospheres and the transvers LSPR of rod and ellipsoid like particles, while the long peak mainly came from the plasmonic coupling of dimer along the inter-particle axis. The obtained Au NP/paper strip with the long peak located around 650 nm had the highest SERS activity, which could be attributed to the plasmon resonance induced local field enhancement and nanogap effect. Also, the SERS performance results indicated the printed SERS strips exhibited satisfied uniformity and stability, demonstrating the potential of Au NP/paper strip in real-world applications.

Semiochemical-mediated flight strategies of two invasive elm bark beetles: a potential factor in competitive displacement.

PubMed

Lee, Jana C; Hamud, Shakeeb M; Negrón, José F; Witcosky, Jeffrey J; Seybold, Steven J

2010-04-01

A seven-state survey showed that the recently detected invasive Asian banded elm bark beetle, Scolytus schevyrewi Semenov, was abundant in areas of Colorado and Wyoming, whereas the long-established European elm bark beetle, S. multistriatus (Marsham), was not as abundant. In one of a series of studies to evaluate whether S. schevyrewi is competitively displacing S. multistriatus in their North American zone of sympatry, we characterized long-range flight responses infested or uninfested to small cut logs of American, Chinese, and Siberian elm, Ulmus americana, U. parvifolia, and U. pumila. Trials were conducted in Colorado and Wyoming to test the flight response of S. schevyrewi; in California to test the response of S. multistriatus; and in Nevada to test the responses of both species simultaneously. Studies with S. schevyrewi showed that males and females aggregated toward Ulmus spp. host volatiles but provided no evidence of a putative aggregation pheromone during the 0- to 48- or 48- to 96-h period of infestation. In contrast, S. multistriatus was attracted to U. pumila over unbaited controls, more to U. pumila infested with conspecific females than without, and more during the 48- to 96- versus 0- to 48-h period of infestation. This confirmed that male and female S. multistriatus aggregated toward host volatiles and that females produced an aggregation pheromone. In a cross-attraction study, S. schevyrewi displayed neither flight preference nor interruption to U. pumila infested with conspecifics, heterospecifics, or a mix of both species. Response of S. multistriatus was too low to draw conclusions. Although S. multistriatus aggregates moderately to host volatiles and strongly to female-derived pheromones emitted after a few days, S. multistriatus may have a relative disadvantage by selecting elm hosts more slowly than S. schevyrewi, which aggregates very strongly to host volatiles. The differential long-range host location strategy may be one factor in a chain of behavioral events that leads to advantageous host colonization and development by S. schevyrewi.

Rate-limiting step analysis of the microbial desulfurization of dibenzothiophene in a model oil system

PubMed Central

Abin-Fuentes, Andres; Leung, James C.; Mohamed, Magdy El-Said; Wang, Daniel IC; Prather, Kristala LJ

2014-01-01

A mechanistic analysis of the various mass transport and kinetic steps in the microbial desulfurization of dibenzothiophene (DBT) by Rhodococcus erythropolis IGTS8 in a model biphasic (oil-water), small-scale system was performed. The biocatalyst was distributed into three populations, free cells in the aqueous phase, cell aggregates and oil-adhered cells, and the fraction of cells in each population was measured. The power input per volume (P/V) and the impeller tip speed (vtip) were identified as key operating parameters in determining whether the system is mass transport controlled or kinetically controlled. Oil-water DBT mass transport was found to not be limiting under the conditions tested. Experimental results at both the 100 mL and 4L (bioreactor) scales suggest that agitation leading to P/V greater than 10,000 W/ m3 and/or vtip greater than 0.67 m/s is sufficient to overcome the major mass transport limitation in the system, which was the diffusion of DBT within the biocatalyst aggregates. PMID:24284557

Role of streams in myxobacteria aggregate formation

NASA Astrophysics Data System (ADS)

Kiskowski, Maria A.; Jiang, Yi; Alber, Mark S.

2004-10-01

Cell contact, movement and directionality are important factors in biological development (morphogenesis), and myxobacteria are a model system for studying cell-cell interaction and cell organization preceding differentiation. When starved, thousands of myxobacteria cells align, stream and form aggregates which later develop into round, non-motile spores. Canonically, cell aggregation has been attributed to attractive chemotaxis, a long range interaction, but there is growing evidence that myxobacteria organization depends on contact-mediated cell-cell communication. We present a discrete stochastic model based on contact-mediated signaling that suggests an explanation for the initialization of early aggregates, aggregation dynamics and final aggregate distribution. Our model qualitatively reproduces the unique structures of myxobacteria aggregates and detailed stages which occur during myxobacteria aggregation: first, aggregates initialize in random positions and cells join aggregates by random walk; second, cells redistribute by moving within transient streams connecting aggregates. Streams play a critical role in final aggregate size distribution by redistributing cells among fewer, larger aggregates. The mechanism by which streams redistribute cells depends on aggregate sizes and is enhanced by noise. Our model predicts that with increased internal noise, more streams would form and streams would last longer. Simulation results suggest a series of new experiments.

Phenylbutyrate Up-regulates the DJ-1 Protein and Protects Neurons in Cell Culture and in Animal Models of Parkinson Disease*

PubMed Central

Zhou, Wenbo; Bercury, Kathryn; Cummiskey, Jessica; Luong, Nancy; Lebin, Jacob; Freed, Curt R.

2011-01-01

Parkinson disease is caused by the death of midbrain dopamine neurons from oxidative stress, abnormal protein aggregation, and genetic predisposition. In 2003, Bonifati et al. (23) found that a single amino acid mutation in the DJ-1 protein was associated with early-onset, autosomal recessive Parkinson disease (PARK7). The mutation L166P prevents dimerization that is essential for the antioxidant and gene regulatory activity of the DJ-1 protein. Because low levels of DJ-1 cause Parkinson, we reasoned that overexpression might stop the disease. We found that overexpression of DJ-1 improved tolerance to oxidative stress by selectively up-regulating the rate-limiting step in glutathione synthesis. When we imposed a different metabolic insult, A53T mutant α-synuclein, we found that DJ-1 turned on production of the chaperone protein Hsp-70 without affecting glutathione synthesis. After screening a number of small molecules, we have found that the histone deacetylase inhibitor phenylbutyrate increases DJ-1 expression by 300% in the N27 dopamine cell line and rescues cells from oxidative stress and mutant α-synuclein toxicity. In mice, phenylbutyrate treatment leads to a 260% increase in brain DJ-1 levels and protects dopamine neurons against 1-methyl 4-phenyl 1,2,3,6-tetrahydropyridine (MPTP) toxicity. In a transgenic mouse model of diffuse Lewy body disease, long-term administration of phenylbutyrate reduces α-synuclein aggregation in brain and prevents age-related deterioration in motor and cognitive function. We conclude that drugs that up-regulate DJ-1 gene expression may slow the progression of Parkinson disease by moderating oxidative stress and protein aggregation. PMID:21372141

A novel approach to interpretation of the time-dependent self-diffusion coefficient as a probe of porous media geometry.

PubMed

Loskutov, V V; Sevriugin, V A

2013-05-01

This article presents a new approximation describing fluid diffusion in porous media. Time dependence of the self-diffusion coefficient D(t) in the permeable porous medium is studied based on the assumption that diffusant molecules move randomly. An analytical expression for time dependence of the self-diffusion coefficient was obtained in the following form: D(t)=(D0-D∞)exp(-D0t/λ)+D∞, where D0 is the self-diffusion coefficient of bulk fluid, D∞ is the asymptotic value of the self-diffusion coefficient in the limit of long time values (t→∞), λ is the characteristic parameter of this porous medium with dimensionality of length. Applicability of the solution obtained to the analysis of experimental data is shown. The possibility of passing to short-time and long-time regimes is discussed. Copyright © 2013 Elsevier Inc. All rights reserved.

Nuclear magnetic resonance diffusion pore imaging: Experimental phase detection by double diffusion encoding

NASA Astrophysics Data System (ADS)

Demberg, Kerstin; Laun, Frederik Bernd; Windschuh, Johannes; Umathum, Reiner; Bachert, Peter; Kuder, Tristan Anselm

2017-02-01

Diffusion pore imaging is an extension of diffusion-weighted nuclear magnetic resonance imaging enabling the direct measurement of the shape of arbitrarily formed, closed pores by probing diffusion restrictions using the motion of spin-bearing particles. Examples of such pores comprise cells in biological tissue or oil containing cavities in porous rocks. All pores contained in the measurement volume contribute to one reconstructed image, which reduces the problem of vanishing signal at increasing resolution present in conventional magnetic resonance imaging. It has been previously experimentally demonstrated that pore imaging using a combination of a long and a narrow magnetic field gradient pulse is feasible. In this work, an experimental verification is presented showing that pores can be imaged using short gradient pulses only. Experiments were carried out using hyperpolarized xenon gas in well-defined pores. The phase required for pore image reconstruction was retrieved from double diffusion encoded (DDE) measurements, while the magnitude could either be obtained from DDE signals or classical diffusion measurements with single encoding. The occurring image artifacts caused by restrictions of the gradient system, insufficient diffusion time, and by the phase reconstruction approach were investigated. Employing short gradient pulses only is advantageous compared to the initial long-narrow approach due to a more flexible sequence design when omitting the long gradient and due to faster convergence to the diffusion long-time limit, which may enable application to larger pores.

Leaching assessment of concrete made of recycled coarse aggregate: physical and environmental characterisation of aggregates and hardened concrete.

PubMed

Galvín, A P; Agrela, F; Ayuso, J; Beltrán, M G; Barbudo, A

2014-09-01

Each year, millions of tonnes of waste are generated worldwide, partially through the construction and demolition of buildings. Recycling the resulting waste could reduce the amount of materials that need to be manufactured. Accordingly, the present work has analysed the potential reuse of construction waste in concrete manufacturing by replacing the natural aggregate with recycled concrete coarse aggregate. However, incorporating alternative materials in concrete manufacturing may increase the pollutant potential of the product, presenting an environmental risk via ground water contamination. The present work has tested two types of concrete batches that were manufactured with different replacement percentages. The experimental procedure analyses not only the effect of the portion of recycled aggregate on the physical properties of concrete but also on the leaching behaviour as indicative of the contamination degree. Thus, parameters such as slump, density, porosity and absorption of hardened concrete, were studied. Leaching behaviour was evaluated based on the availability test performed to three aggregates (raw materials of the concrete batches) and on the diffusion test performed to all concrete. From an environmental point of view, the question of whether the cumulative amount of heavy metals that are released by diffusion reaches the availability threshold was answered. The analysis of concentration levels allowed the establishment of different groups of metals according to the observed behaviour, the analysis of the role of pH and the identification of the main release mechanisms. Finally, through a statistical analysis, physical parameters and diffusion data were interrelated. It allowed estimating the relevance of porosity, density and absorption of hardened concrete on diffusion release of the metals in study. Copyright © 2014 Elsevier Ltd. All rights reserved.

Asymmetrical flow field-flow fractionation hyphenated to Orbitrap high resolution mass spectrometry for the determination of (functionalised) aqueous fullerene aggregates.

PubMed

Herrero, P; Bäuerlein, P S; Emke, E; Pocurull, E; de Voogt, P

2014-08-22

In this short communication we report on the technical implementations of coupling an asymmetric flow field-flow fractionation (AF4) instrument to a high resolution mass spectrometer (Orbitrap) using an atmospheric photoionisation interface. This will allow for the first time online identification of different fullerenes in aqueous samples after their aggregates have been fractionated in the FFF channel. Quality parameters such as limits of detection (LODs), limits of quantification (LOQs) or linear range were evaluated and they were in the range of hundreds ng/L for LODs and LOQs and the detector response was linear in the range tested (up to ∼20 μg/L). The low detection and quantification limits make this technique useful for future environmental or ecotoxicology studies in which low concentration levels are expected for fullerenes and common on-line detectors such as UV or MALS do not have enough sensitivity and selectivity. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

The fluid mechanics of thrombus formation

NASA Technical Reports Server (NTRS)

1972-01-01

Experimental data are presented for the growth of thrombi (blood clots) in a stagnation point flow of fresh blood. Thrombus shape, size and structure are shown to depend on local flow conditions. The evolution of a thrombus is described in terms of a physical model that includes platelet diffusion, a platelet aggregation mechanism, and diffusion and convection of the chemical species responsible for aggregation. Diffusion-controlled and convection-controlled regimes are defined by flow parameters and thrombus location, and the characteristic growth pattern in each regime is explained. Quantitative comparisons with an approximate theoretical model are presented, and a more general model is formulated.

Effect of cutoff radius, long range interaction and temperature controller on thermodynamic properties of fluids: Methanol as an example

NASA Astrophysics Data System (ADS)

Obeidat, Abdalla; Jaradat, Adnan; Hamdan, Bushra; Abu-Ghazleh, Hind

2018-04-01

The best spherical cutoff radius, long range interaction and temperature controller were determined using surface tension, density, and diffusion coefficients of van Leeuwen and Smit methanol. A quite good range of cutoff radii from 0.75 to 1.45 nm has been studied on Coulomb cut-off and particle mesh Ewald (PME) long range interaction to determine the best cutoff radius and best long range interaction as well for four sets of temperature: 200, 230, 270 and 300 K. To determine the best temperature controller, the cutoff radius of 1.25 nm was fixed using PME long range interaction on calculating the above properties at low temperature range: 200-300 K.

Morphology and Optical Properties of Black-Carbon Particles Relevant to Engine Emissions

NASA Astrophysics Data System (ADS)

Michelsen, H. A.; Bambha, R.; Dansson, M. A.; Schrader, P. E.

2013-12-01

Black-carbon particles are believed to have a large influence on climate through direct radiative forcing, reduction of surface albedo of snow and ice in the cryosphere, and interaction with clouds. The optical properties and morphology of atmospheric particles containing black carbon are uncertain, and characterization of black carbon resulting from engines emissions is needed. Refractory black-carbon particles found in the atmosphere are often coated with unburned fuel, sulfuric acid, water, ash, and other combustion by-products and atmospheric constituents. Coatings can alter the optical and physical properties of the particles and therefore change their optical properties and cloud interactions. Details of particle morphology and coating state can also have important effects on the interpretation of optical diagnostics. A more complete understanding of how coatings affect extinction, absorption, and incandescence measurements is needed before these techniques can be applied reliably to a wide range of particles. We have investigated the effects of coatings on the optical and physical properties of combustion-generated black-carbon particles using a range of standard particle diagnostics, extinction, and time-resolved laser-induced incandescence (LII) measurements. Particles were generated in a co-flow diffusion flame, extracted, cooled, and coated with oleic acid. The diffusion flame produces highly dendritic soot aggregates with similar properties to those produced in diesel engines, diffusion flames, and most natural combustion processes. A thermodenuder was used to remove the coating. A scanning mobility particle sizer (SMPS) was used to monitor aggregate sizes; a centrifugal particle mass analyzer (CPMA) was used to measure coating mass fractions, and transmission electron microscopy (TEM) was used to characterize particle morphologies. The results demonstrate important differences in optical measurements between coated and uncoated particles.

Target Patterns in Reaction-Diffusion Systems,

DTIC Science & Technology

1981-01-01

Riol. 37 (1974), 225-235. 8. M. H. COHEN AND S. A. ROBERTSON, Wave propagation in the early stages of aggregation of cellular slime molds . J. Theoret...the Zaikin-Zhabotinskii-Winfree reagent, Chem. Educ. 56 (1979), 574. 5. F. ALCANTARA AND M. MONK, Signal propagation during aggregation in the slime ... mold Dit’resteltu n discoideum. J. Gen. Microbiol. 85 (1974). 321-334. 6. M. S. COHEN AND P. S. HAGAN, Diffusion induced morphogenesis in the

Lowering of acoustic droplet vaporization threshold via aggregation

NASA Astrophysics Data System (ADS)

Guo, Shifang; Shi, Aiwei; Xu, Shanshan; Du, Xuan; Wang, Xin; Zong, Yujin; Bouakaz, Ayache; Wan, Mingxi

2017-12-01

Acoustically sensitive emulsion nanodroplets composed of perfluorocarbon have shown great potential for advanced medical diagnosis and therapy but are limited by the required high acoustic droplet vaporization (ADV) threshold for clinical applications. This study investigates the use of an ultrasonic standing wave to lower the ADV threshold while maintaining the generated bubble size in the required size range, ensuring the generation of inertial cavitation and corresponding physical effects. The results showed that disperse nanodroplets were manipulated to form micron-sized aggregations, and the required ADV threshold was significantly lowered, while a similar size range of the microbubbles generated by disperse nanodroplets was maintained. The threshold could be further regulated by adjusting the aggregation size via controlling the concentration of the disperse nanodroplets. Furthermore, the internal pressures in the aggregations with different sizes were calculated to determine their ADV thresholds theoretically, which were shown to be in good agreement with the experimental results.

Effect of molecular structure on the hydration of structurally related antidepressant drugs

NASA Astrophysics Data System (ADS)

Cheema, M. A.; Taboada, P.; Barbosa, S.; Siddiq, M.; Mosquera, V.

Apparent molal volumes and adiabatic compressibilities of aqueous solutions of the amphiphilic cationic antidepressant drugs butriptyline and doxepin hydrochlorides have been determined from density and ultrasound velocity measurements in the temperature range 20-50°C. Critical concentrations for aggregation of these drugs were obtained from ultrasound velocity measurements. Negative deviations from the Debye-Hückel limiting law of the apparent molal volume were obtained from both drugs in all temperature ranges, except for doxepin at 50°C, which provides evidence of no pre-association at concentrations below the critical concentration. Apparent molal adiabatic compressibilities of the aggregates formed by these drugs were typical of those corresponding for an aggregate formed by a stacking process.

Zigzag antiferromagnetic ground state with anisotropic correlation lengths in the quasi-two-dimensional honeycomb lattice compound N a2C o2Te O6

NASA Astrophysics Data System (ADS)

Bera, A. K.; Yusuf, S. M.; Kumar, Amit; Ritter, C.

2017-03-01

The crystal structure, magnetic ground state, and the temperature-dependent microscopic spin-spin correlations of the frustrated honeycomb lattice antiferromagnet N a2C o2Te O6 have been investigated by powder neutron diffraction. A long-range antiferromagnetic (AFM) ordering has been found below TN˜24.8 K . The magnetic ground state, determined to be zigzag antiferromagnetic and characterized by a propagation vector k =(1 /2 0 0 ) , occurs due to the competing exchange interactions up to third-nearest neighbors within the honeycomb lattice. The exceptional existence of a limited magnetic correlation length along the c axis (perpendicular to the honeycomb layers in the a b planes) has been found even at 1.8 K, well below the TN˜24.8 K . The observed limited correlation along the c axis is explained by the disorder distribution of the Na ions within the intermediate layers between honeycomb planes. The reduced ordered moments mCo (1 )=2.77 (3 ) μB/C o2 + and mCo (2 )=2.45 (2 ) μB/C o2 + at 1.8 K reflect the persistence of spin fluctuations in the ordered state. Above TN˜24.8 K , the presence of short-range magnetic correlations, manifested by broad diffuse magnetic peaks in the diffraction patterns, has been found. Reverse Monte Carlo analysis of the experimental diffuse magnetic scattering data reveals that the spin correlations are mainly confined within the two-dimensional honeycomb layers (a b plane) with a correlation length of ˜12 Å at 25 K. The nature of the spin arrangements is found to be similar in both the short-range and long-range ordered magnetic states. This implies that the short-range correlation grows with decreasing temperature and leads to the zigzag AFM ordering at T ≤TN . The present study provides a comprehensive picture of the magnetic correlations over the temperature range above and below the TN and their relation to the crystal structure. The role of intermediate soft Na layers on the magnetic coupling between honeycomb planes is discussed.

Three-dimensional formulation of dislocation climb

NASA Astrophysics Data System (ADS)

Gu, Yejun; Xiang, Yang; Quek, Siu Sin; Srolovitz, David J.

2015-10-01

We derive a Green's function formulation for the climb of curved dislocations and multiple dislocations in three-dimensions. In this new dislocation climb formulation, the dislocation climb velocity is determined from the Peach-Koehler force on dislocations through vacancy diffusion in a non-local manner. The long-range contribution to the dislocation climb velocity is associated with vacancy diffusion rather than from the climb component of the well-known, long-range elastic effects captured in the Peach-Koehler force. Both long-range effects are important in determining the climb velocity of dislocations. Analytical and numerical examples show that the widely used local climb formula, based on straight infinite dislocations, is not generally applicable, except for a small set of special cases. We also present a numerical discretization method of this Green's function formulation appropriate for implementation in discrete dislocation dynamics (DDD) simulations. In DDD implementations, the long-range Peach-Koehler force is calculated as is commonly done, then a linear system is solved for the climb velocity using these forces. This is also done within the same order of computational cost as existing discrete dislocation dynamics methods.

Escarpment evolution on high-elevation rifted margins: Insights derived from a surface processes model that combines diffusion, advection and reaction

NASA Technical Reports Server (NTRS)

Kooi, Henk; Beaumont, Christopher

1994-01-01

Experiments with a surface processes model of large-scale (1-1000 km) long-term (1-100 m.y.) erosional denudation are used to establish the controls on the evolution of a model escarpment that is related to the rifting of a continent. The mdoel describes changes in topographic form as a result of sumultaneous short- and long-range mass transport representing hillslope (diffusive) processes and fluvial transport (advection), repsectively. Fluvial entrainment is modeled as a first-order kinetic reaction which reflects the erodibility of the substrate, and therefore the fluvial system is not necessarily carrying at capacity. One dimensional and planform models demonstrate that the principal controls on the evolution of an initially steep model escarpment are (1) antecedent topography/drainage; (2) the timesale (or equivalently a length scale) in the fluvial entrainment reaction; (3) the flexural response of the lithosphere to denudation; and (4) the relative efficiencies of the short- and long-range transport processes. When rainfall and substrate lithology are uniform, a significant amount of discharge draining over the escarpment top causes it to degrade. Only when the top of the model escarpment coincides with a drainage divide can escarpment retreat occur for these conditions. An additional requirement for retreat of a model escarpment without decline is a long reaction time scale for fluvial entrainment. This corresponds to a substrate that is hard to detach by flucial erosion, and therefore to fluvial erosion that is not transport limited. Coninuous backtilting of an escarpment due ot flexural isostatic uplift in response to denudational unloading helps maintain the scarp top as a divide. It is essntial if the escarpment gradient is to be preserved during retreat in a uniform lithology. Low flexural rigidieties propote steep and slowly retreating escarpments. For given rainfall and substrate conditions, the morphology of a retraeating model escarpment is determined by the ratio of hte short-range diffusive and long range advective transport efficiencies. A low ration (which is interpreted to correspond to a more humid, temperate climate) produces a convex upper slope, and concave lower slope morphology and only major escarpments are predicted to preserve a high scarp gradient. Lithological contrasts in hte model produce more complex morphologies and predict the formation of scarps crowned by an erosionaly resistant caprock. However, resistant caprocks are not an essential requirement for model scarps to retreat. We conclude that the inferred controls and model behavior are both consistent with the present-day morphology of rifted continental margins and with modern conceptual models of landscape evolution.

Correlation Structure of Fractional Pearson Diffusions.

PubMed

Leonenko, Nikolai N; Meerschaert, Mark M; Sikorskii, Alla

2013-09-01

The stochastic solution to a diffusion equations with polynomial coefficients is called a Pearson diffusion. If the first time derivative is replaced by a Caputo fractional derivative of order less than one, the stochastic solution is called a fractional Pearson diffusion. This paper develops an explicit formula for the covariance function of a fractional Pearson diffusion in steady state, in terms of Mittag-Leffler functions. That formula shows that fractional Pearson diffusions are long range dependent, with a correlation that falls off like a power law, whose exponent equals the order of the fractional derivative.

Fluctuation-controlled front propagation

NASA Astrophysics Data System (ADS)

Ridgway, Douglas Thacher

1997-09-01

A number of fundamental pattern-forming systems are controlled by fluctuations at the front. These problems involve the interaction of an infinite dimensional probability distribution with a strongly nonlinear, spatially extended pattern-forming system. We have examined fluctuation-controlled growth in the context of the specific problems of diffusion-limited growth and biological evolution. Mean field theory of diffusion-limited growth exhibits a finite time singularity. Near the leading edge of a diffusion-limited front, this leads to acceleration and blowup. This may be resolved, in an ad hoc manner, by introducing a cutoff below which growth is weakened or eliminated (8). This model, referred to as the BLT model, captures a number of qualitative features of global pattern formation in diffusion-limited aggregation: contours of the mean field match contours of averaged particle density in simulation, and the modified mean field theory can form dendritic features not possible in the naive mean field theory. The morphology transition between dendritic and non-dendritic global patterns requires that BLT fronts have a Mullins-Sekerka instability of the wavefront shape, in order to form concave patterns. We compute the stability of BLT fronts numerically, and compare the results to fronts without a cutoff. A significant morphological instability of the BLT fronts exists, with a dominant wavenumber on the scale of the front width. For standard mean field fronts, no instability is found. The naive and ad hoc mean field theories are continuum-deterministic models intended to capture the behavior of a discrete stochastic system. A transformation which maps discrete systems into a continuum model with a singular multiplicative noise is known, however numerical simulations of the continuum stochastic system often give mean field behavior instead of the critical behavior of the discrete system. We have found a new interpretation of the singular noise, based on maintaining the symmetry of the absorbing state, but which is unsuccessful at capturing the behavior of diffusion-limited growth. In an effort to find a simpler model system, we turned to modelling fitness increases in evolution. The work was motivated by an experiment on vesicular stomatitis virus, a short (˜9600bp) single-stranded RNA virus. A highly bottlenecked viral population increases in fitness rapidly until a certain point, after which the fitness increases at a slower rate. This is well modeled by a constant population reproducing and mutating on a smooth fitness landscape. Mean field theory of this system displays the same infinite propagation velocity blowup as mean field diffusion-limited aggregation. However, we have been able to make progress on a number of fronts. One is solving systems of moment equations, where a hierarchy of moments is truncated arbitrarily at some level. Good results for front propagation velocity are found with just two moments, corresponding to inclusion of the basic finite population clustering effect ignored by mean field theory. In addition, for small mutation rates, most of the population will be entirely on a single site or two adjacent sites, and the density of these cases can be described and solved. (Abstract shortened by UMI.)

Ordering process in the diffusively coupled logistic lattice

NASA Astrophysics Data System (ADS)

Conrado, Claudine V.; Bohr, Tomas

1991-08-01

We study the ordering process in a lattice of diffusively coupled logistic maps for increasing lattice size. Within a window of parameters, the system goes into a weakly chaotic state with long range "antiferromagnetic" order. This happens for arbitrary lattice size L and the ordering time behaves as t ~ L2 as we would expect from a picture of diffusing defects.

Localization and Ballistic Diffusion for the Tempered Fractional Brownian-Langevin Motion

NASA Astrophysics Data System (ADS)

Chen, Yao; Wang, Xudong; Deng, Weihua

2017-10-01

This paper discusses the tempered fractional Brownian motion (tfBm), its ergodicity, and the derivation of the corresponding Fokker-Planck equation. Then we introduce the generalized Langevin equation with the tempered fractional Gaussian noise for a free particle, called tempered fractional Langevin equation (tfLe). While the tfBm displays localization diffusion for the long time limit and for the short time its mean squared displacement (MSD) has the asymptotic form t^{2H}, we show that the asymptotic form of the MSD of the tfLe transits from t^2 (ballistic diffusion for short time) to t^{2-2H}, and then to t^2 (again ballistic diffusion for long time). On the other hand, the overdamped tfLe has the transition of the diffusion type from t^{2-2H} to t^2 (ballistic diffusion). The tfLe with harmonic potential is also considered.

Aggregate-scale heterogeneity in iron (hydr)oxide reductive transformations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tufano, K.J.; Benner, S.G.; Mayer, K.U.

There is growing awareness of the complexity of potential reaction pathways and the associated solid-phase transformations during the reduction of Fe (hydr)oxides, especially ferrihydrite. An important observation in static and advective-dominated systems is that microbially produced Fe(II) accelerates Ostwald ripening of ferrihydrite, thus promoting the formation of thermodynamically more stable ferric phases (lepidocrocite and goethite) and, at higher Fe(II) surface loadings, the precipitation of magnetite; high Fe(II) levels can also lead to green rust formation, and with high carbonate levels siderite may also be formed. This study expands this emerging conceptual model to a diffusion-dominated system that mimics an idealizedmore » micropore of a ferrihydrite-coated soil aggregate undergoing reduction. Using a novel diffusion cell, coupled with micro-x-ray fluorescence and absorption spectroscopies, we determined that diffusion-controlled gradients in Fe{sup 2+}{sub (aq)} result in a complex array of spatially distributed secondary mineral phases. At the diffusive pore entrance, where Fe{sup 2+} concentrations are highest, green rust and magnetite are the dominant secondary Fe (hydr)oxides (30 mol% Fe each). At intermediate distances from the inlet, green rust is not observed and the proportion of magnetite decreases from approximately 30 to <10%. Across this same transect, the proportion of goethite increases from undetectable up to >50%. At greater distances from the advective-diffusive boundary, goethite is the dominant phase, comprising between 40 and 95% of the Fe. In the presence of magnetite, lepidocrocite forms as a transient-intermediate phase during ferrihydrite-to-goethite conversion; in the absence of magnetite, conversion to goethite is more limited. These experimental observations, coupled with results of reactive transport modeling, confirm the conceptual model and illustrate the potential importance of diffusion-generated concentration gradients in dissolved Fe{sup 2+} on the fate of ferrihydrite during reduction in structured soils.« less

Direct measurements of interfacial interactions between pectin and kappa-casein and implications for the stabilisation of calcium-free casein micelle mimics.

PubMed

Cucheval, A; Al-Ghobashy, M A; Hemar, Y; Otter, D; Williams, M A K

2009-10-15

Using Surface Plasmon Resonance (SPR) it has been shown that the fine structure of the anionic polysaccharide pectin strongly influences its interfacial interaction with a kappa-casein layer coated onto a gold surface (via a dextran linker) in the pH range 3.5-6.8, with the highest SPR signal being observed for pectin with the lowest charge density tested (a degree of methylesterification (DM) around 90%). Furthermore, the Brownian motions of kappa-casein coated polystyrene beads (used to provide calcium-free 'model casein micelles') were studied in pectin solutions using Diffusing Wave Spectroscopy (DWS) and microscopy, and were compared with measurements made on naked beads. At every pH value studied (with the exception of 3.5), bridging of the protein-covered probe particles was observed for pectins of both DM 28 and DM 78. However, no aggregated complexes were found in these model casein micelle systems when pectin of an unusually high DM was used (90%). It was hypothesised that having a limited number of binding regions of spatially limited extent maximises the number of chains binding to the protein layer (as found with the SPR measurement), encourages the formation of loops and trains, and additionally limits the potential for destabilisation via bridging.

Vacancy–Vacancy Interaction Induced Oxygen Diffusivity Enhancement in Undoped Nonstoichiometric Ceria

DOE PAGES

Yuan, Fenglin; Zhang, Yanwen; Weber, William J.

2015-05-19

In this paper, molecular dynamics simulations and molecular static calculations have been used to systematically study oxygen vacancy transport in undoped nonstoichiometric ceria. A strong oxygen diffusivity enhancement appears in the vacancy concentration range of 2–4% over the temperature range from 1000 to 2000 K. An Arrhenius ion diffusion mechanism by vacancy hopping along the (100) direction is unambiguously identified, and an increasing trend of both the oxygen migration barrier and the prefactor with increasing vacancy concentration is observed. Within the framework of classical diffusion theory, a weak concentration dependence of the prefactor in oxygen vacancy migration is shown tomore » be crucial for explaining the unusual fast oxygen ion migration in the low concentration range and consequently the appearance of a maximum in oxygen diffusivity. Finally, a representative (100) direction interaction model is constructed to identify long-range vacancy–vacancy interaction as the structural origin of the positive correlation between oxygen migration barrier and vacancy concentration.« less

CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Kinetics of catalytically activated duplication in aggregation growth

NASA Astrophysics Data System (ADS)

Wang, Hai-Feng; Lin, Zhen-Quan; Gao, Yan; Xu, Chao

2009-08-01

We propose a catalytically activated duplication model to mimic the coagulation and duplication of the DNA polymer system under the catalysis of the primer RNA. In the model, two aggregates of the same species can coagulate themselves and a DNA aggregate of any size can yield a new monomer or double itself with the help of RNA aggregates. By employing the mean-field rate equation approach we analytically investigate the evolution behaviour of the system. For the system with catalysis-driven monomer duplications, the aggregate size distribution of DNA polymers ak(t) always follows a power law in size in the long-time limit, and it decreases with time or approaches a time-independent steady-state form in the case of the duplication rate independent of the size of the mother aggregates, while it increases with time increasing in the case of the duplication rate proportional to the size of the mother aggregates. For the system with complete catalysis-driven duplications, the aggregate size distribution ak(t) approaches a generalized or modified scaling form.

Substrate Diffusion Heterogeneity Controls Bacterial Competition and Coexistence

NASA Astrophysics Data System (ADS)

Dechesne, A.; Or, D.; Smets, B. F.

2005-12-01

Diffusion has long been recognized as a key process affecting bacterial physiological functions ranging from nutrient uptake to removal of metabolic waste products. In the vadose zone, significant convective flows are limited and bacteria rely primarily on diffusion for nutrient supply. Even under relatively "wet" conditions (e.g. matric potentials -20 J/kg), soil water is fragmented and exists as thin liquid films or held in crevices imposing constraints on substrate diffusion. Our objective was to investigate the role of diffusion on soil microbial diversity, by focusing on one of the processes that shapes the structure of bacterial communities: competitive interactions. We used a simplified setup, in which the substrate (citrate) fluxes were controlled by different agar gels thicknesses and spatially heterogeneous diffusive pathways were created by an impermeable film with prescribed hole sizes and patterns. Our competition experiments involved two soil bacteria: Burkholderia xenovorans LB400 and Pseudomonas putida KT2440, which were tagged with different constitutive fluorescent markers, allowing for their on line microscopic detection. The growth parameters on citrate of these strains were thoroughly assessed. B. xenovorans LB400 is the weaker competitor. As a result, this strain was outcompeted by KT2440 under high substrate diffusivity and homogeneous conditions. Conversely, the disadvantage of the weakest competitor was not so marked under low substrate diffusivity condition. These results suggest that dry conditions in soil would provide conditions allowing the sustaining of weak bacterial competitors, resulting in the maintenance of high bacterial diversity.

Cost-Efficient and Multi-Functional Secure Aggregation in Large Scale Distributed Application

PubMed Central

Zhang, Ping; Li, Wenjun; Sun, Hua

2016-01-01

Secure aggregation is an essential component of modern distributed applications and data mining platforms. Aggregated statistical results are typically adopted in constructing a data cube for data analysis at multiple abstraction levels in data warehouse platforms. Generating different types of statistical results efficiently at the same time (or referred to as enabling multi-functional support) is a fundamental requirement in practice. However, most of the existing schemes support a very limited number of statistics. Securely obtaining typical statistical results simultaneously in the distribution system, without recovering the original data, is still an open problem. In this paper, we present SEDAR, which is a SEcure Data Aggregation scheme under the Range segmentation model. Range segmentation model is proposed to reduce the communication cost by capturing the data characteristics, and different range uses different aggregation strategy. For raw data in the dominant range, SEDAR encodes them into well defined vectors to provide value-preservation and order-preservation, and thus provides the basis for multi-functional aggregation. A homomorphic encryption scheme is used to achieve data privacy. We also present two enhanced versions. The first one is a Random based SEDAR (REDAR), and the second is a Compression based SEDAR (CEDAR). Both of them can significantly reduce communication cost with the trade-off lower security and lower accuracy, respectively. Experimental evaluations, based on six different scenes of real data, show that all of them have an excellent performance on cost and accuracy. PMID:27551747

Cost-Efficient and Multi-Functional Secure Aggregation in Large Scale Distributed Application.

PubMed

Zhang, Ping; Li, Wenjun; Sun, Hua

2016-01-01

Secure aggregation is an essential component of modern distributed applications and data mining platforms. Aggregated statistical results are typically adopted in constructing a data cube for data analysis at multiple abstraction levels in data warehouse platforms. Generating different types of statistical results efficiently at the same time (or referred to as enabling multi-functional support) is a fundamental requirement in practice. However, most of the existing schemes support a very limited number of statistics. Securely obtaining typical statistical results simultaneously in the distribution system, without recovering the original data, is still an open problem. In this paper, we present SEDAR, which is a SEcure Data Aggregation scheme under the Range segmentation model. Range segmentation model is proposed to reduce the communication cost by capturing the data characteristics, and different range uses different aggregation strategy. For raw data in the dominant range, SEDAR encodes them into well defined vectors to provide value-preservation and order-preservation, and thus provides the basis for multi-functional aggregation. A homomorphic encryption scheme is used to achieve data privacy. We also present two enhanced versions. The first one is a Random based SEDAR (REDAR), and the second is a Compression based SEDAR (CEDAR). Both of them can significantly reduce communication cost with the trade-off lower security and lower accuracy, respectively. Experimental evaluations, based on six different scenes of real data, show that all of them have an excellent performance on cost and accuracy.

A Computational Investigation of Sooting Limits of Spherical Diffusion Flames

NASA Technical Reports Server (NTRS)

Lecoustre, V. R.; Chao, B. H.; Sunderland, P. B.; Urban, D. L.; Stocker, D. P.; Axelbaum, R. L.

2007-01-01

Limiting conditions for soot particle inception in spherical diffusion flames were investigated numerically. The flames were modeled using a one-dimensional, time accurate diffusion flame code with detailed chemistry and transport and an optically thick radiation model. Seventeen normal and inverse flames were considered, covering a wide range of stoichiometric mixture fraction, adiabatic flame temperature, and residence time. These flames were previously observed to reach their sooting limits after 2 s of microgravity. Sooting-limit diffusion flames with residence times longer than 200 ms were found to have temperatures near 1190 K where C/O = 0.6, whereas flames with shorter residence times required increased temperatures. Acetylene was found to be a reasonable surrogate for soot precursor species in these flames, having peak mole fractions of about 0.01.

Effect of surfactant concentration to aggregations of nanogold particles

NASA Astrophysics Data System (ADS)

Duangthanu, Methawee; Pattanaporkratana, Apichart

2017-09-01

This research presents a study of aggregation of colloidal gold nanoparticles using 400 nm diameter gold nanoparticles mixed with a surfactant (Plantacare 2000) at various concentrations. When observed under a microscope, we found that the nanoparticles aggregated to form nearly spherical clusters at the beginning of the formation, and then sedimented to the bottom of the container. These clusters moved with Brownian’s motion and collided with each other in the horizontal plane, forming branch-like clusters in 2D. The appearance and size of the clusters were different depending on the concentration of surfactant. The clusters’ size and appearance were rarely changed after mixing with surfactant for 90 minutes, and we found that the cluster’s shapes were nearly spherical at low surfactant concentration (c = 0.25%). At surfactant concentration between 0.50% - 5.00%, the aggregates formed branch-like clusters with skinnier branches and smaller sizes at higher surfactant concentration. Moreover, we also found that, at surfactant concentrations between 2.50% - 5.00%, nanoparticles and aggregates stuck to the bottom of the glass container quickly and rarely moved after 10 minutes. At c = 0.25%, the 2D fractal dimension of the aggregates was measured to be D = 1.88 ± 0.04, since the aggregates were nearly spherical. The fractal dimension decreased to the minimum of D = 1.50 ± 0.12 at c = 1.50%, similar to D ∼ 1.45 found in diffusion-limited cluster aggregation (DLCA). At surfactant concentration above 1.50%, the fractal dimension increased until it reached the value of D ∼ 1.66 at c = 5.00%.

Equilibrium sorption and diffusion rate studies with halogenated organic chemical and sandy aquifer material

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ball, W.P.

1990-01-01

Concepts for rate limitation of sorptive uptake of hydrophobic organic solutes by aquifer solids are reviewed, emphasizing physical diffusion models and in the context of effects on contaminant transport. Data for the sorption of tetrachloroethene (PCE) and 1,2,4,5-tetrachlorobenzene (TeCB) on Borden sand are presented, showing that equilibrium is attained very slowly, requiring equilibration times on the order of tens of days for PCE and hundreds of days for TeCB. The rate of approach to equilibrium decreased with increasing particle size and sorption distribution coefficient, in accordance with retarded intragranular diffusion models. Pulverization of the samples significantly decreased the required timemore » to equilibrium without changing the sorption capacity of the solids. Batch sorption methodology was refined to allow accurate measurement of long-term distribution coefficients, using purified {sup 14}C-labelled solute spikes and sealed glass ampules. Sorption isotherms for PCE and TeCB were conducted with size fractions of Borden sand over four to five orders of magnitude in aqueous concentration, and were found to be slightly nonlinear (Freundlich exponent = 0.8). A concentrated set of data in the low concentration range (<50 ug/L) revealed that sorption in this range could be equally well described by a linear isotherm. Distribution coefficients of the two solutes with seven size fractions of Borden sand, measured at low concentration and at full equilibrium, were between seven and sixty times the value predicted on the basis of recent correlations with organic carbon content. Rate results for coarse size fractions support a simple pore diffusion model, with pore diffusion coefficients estimated to be approximately 3 {times} 10{sup {minus}8} cm{sup 2}/sec, more than 200{times} lower than the aqueous diffusivities.« less

Defect-rich TiO2-δ nanocrystals confined in a mooncake-shaped porous carbon matrix as an advanced Na ion battery anode

NASA Astrophysics Data System (ADS)

He, Hanna; Zhang, Qi; Wang, Haiyan; Zhang, Hehe; Li, Jiadong; Peng, Zhiguang; Tang, Yougen; Shao, Minhua

2017-06-01

Inferior electronic conductivity and sluggish sodium ion diffusion are still two big challenges for TiO2 anode material for Na ion batteries (SIBs). Herein, we synthesize TiO2/C composites by the pyrolysis of MIL-125(Ti) precursor and successfully introduce defects to TiO2/C composite by a simple magnesium reduction. The as-prepared defect-rich TiO2-δ/C composite shows mooncake-shaped morphology consisting of TiO2-δ nanocrystals with an average particle size of 5 nm well dispersed in the carbon matrix. When used as a SIBs anode, the defect-rich TiO2-δ/C composite exhibits a high reversible capacity of 330.2 mAh g-1 at 50 mA g-1 at the voltage range of 0.001-3.0 V and long-term cycling stability with negligible decay after 5000 cycles. Compared with other four TiO2/C samples, the electrochemical performance of defect-rich TiO2-δ/C is highly improved, which may benefit from the enhanced electronic/ionic conductivities owing to the defect-rich features, high surface area rendering shortened electronic and ionic diffusion path, and the suppress of the TiO2 crystal aggregation during sodiation and desodiation process by the carbon matrix.

Shear-induced aggregation or disaggregation in edible oils: Models, computer simulation, and USAXS measurements

NASA Astrophysics Data System (ADS)

Townsend, B.; Peyronel, F.; Callaghan-Patrachar, N.; Quinn, B.; Marangoni, A. G.; Pink, D. A.

2017-12-01

The effects of shear upon the aggregation of solid objects formed from solid triacylglycerols (TAGs) immersed in liquid TAG oils were modeled using Dissipative Particle Dynamics (DPD) and the predictions compared to experimental data using Ultra-Small Angle X-ray Scattering (USAXS). The solid components were represented by spheres interacting via attractive van der Waals forces and short range repulsive forces. A velocity was applied to the liquid particles nearest to the boundary, and Lees-Edwards boundary conditions were used to transmit this motion to non-boundary layers via dissipative interactions. The shear was created through the dissipative forces acting between liquid particles. Translational diffusion was simulated, and the Stokes-Einstein equation was used to relate DPD length and time scales to SI units for comparison with USAXS results. The SI values depended on how large the spherical particles were (250 nm vs. 25 nm). Aggregation was studied by (a) computing the Structure Function and (b) quantifying the number of pairs of solid spheres formed. Solid aggregation was found to be enhanced by low shear rates. As the shear rate was increased, a transition shear region was manifested in which aggregation was inhibited and shear banding was observed. Aggregation was inhibited, and eventually eliminated, by further increases in the shear rate. The magnitude of the transition region shear, γ˙ t, depended on the size of the solid particles, which was confirmed experimentally.

Reuse of industrial sludge as construction aggregates.

PubMed

Tay, J H; Show, K Y; Hong, S Y

2001-01-01

Industrial wastewater sludge and dredged marine clay are high volume wastes that needed enormous space at landfill disposal sites. Due to the limitation of land space, there is an urgent need for alternative disposal methods for these two wastes. This study investigates the possibility of using the industrial sludge in combination with marine clay as construction aggregates. Different proportions of sludge and clay were made into round and angular aggregates. It was found that certain mix proportions could provide aggregates of adequate strength, comparable to that of conventional aggregates. Concrete samples cast from the sludge-clay aggregates yield compressive strengths in the range of 31.0 to 39.0 N/mm2. The results showed that the round aggregates of 100% sludge and the crush aggregates of sludge with up to 20% clay produced concrete of compressive strengths which are superior to that of 38.0 N/mm2 for conventional aggregate. The study indicates that the conversion of high volume wastes into construction materials is a potential option for waste management.

Adiabatic description of long range frequency sweeping

NASA Astrophysics Data System (ADS)

Nyqvist, R. M.; Lilley, M. K.; Breizman, B. N.

2012-09-01

A theoretical framework is developed to describe long range frequency sweeping events in the 1D electrostatic bump-on-tail model with fast particle sources and collisions. The model includes three collision operators (Krook, drag (dynamical friction) and velocity space diffusion), and allows for a general shape of the fast particle distribution function. The behaviour of phase space holes and clumps is analysed in the absence of diffusion, and the effect of particle trapping due to separatrix expansion is discussed. With a fast particle distribution function whose slope decays above the resonant phase velocity, hooked frequency sweeping is found for holes in the presence of drag collisions alone.

The aggregation and characteristics of radiation-induced defects in lithium fluoride nanocrystals

NASA Astrophysics Data System (ADS)

Voitovich, A. P.; Kalinov, V. S.; Korzhik, M. V.; Martynovich, E. F.; Runets, L. P.; Stupak, A. P.

2013-02-01

It has been established that diffusion activation energies for anion vacancies and centres ? in lithium fluoride nanocrystals are higher than those in bulk crystals. In nanocrystals, ? centres migrating in the range of the temperature close to room temperature is not observed and these centres remain stable. The ratio of centres ? and F 2 concentrations in nanocrystals is higher than in bulk crystals. A new type of colour centres, which is absent in bulk crystals, is discovered in nanocrystals.

Choice of reference measurements affects quantification of long diffusion time behaviour using stimulated echoes.

PubMed

Kleinnijenhuis, Michiel; Mollink, Jeroen; Lam, Wilfred W; Kinchesh, Paul; Khrapitchev, Alexandre A; Smart, Sean C; Jbabdi, Saad; Miller, Karla L

2018-02-01

To demonstrate how reference data affect the quantification of the apparent diffusion coefficient (ADC) in long diffusion time measurements with diffusion-weighted stimulated echo acquisition mode (DW-STEAM) measurements, and to present a modification to avoid contribution from crusher gradients in DW-STEAM. For DW-STEAM, reference measurements at long diffusion times have significant b 0 value, because b = 0 cannot be achieved in practice as a result of the need for signal spoiling. Two strategies for acquiring reference data over a range of diffusion times were considered: constant diffusion weighting (fixed-b 0 ) and constant gradient area (fixed-q 0 ). Fixed-b 0 and fixed-q 0 were compared using signal calculations for systems with one and two diffusion coefficients, and experimentally using data from postmortem human corpus callosum samples. Calculations of biexponential diffusion decay show that the ADC is underestimated for reference images with b > 0, which can induce an apparent time-dependence for fixed-q 0 . Restricted systems were also found to be affected. Experimentally, the exaggeration of the diffusion time-dependent effect under fixed-q 0 versus fixed-b 0 was in a range predicted theoretically, accounting for 62% (longitudinal) and 35% (radial) of the time dependence observed in white matter. Variation in the b-value of reference measurements in DW-STEAM can induce artificial diffusion time dependence in ADC, even in the absence of restriction. Magn Reson Med 79:952-959, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

Spatially Different Tissue-Scale Diffusivity Shapes ANGUSTIFOLIA3 Gradient in Growing Leaves.

PubMed

Kawade, Kensuke; Tanimoto, Hirokazu; Horiguchi, Gorou; Tsukaya, Hirokazu

2017-09-05

The spatial gradient of signaling molecules is pivotal for establishing developmental patterns of multicellular organisms. It has long been proposed that these gradients could arise from the pure diffusion process of signaling molecules between cells, but whether this simplest mechanism establishes the formation of the tissue-scale gradient remains unclear. Plasmodesmata are unique channel structures in plants that connect neighboring cells for molecular transport. In this study, we measured cellular- and tissue-scale kinetics of molecular transport through plasmodesmata in Arabidopsis thaliana developing leaf primordia by fluorescence recovery assays. These trans-scale measurements revealed biophysical properties of diffusive molecular transport through plasmodesmata and revealed that the tissue-scale diffusivity, but not the cellular-scale diffusivity, is spatially different along the leaf proximal-to-distal axis. We found that the gradient in cell size along the developmental axis underlies this spatially different tissue-scale diffusivity. We then asked how this diffusion-based framework functions in establishing a signaling gradient of endogenous molecules. ANGUSTIFOLIA3 (AN3) is a transcriptional co-activator, and as we have shown here, it forms a long-range signaling gradient along the leaf proximal-to-distal axis to determine a cell-proliferation domain. By genetically engineering AN3 mobility, we assessed each contribution of cell-to-cell movement and tissue growth to the distribution of the AN3 gradient. We constructed a diffusion-based theoretical model using these quantitative data to analyze the AN3 gradient formation and demonstrated that it could be achieved solely by the diffusive molecular transport in a growing tissue. Our results indicate that the spatially different tissue-scale diffusivity is a core mechanism for AN3 gradient formation. This provides evidence that the pure diffusion process establishes the formation of the long-range signaling gradient in leaf development. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Symbiotic Cell Differentiation and Cooperative Growth in Multicellular Aggregates

PubMed Central

Yamagishi, Jumpei F; Saito, Nen; Kaneko, Kunihiko

2016-01-01

As cells grow and divide under a given environment, they become crowded and resources are limited, as seen in bacterial biofilms and multicellular aggregates. These cells often show strong interactions through exchanging chemicals, as evident in quorum sensing, to achieve mutualism and division of labor. Here, to achieve stable division of labor, three characteristics are required. First, isogenous cells differentiate into several types. Second, this aggregate of distinct cell types shows better growth than that of isolated cells without interaction and differentiation, by achieving division of labor. Third, this cell aggregate is robust with respect to the number distribution of differentiated cell types. Indeed, theoretical studies have thus far considered how such cooperation is achieved when the ability of cell differentiation is presumed. Here, we address how cells acquire the ability of cell differentiation and division of labor simultaneously, which is also connected with the robustness of a cell society. For this purpose, we developed a dynamical-systems model of cells consisting of chemical components with intracellular catalytic reaction dynamics. The reactions convert external nutrients into internal components for cellular growth, and the divided cells interact through chemical diffusion. We found that cells sharing an identical catalytic network spontaneously differentiate via induction from cell-cell interactions, and then achieve division of labor, enabling a higher growth rate than that in the unicellular case. This symbiotic differentiation emerged for a class of reaction networks under the condition of nutrient limitation and strong cell-cell interactions. Then, robustness in the cell type distribution was achieved, while instability of collective growth could emerge even among the cooperative cells when the internal reserves of products were dominant. The present mechanism is simple and general as a natural consequence of interacting cells with limited resources, and is consistent with the observed behaviors and forms of several aggregates of unicellular organisms. PMID:27749898

Hollow-fiber flow field-flow fractionation with multi-angle laser scattering detection for aggregation studies of therapeutic proteins.

PubMed

Reschiglian, P; Roda, B; Zattoni, A; Tanase, M; Marassi, V; Serani, S

2014-02-01

The rapid development of protein-based pharmaceuticals highlights the need for robust analytical methods to ensure their quality and stability. Among proteins used in pharmaceutical applications, an important and ever increasing role is represented by monoclonal antibodies and large proteins, which are often modified to enhance their activity or stability when used as drugs. The bioactivity and the stability of those proteins are closely related to the maintenance of their complex structure, which however are influenced by many external factors that can cause degradation and/or aggregation. The presence of aggregates in these drugs could reduce their bioactivity and bioavailability, and induce immunogenicity. The choice of the proper analytical method for the analysis of aggregates is fundamental to understand their (size) dimensional range, their amount, and if they are present in the sample as generated by an aggregation or as an artifact due to the method itself. Size exclusion chromatography is one of the most important techniques for the quality control of pharmaceutical proteins; however, its application is limited to relatively low molar mass aggregates. Among the techniques for the size characterization of proteins, field-flow fractionation (FFF) represents a competitive choice because of its soft mechanism due to the absence of a stationary phase and application in a broader size range, from nanometer- to micrometer-sized analytes. In this paper, the microcolumn variant of FFF, the hollow-fiber flow FFF, was online coupled with multi-angle light scattering, and a method for the characterization of aggregates with high reproducibility and low limit of detection was demonstrated employing an avidin derivate as sample model.

Diffusive charge transport in graphene on SiO 2

NASA Astrophysics Data System (ADS)

Chen, J.-H.; Jang, C.; Ishigami, M.; Xiao, S.; Cullen, W. G.; Williams, E. D.; Fuhrer, M. S.

2009-07-01

We review our recent work on the physical mechanisms limiting the mobility of graphene on SiO 2. We have used intentional addition of charged scattering impurities and systematic variation of the dielectric environment to differentiate the effects of charged impurities and short-range scatterers. The results show that charged impurities indeed lead to a conductivity linear in density ( σ(n)∝n) in graphene, with a scattering magnitude that agrees quantitatively with theoretical estimates; increased dielectric screening reduces the scattering from charged impurities, but increases the scattering from short-range scatterers. We evaluate the effects of the corrugations (ripples) of graphene on SiO 2 on transport by measuring the height-height correlation function. The results show that the corrugations cannot mimic long-range (charged impurity) scattering effects, and have too small an amplitude-to-wavelength ratio to significantly affect the observed mobility via short-range scattering. Temperature-dependent measurements show that longitudinal acoustic phonons in graphene produce a resistivity that is linear in temperature and independent of carrier density; at higher temperatures, polar optical phonons of the SiO 2 substrate give rise to an activated, carrier density-dependent resistivity. Together the results paint a complete picture of charge carrier transport in graphene on SiO 2 in the diffusive regime.

Investigation of guanosine-quartet assemblies by vibrational and electronic circular dichroism spectroscopy, a novel approach for studying supramolecular entities.

PubMed

Setnicka, Vladimír; Urbanová, Marie; Volka, Karel; Nampally, Sreenivasachary; Lehn, Jean-Marie

2006-11-24

The self-assembly of guanosine-5'-hydrazide G-1 in D(2)O, in the presence and absence of sodium cations, has been investigated by chiroptical techniques: electronic (ECD) and the newly introduced vibrational (VCD) circular dichroism spectroscopy. Using a combination of ECD and VCD with other methods such as IR, electron microscopy, and electrospray ionization mass spectrometry (ESI-MS) it was found that G-1 produces long-range chiral aggregates consisting of G-quartets, (G-1)(4), subsequently stacked into columns, [(G-1)(4)](n), induced by binding of metal cations between the (G-1)(4) species. This process, accompanied by gelation of the sample, is highly efficient in the presence of an excess of sodium cations, leading to aggregates with strong quartet-quartet interaction. Thermally induced conformational changes and conformational stability of guanosine-5'-hydrazide assemblies were studied by chiroptical techniques and the melting temperature of the hydrogels formed was obtained. The temperature-dependent experiments indicate that the long-range supramolecular aggregates are dissociated by increasing temperature into less ordered species, monomers, or other intermediates in equilibrium, as indicated by MS experiments.

Mechanistic modeling of microbial interactions at pore to profile scale resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-05-01

The sensitivity of polar regions to raising global temperatures is reflected in rapidly changing hydrological processes associated with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and stimulation of other soil-borne greenhouse gas emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and other environmental factors. Soil structural elements such as aggregates and layering affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hot spots). We developed a mechanistic individual-based model to quantify microbial activity dynamics in soil pore networks considering transport processes and enzymatic activity associated with methane production in soil. The model was upscaled from single aggregates to the soil profile where freezing/thawing provides macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged profile) for resolving methane production and oxidation rates. Methane transport pathways by diffusion and ebullition of bubbles vary with hydration dynamics. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability and enzyme activity) on long-term methane emissions and carbon decomposition rates in the rapidly changing polar regions.

Twitching motility of bacteria with type-IV pili: Fractal walks, first passage time, and their consequences on microcolonies

NASA Astrophysics Data System (ADS)

Bisht, Konark; Klumpp, Stefan; Banerjee, Varsha; Marathe, Rahul

2017-11-01

A human pathogen, Neisseria gonorrhoeae (NG), moves on surfaces by attaching and retracting polymeric structures called Type IV pili. The tug-of-war between the pili results in a two-dimensional stochastic motion called twitching motility. In this paper, with the help of real-time NG trajectories, we develop coarse-grained models for their description. The fractal properties of these trajectories are determined and their influence on first passage time and formation of bacterial microcolonies is studied. Our main observations are as follows: (i) NG performs a fast ballistic walk on small time scales and a slow diffusive walk over long time scales with a long crossover region; (ii) there exists a characteristic persistent length lp*, which yields the fastest growth of bacterial aggregates or biofilms. Our simulations reveal that lp*˜L0.6 , where L ×L is the surface on which the bacteria move; (iii) the morphologies have distinct fractal characteristics as a consequence of the ballistic and diffusive motion of the constituting bacteria.

Shear-induced reaction-limited aggregation kinetics of Brownian particles at arbitrary concentrations

NASA Astrophysics Data System (ADS)

Zaccone, Alessio; Gentili, Daniele; Wu, Hua; Morbidelli, Massimo

2010-04-01

The aggregation of interacting Brownian particles in sheared concentrated suspensions is an important issue in colloid and soft matter science per se. Also, it serves as a model to understand biochemical reactions occurring in vivo where both crowding and shear play an important role. We present an effective medium approach within the Smoluchowski equation with shear which allows one to calculate the encounter kinetics through a potential barrier under shear at arbitrary colloid concentrations. Experiments on a model colloidal system in simple shear flow support the validity of the model in the concentration range considered. By generalizing Kramers' rate theory to the presence of shear and collective hydrodynamics, our model explains the significant increase in the shear-induced reaction-limited aggregation kinetics upon increasing the colloid concentration.

Intermediate temperature proton conductors for PEM fuel cells based on phosphonic acid as protogenic group: a progress report.

PubMed

Steininger, H; Schuster, M; Kreuer, K D; Kaltbeitzel, A; Bingöl, B; Meyer, W H; Schauff, S; Brunklaus, G; Maier, J; Spiess, H W

2007-04-21

The melting behaviour and transport properties of straight chain alkanes mono- and difunctionalized with phosphonic acid groups have been investigated as a function of their length. The increase of melting temperature and decrease of proton conductivity with increasing chain length is suggested to be the consequence of an increasing ordering of the alkane segments which constrains the free aggregation of the phosphonic acid groups. However, the proton mobility is reduced to a greater extent than the proton diffusion coefficient indicating an increasing cooperativity of proton transport with increasing length of the alkane segment. The results clearly indicate that the "spacer concept", which had been proven successful in the optimization of the proton conductivity of heterocycle based systems, fails in the case of phosphonic acid functionalized polymers. Instead, a very high concentration of phosphonic acid functional groups forming "bulky" hydrogen bonded aggregates is suggested to be essential for obtaining very high proton conductivity. Aggregation is also suggested to reduce condensation reactions generally observed in phosphonic acid containing systems. On the basis of this understanding, the proton conductivities of poly(vinyl phosphonic acid) and poly(meta-phenylene phosphonic acid) are discussed. Though both polymers exhibit a substantial concentration of phosphonic acid groups, aggregation seems to be constrained to such an extent that intrinsic proton conductivity is limited to values below sigma = 10(-3) S cm(-1) at T = 150 degrees C. The results suggest that different immobilization concepts have to be developed in order to minimize the conductivity reduction compared to the very high intrinsic proton conductivity of neat phosphonic acid under quasi dry conditions. In the presence of high water activities, however, (as usually present in PEM fuel cells) the very high ion exchange capacities (IEC) possible for phosphonic acid functionalized ionomers (IEC >10 meq g(-1)) may allow for high proton conductivities in the intermediate temperature range (T approximately 120 -160 degrees C).

Multi-regime transport model for leaching behavior of heterogeneous porous materials.

PubMed

Sanchez, F; Massry, I W; Eighmy, T; Kosson, D S

2003-01-01

Utilization of secondary materials in civil engineering applications (e.g. as substitutes for natural aggregates or binder constituents) requires assessment of the physical and environment properties of the product. Environmental assessment often necessitates evaluation of the potential for constituent release through leaching. Currently most leaching models used to estimate long-term field performance assume that the species of concern is uniformly dispersed in a homogeneous porous material. However, waste materials are often comprised of distinct components such as coarse or fine aggregates in a cement concrete or waste encapsulated in a stabilized matrix. The specific objectives of the research presented here were to (1) develop a one-dimensional, multi-regime transport model (i.e. MRT model) to describe the release of species from heterogeneous porous materials and, (2) evaluate simple limit cases using the model for species when release is not dependent on pH. Two different idealized model systems were considered: (1) a porous material contaminated with the species of interest and containing inert aggregates and, (2) a porous material containing the contaminant of interest only in the aggregates. The effect of three factors on constituent release were examined: (1) volume fraction of material occupied by the aggregates compared to a homogeneous porous material, (2) aggregate size and, (3) differences in mass transfer rates between the binder and the aggregates. Simulation results confirmed that assuming homogeneous materials to evaluate the release of contaminants from porous waste materials may result in erroneous long-term field performance assessment.

Determination of critical nucleation number for a single nucleation amyloid-β aggregation model.

PubMed

Ghosh, Preetam; Vaidya, Ashwin; Kumar, Amit; Rangachari, Vijayaraghavan

2016-03-01

Aggregates of amyloid-β (Aβ) peptide are known to be the key pathological agents in Alzheimer disease (AD). Aβ aggregates to form large, insoluble fibrils that deposit as senile plaques in AD brains. The process of aggregation is nucleation-dependent in which the formation of a nucleus is the rate-limiting step, and controls the physiochemical fate of the aggregates formed. Therefore, understanding the properties of nucleus and pre-nucleation events will be significant in reducing the existing knowledge-gap in AD pathogenesis. In this report, we have determined the plausible range of critical nucleation number (n(*)), the number of monomers associated within the nucleus for a homogenous aggregation model with single unique nucleation event, by two independent methods: A reduced-order stability analysis and ordinary differential equation based numerical analysis, supported by experimental biophysics. The results establish that the most likely range of n(*) is between 7 and 14 and within, this range, n(*) = 12 closely supports the experimental data. These numbers are in agreement with those previously reported, and importantly, the report establishes a new modeling framework using two independent approaches towards a convergent solution in modeling complex aggregation reactions. Our model also suggests that the formation of large protofibrils is dependent on the nature of n(*), further supporting the idea that pre-nucleation events are significant in controlling the fate of larger aggregates formed. This report has re-opened an old problem with a new perspective and holds promise towards revealing the molecular events in amyloid pathologies in the future. Copyright © 2015 Elsevier Inc. All rights reserved.

NMR investigations of self-aggregation characteristics of SDS in a model assembled tri-block copolymer solution.

PubMed

Kumar, B V N Phani; Priyadharsini, S Umayal; Prameela, G K S; Mandal, Asit Baran

2011-08-01

The present work was undertaken with a view to understand the influence of a model non-ionic tri-block copolymer PEO-PPO-PEO (poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide)) with molecular weight 5800 i.e., P123 [(EO)(20)-(PO)(70)-(EO)(20)] on the self-aggregation characteristics of the anionic surfactant sodium dodecylsulfate (SDS) in aqueous solution (D(2)O) using NMR chemical shift, self-diffusion and nuclear spin-relaxation as suitable experimental probes. In addition, polymer diffusion has been monitored as a function of SDS concentration. The concentration-dependent chemical shift, diffusion data and relaxation data indicated the significant interaction of polymeric micelles with SDS monomers and micelles at lower and intermediate concentrations of SDS, whereas the weak interaction of the polymer with SDS micelles at higher concentrations of SDS. It has been observed that SDS starts aggregating on the polymer at a lower concentration i.e., critical aggregation concentration (cac=1.94 mM) compared to polymer-free situation, and the onset of secondary micelle concentration (C(2)=27.16 mM) points out the saturation of the 0.2 wt% polymer or free SDS monomers/micelles at higher concentrations of SDS. It has also been observed that the parameter cac is almost independent in the polymer concentrations of study. The TMS (tetramethylsilane) has been used as a solubilizate to measure the bound diffusion coefficient of SDS-polymer mixed system. The self-diffusion data were analyzed using two-site exchange model and the obtained information on aggregation dynamics was commensurate with that inferred from chemical shift and relaxation data. The information on slow motions of polymer-SDS system was also extracted using spin-spin and spin-lattice relaxation rate measurements. The relaxation data points out the disintegration of polymer network at higher concentrations of SDS. The present NMR investigations have been well corroborated by surface tension and conductivity measurements. Copyright © 2011 Elsevier Inc. All rights reserved.

Biexponential Characterization of Prostate Tissue Water Diffusion Decay Curves Over an Extended b-factor Range

PubMed Central

Mulkern, Robert V.; Barnes, Agnieszka Szot; Haker, Steven J.; Hung, Yin P.; Rybicki, Frank J.; Maier, Stephan E.; Tempany, Clare M.C.

2006-01-01

Detailed measurements of water diffusion within the prostate over an extended b-factor range were performed to assess whether the standard assumption of monoexponential signal decay is appropriate in this organ. From nine men undergoing prostate MR staging exams at 1.5 T, a single 10 mm thick axial slice was scanned with a line scan diffusion imaging (LSDI) sequence in which 14 equally spaced b- factors from 5 to 3500 s/mm2 were sampled along three orthogonal diffusion sensitization directions in 6 minutes. Due to the combination of long scan time and limited volume coverage associated with the multi-b- factor, multi-directional sampling, the slice was chosen online from the available T2-weighted axial images with the specific goal of enabling the sampling of presumed non-cancerous regions of interest (ROI’s) within the central gland (CG) and peripheral zone (PZ). Histology from pre-scan biopsy (N = 9) and post-surgical resection (N = 4) was subsequently employed to help confirm that the ROIs sampled were non-cancerous. The CG ROIs were characterized from the T2-weighted images as primarily mixtures of glandular and stromal benign prostatic hyperplasia (BPH) which is prevalent in this population. The water signal decays with b- factor from all ROI’s were clearly non-monoexponential and better served with bi- vs monoexponential fits, as tested using λ2 based F-test analyses. Fits to biexponential decay functions yielded inter-subject fast diffusion component fractions on the order of 0.73 ± 0.08 for both CG and PZ ROIs, fast diffusion coefficients of 2.68 ± 0.39 and 2.52 ± 0.38 μm2/ms and slow diffusion coefficients of 0.44 ± 0.16 and 0.23 ± 0.16 um2/ms for CG and PZ ROI’s, respectively. The difference between the slow diffusion coefficients within CG and PZ was statistically significant as assessed with a Mann-Whitney non-parametric test (P < 0.05). We conclude that a monoexponential model for water diffusion decay in prostate tissue is inadequate when a large range of b- factors is sampled and that biexponential analyses are better suited for characterizing prostate diffusion decay curves. PMID:16735177

Hydration and rotational diffusion of levoglucosan in aqueous solutions

NASA Astrophysics Data System (ADS)

Corezzi, S.; Sassi, P.; Paolantoni, M.; Comez, L.; Morresi, A.; Fioretto, D.

2014-05-01

Extended frequency range depolarized light scattering measurements of water-levoglucosan solutions are reported at different concentrations and temperatures to assess the effect of the presence and distribution of hydroxyl groups on the dynamics of hydration water. The anhydro bridge, reducing from five to three the number of hydroxyl groups with respect to glucose, considerably affects the hydration properties of levoglucosan with respect to those of mono and disaccharides. In particular, we find that the average retardation of water dynamics is ≈3-4, that is lower than ≈5-6 previously found in glucose, fructose, trehalose, and sucrose. Conversely, the average number of retarded water molecules around levoglucosan is 24, almost double that found in water-glucose mixtures. These results suggest that the ability of sugar molecules to form H-bonds through hydroxyl groups with surrounding water, while producing a more effective retardation, it drastically reduces the spatial extent of the perturbation on the H-bond network. In addition, the analysis of the concentration dependence of the hydration number reveals the aptitude of levoglucosan to produce large aggregates in solution. The analysis of shear viscosity and rotational diffusion time suggests a very short lifetime for these aggregates, typically faster than ≈20 ps.

Electrodiffusion of lipids on membrane surfaces.

PubMed

Zhou, Y C

2012-05-28

Lateral translocation of lipids and proteins is a universal process on membrane surfaces. Local aggregation or organization of lipids and proteins can be induced when the random lateral motion is mediated by the electrostatic interactions and membrane curvature. Although the lateral diffusion rates of lipids on membranes of various compositions are measured and the electrostatic free energies of predetermined protein-membrane-lipid systems can be computed, the process of the aggregation and the evolution to the electrostatically favorable states remain largely undetermined. Here we propose an electrodiffusion model, based on the variational principle of the free energy functional, for the self-consistent lateral drift-diffusion of multiple species of charged lipids on membrane surfaces. Finite sizes of lipids are modeled to enforce the geometrical constraint of the lipid concentration on membrane surfaces. A surface finite element method is developed to appropriate the Laplace-Beltrami operators in the partial differential equations of the model. Our model properly describes the saturation of lipids on membrane surfaces, and correctly predicts that the MARCKS peptide can consistently sequester three multivalent phosphatidylinositol 4,5-bisphosphate lipids through its basic amino acid residues, regardless of a wide range of the percentage of monovalent phosphatidylserine in the membrane.

Electrodiffusion of lipids on membrane surfaces

NASA Astrophysics Data System (ADS)

Zhou, Y. C.

2012-05-01

Lateral translocation of lipids and proteins is a universal process on membrane surfaces. Local aggregation or organization of lipids and proteins can be induced when the random lateral motion is mediated by the electrostatic interactions and membrane curvature. Although the lateral diffusion rates of lipids on membranes of various compositions are measured and the electrostatic free energies of predetermined protein-membrane-lipid systems can be computed, the process of the aggregation and the evolution to the electrostatically favorable states remain largely undetermined. Here we propose an electrodiffusion model, based on the variational principle of the free energy functional, for the self-consistent lateral drift-diffusion of multiple species of charged lipids on membrane surfaces. Finite sizes of lipids are modeled to enforce the geometrical constraint of the lipid concentration on membrane surfaces. A surface finite element method is developed to appropriate the Laplace-Beltrami operators in the partial differential equations of the model. Our model properly describes the saturation of lipids on membrane surfaces, and correctly predicts that the MARCKS peptide can consistently sequester three multivalent phosphatidylinositol 4,5-bisphosphate lipids through its basic amino acid residues, regardless of a wide range of the percentage of monovalent phosphatidylserine in the membrane.

Development of controlled release formulations of azadirachtin-A employing poly(ethylene glycol) based amphiphilic copolymers.

PubMed

Kumar, Jitendra; Shakil, Najam A; Singh, Manish K; Singh, Mukesh K; Pandey, Alka; Pandey, Ravi P

2010-05-01

Controlled release (CR) formulations of azadirachtin-A, a bioactive constituent derived from the seed of Azadirachta indica A. Juss (Meliaceae), have been prepared using commercially available polyvinyl chloride, polyethylene glycol (PEG) and laboratory synthesized poly ethylene glycol-based amphiphilic copolymers. Copolymers of polyethylene glycol and various dimethyl esters, which self assemble into nano micellar aggregates in aqueous media, have been synthesized. The kinetics of azadirachtin-A, release in water from the different formulations was studied. Release from the commercial polyethylene glycol (PEG) formulation was faster than the other CR formulations. The rate of release of encapsulated azadirachtin-A from nano micellar aggregates is reduced by increasing the molecular weight of PEG. The diffusion exponent (n value) of azadirachtin-A, in water ranged from 0.47 to 1.18 in the tested formulations. The release was diffusion controlled with a half release time (t(1/2)) of 3.05 to 42.80 days in water from different matrices. The results suggest that depending upon the polymer matrix used, the application rate of azadirachtin-A can be optimized to achieve insect control at the desired level and period.

O'Connell's process as a vicious Brownian motion.

PubMed

Katori, Makoto

2011-12-01

Vicious Brownian motion is a diffusion scaling limit of Fisher's vicious walk model, which is a system of Brownian particles in one dimension such that if two motions meet they kill each other. We consider the vicious Brownian motions conditioned never to collide with each other and call it noncolliding Brownian motion. This conditional diffusion process is equivalent to the eigenvalue process of the Hermitian-matrix-valued Brownian motion studied by Dyson [J. Math. Phys. 3, 1191 (1962)]. Recently, O'Connell [Ann. Probab. (to be published)] introduced a generalization of the noncolliding Brownian motion by using the eigenfunctions (the Whittaker functions) of the quantum Toda lattice in order to analyze a directed polymer model in 1 + 1 dimensions. We consider a system of one-dimensional Brownian motions with a long-ranged killing term as a generalization of the vicious Brownian motion and construct the O'Connell process as a conditional process of the killing Brownian motions to survive forever.

Phase-field modeling of two-dimensional crystal growth with anisotropic diffusion.

PubMed

Meca, Esteban; Shenoy, Vivek B; Lowengrub, John

2013-11-01

In the present article, we introduce a phase-field model for thin-film growth with anisotropic step energy, attachment kinetics, and diffusion, with second-order (thin-interface) corrections. We are mainly interested in the limit in which kinetic anisotropy dominates, and hence we study how the expected shape of a crystallite, which in the long-time limit is the kinetic Wulff shape, is modified by anisotropic diffusion. We present results that prove that anisotropic diffusion plays an important, counterintuitive role in the evolving crystal shape, and we add second-order corrections to the model that provide a significant increase in accuracy for small supersaturations. We also study the effect of different crystal symmetries and discuss the influence of the deposition rate.

New York | Midmarket Solar Policies in the United States | Solar Research |

Science.gov Websites

solar within the state. The statewide solar incentives program, NY-Sun, offers loans and grants for non viability. System size limit: Solar: 25 kW for residential; 100 kW for farms; 2 MW for non-residential. PSEG Long Island: 25 kW for residential solar, 2 MW for non-residential solar Aggregate cap: None PSEG Long

Brief Communication: Buoyancy-Induced Differences in Soot Morphology

NASA Technical Reports Server (NTRS)

Ku, Jerry C.; Griffin, Devon W.; Greenberg, Paul S.; Roma, John

1995-01-01

Reduction or elimination of buoyancy in flames affects the dominant mechanisms driving heat transfer, burning rates and flame shape. The absence of buoyancy produces longer residence times for soot formation, clustering and oxidation. In addition, soot pathlines are strongly affected in microgravity. We recently conducted the first experiments comparing soot morphology in normal and reduced-gravity laminar gas jet diffusion flames. Thermophoretic sampling is a relatively new but well-established technique for studying the morphology of soot primaries and aggregates. Although there have been some questions about biasing that may be induced due to sampling, recent analysis by Rosner et al. showed that the sample is not biased when the system under study is operating in the continuum limit. Furthermore, even if the sampling is preferentially biased to larger aggregates, the size-invariant premise of fractal analysis should produce a correct fractal dimension.

Aging underdamped scaled Brownian motion: Ensemble- and time-averaged particle displacements, nonergodicity, and the failure of the overdamping approximation.

PubMed

Safdari, Hadiseh; Cherstvy, Andrey G; Chechkin, Aleksei V; Bodrova, Anna; Metzler, Ralf

2017-01-01

We investigate both analytically and by computer simulations the ensemble- and time-averaged, nonergodic, and aging properties of massive particles diffusing in a medium with a time dependent diffusivity. We call this stochastic diffusion process the (aging) underdamped scaled Brownian motion (UDSBM). We demonstrate how the mean squared displacement (MSD) and the time-averaged MSD of UDSBM are affected by the inertial term in the Langevin equation, both at short, intermediate, and even long diffusion times. In particular, we quantify the ballistic regime for the MSD and the time-averaged MSD as well as the spread of individual time-averaged MSD trajectories. One of the main effects we observe is that, both for the MSD and the time-averaged MSD, for superdiffusive UDSBM the ballistic regime is much shorter than for ordinary Brownian motion. In contrast, for subdiffusive UDSBM, the ballistic region extends to much longer diffusion times. Therefore, particular care needs to be taken under what conditions the overdamped limit indeed provides a correct description, even in the long time limit. We also analyze to what extent ergodicity in the Boltzmann-Khinchin sense in this nonstationary system is broken, both for subdiffusive and superdiffusive UDSBM. Finally, the limiting case of ultraslow UDSBM is considered, with a mixed logarithmic and power-law dependence of the ensemble- and time-averaged MSDs of the particles. In the limit of strong aging, remarkably, the ordinary UDSBM and the ultraslow UDSBM behave similarly in the short time ballistic limit. The approaches developed here open ways for considering other stochastic processes under physically important conditions when a finite particle mass and aging in the system cannot be neglected.

Aging underdamped scaled Brownian motion: Ensemble- and time-averaged particle displacements, nonergodicity, and the failure of the overdamping approximation

NASA Astrophysics Data System (ADS)

Safdari, Hadiseh; Cherstvy, Andrey G.; Chechkin, Aleksei V.; Bodrova, Anna; Metzler, Ralf

2017-01-01

We investigate both analytically and by computer simulations the ensemble- and time-averaged, nonergodic, and aging properties of massive particles diffusing in a medium with a time dependent diffusivity. We call this stochastic diffusion process the (aging) underdamped scaled Brownian motion (UDSBM). We demonstrate how the mean squared displacement (MSD) and the time-averaged MSD of UDSBM are affected by the inertial term in the Langevin equation, both at short, intermediate, and even long diffusion times. In particular, we quantify the ballistic regime for the MSD and the time-averaged MSD as well as the spread of individual time-averaged MSD trajectories. One of the main effects we observe is that, both for the MSD and the time-averaged MSD, for superdiffusive UDSBM the ballistic regime is much shorter than for ordinary Brownian motion. In contrast, for subdiffusive UDSBM, the ballistic region extends to much longer diffusion times. Therefore, particular care needs to be taken under what conditions the overdamped limit indeed provides a correct description, even in the long time limit. We also analyze to what extent ergodicity in the Boltzmann-Khinchin sense in this nonstationary system is broken, both for subdiffusive and superdiffusive UDSBM. Finally, the limiting case of ultraslow UDSBM is considered, with a mixed logarithmic and power-law dependence of the ensemble- and time-averaged MSDs of the particles. In the limit of strong aging, remarkably, the ordinary UDSBM and the ultraslow UDSBM behave similarly in the short time ballistic limit. The approaches developed here open ways for considering other stochastic processes under physically important conditions when a finite particle mass and aging in the system cannot be neglected.

Diffusion in Deterministic Interacting Lattice Systems

NASA Astrophysics Data System (ADS)

Medenjak, Marko; Klobas, Katja; Prosen, Tomaž

2017-09-01

We study reversible deterministic dynamics of classical charged particles on a lattice with hard-core interaction. It is rigorously shown that the system exhibits three types of transport phenomena, ranging from ballistic, through diffusive to insulating. By obtaining an exact expressions for the current time-autocorrelation function we are able to calculate the linear response transport coefficients, such as the diffusion constant and the Drude weight. Additionally, we calculate the long-time charge profile after an inhomogeneous quench and obtain diffusive profilewith the Green-Kubo diffusion constant. Exact analytical results are corroborated by Monte Carlo simulations.

Study of diffusion coefficient of anhydrous trehalose glasses by using PFG-NMR spectroscopy

NASA Astrophysics Data System (ADS)

Kwon, Hyun-Joung; Takekawa, Reiji; Kawamura, Junichi; Tokuyama, Michio

2013-02-01

We investigated the temperature dependent long time self-diffusion coefficient of the anhydrous trehalose supercooled liquids by using pulsed field gradient nuclear magnetic resonance (PFG-NMR) spectroscopy. At the same temperature ranges, the diffusion coefficient convoluted from the α-relaxation time as Einstein-Smoluchowski relaxation, measured by using the dielectric loss spectroscopy are well overlapped with diffusion coefficients within experimental error. The temperature dependent diffusion coefficients obtained from different methods are normalized by fictive temperature and well satisfied the single master curve, proposed by Tokuyama.

Naked-eye detection of potassium ions in a novel gold nanoparticle aggregation-based aptasensor

NASA Astrophysics Data System (ADS)

Naderi, Mahboube; Hosseini, Morteza; Ganjali, Mohammad Reza

2018-04-01

In this work, we studied the feasibility of interaction among gold nanoparticles (AuNPs) and a cationic dye in an aptasensor system for the detection of potassium ions. The presence and absence of potassium in the solution was distinguishable by different colors (between orange and green) appeared after reaction. Cationic dye (Y5GL) acts as a new aggregator for AuNP-based sensors which changes the aggregated AuNP solution color from blue-purple to green. In the presence of K+ ions, the aptamer dissociated from the surface of the AuNP so that free AuNPs and cationic dye make the solution green. The aptasensor showed that the analytical linear range was from 10 nM to 50 mM and the detection limit was 4.4 nM. Also, we examined the practicality of this method on a simple paper based platform. The linear range of the colorimetric paper sensor covered of K+ concentration from 10 μM to 40 mM and the detection limit of 6.2 μM was obtained. The selectivity of AuNP aggregation-based sensor improved by the use of cationic dye. Rapidity, simplicity, high sensitivity and excellent selectivity made this assay suitable for practical determination of K+ in real urine samples.

Consistent platelet inhibition during long-term maintenance-dose clopidogrel therapy among 359 compliant outpatients with documented vascular disease.

PubMed

Serebruany, Victor L; Malinin, Alex I; Atar, Dan; Hanley, Dan F

2007-03-01

Numerous reports have dichotomized responses after clopidogrel therapy using varying definitions and platelet tests in patients immediately after acute vascular events; however, no large study has assessed platelet characteristics in outpatients receiving long-term treatment for more than 30 days with the maintenance dose (75 mg/d) of clopidogrel. The aim of this study was to describe the responses of ex vivo measures of platelet aggregation and activation to long-term clopidogrel therapy in a large population of outpatients after coronary stenting or ischemic stroke. We conducted a secondary post hoc analysis of a data set represented by presumably compliant patients after coronary stenting (n = 237) or a documented ischemic stroke (n = 122) treated with clopidogrel-and-aspirin combination antiplatelet therapy. The mean duration of treatment was 5.8 months (range 1-21 months). Every patient exhibited a significant inhibition of adenosine diphosphate-induced platelet aggregation (mean 52.9%, range 36%-70%) as compared with the preclopidogrel measures. Inhibition of aggregation strongly correlated with a diminished expression of PECAM-1 (platelet/endothelial cell adhesion molecule 1, r = 0.75), glycoprotein IIb/IIIa (r = 0.62), and PAR-1 (protease-activated receptor 1, r = 0.71). None of the patients developed hyporesponsiveness (reduction from the baseline <15%) or profound inhibition (residual platelet activity <10%). In contrast to the wide variability of responses that exists in the acute setting, long-term therapy with clopidogrel leads to consistent and much less variable platelet inhibition. Lack of nonresponse and profound inhibition with clopidogrel allow for the maintenance of a delicate balance between proven efficacy and acceptable bleeding risks for long-term secondary prevention in outpatients after acute vascular events.

Relation of short-range and long-range lithium ion dynamics in glass-ceramics: Insights from 7Li NMR field-cycling and field-gradient studies

NASA Astrophysics Data System (ADS)

Haaks, Michael; Martin, Steve W.; Vogel, Michael

2017-09-01

We use various 7Li NMR methods to investigate lithium ion dynamics in 70Li 2S-30 P 2S5 glass and glass-ceramic obtained from this glass after heat treatment. We employ 7Li spin-lattice relaxometry, including field-cycling measurements, and line-shape analysis to investigate short-range ion jumps as well as 7Li field-gradient approaches to characterize long-range ion diffusion. The results show that ceramization substantially enhances the lithium ion mobility on all length scales. For the 70Li 2S-30 P 2S5 glass-ceramic, no evidence is found that bimodal dynamics result from different ion mobilities in glassy and crystalline regions of this sample. Rather, 7Li field-cycling relaxometry shows that dynamic susceptibilities in broad frequency and temperature ranges can be described by thermally activated jumps governed by a Gaussian distribution of activation energies g (Ea) with temperature-independent mean value Em=0.43 eV and standard deviation σ =0.07 eV . Moreover, use of this distribution allows us to rationalize 7Li line-shape results for the local ion jumps. In addition, this information about short-range ion dynamics further explains 7Li field-gradient results for long-range ion diffusion. In particular, we quantitatively show that, consistent with our experimental results, the temperature dependence of the self-diffusion coefficient D is not described by the mean activation energy Em of the local ion jumps, but by a significantly smaller apparent value whenever the distribution of correlation times G (logτ ) of the jump motion derives from an invariant distribution of activation energies and, hence, continuously broadens upon cooling. This effect occurs because the harmonic mean, which determines the results of diffusivity or also conductivity studies, continuously separates from the peak position of G (logτ ) when the width of this distribution increases.

Native Mussels Alter Nutrient Availability and Reduce Blue ...

EPA Pesticide Factsheets

Nutrient cycling is a key process that ties all organisms together. This is especially apparent in stream environments in which nutrients are taken up readily and cycled through the system in a downstream trajectory. Ecological stoichiometry predicts that biogeochemical cycles of different elements are interdependent because the organisms that drive these cycles require fixed ratios of nutrients. There is growing recognition that animals play an important role in biogeochemical cycling across ecosystems. In particular, dense aggregations of consumers can create biogeochemical hotspots in aquatic ecosystems via nutrient translocation. We predicted that filter-feeding freshwater mussels, which occur as speciose, high biomass aggregates, would create biogeochemical hotspots in streams by altering nutrient limitation and algal dynamics. In a field study, we manipulated nitrogen and phosphorus using nutrient-diffusing substrates in areas with high and low mussel abundance, recorded algal growth and community composition, and determined in situ mussel excretion stoichiometry at 18 sites in 3 rivers (Kiamichi, Little, and Mt. Fork rivers, southcentral U.S.). Our results indicate that mussels greatly influence ecosystem processes by modifying the nutrients that limit primary productivity. Sites without mussels were N-limited with ~26% higher abundances of N-fixing blue-green algae, while sites with high mussel densities were co-limited (N and P) and dominated by diatoms

Aeromonas species exhibit aggregative adherence to HEp-2 cells.

PubMed Central

Neves, M S; Nunes, M P; Milhomem, A M

1994-01-01

Clinical and environmental isolates of Aeromonas species (five A. hydrophila isolates, three A. caviae isolates, and two A. sobria isolates) were tested for their adherence to HEp-2 cells. Clinical isolates of A. hydrophila and A. sobria exhibited aggregative adherence similar to that presented by enteroadherent-aggregative Escherichia coli. Bacterial aggregates adhered to cells with a typical "stacked-brick" appearance. In contrast, A. caviae strains showed a diffuse adherence pattern. Images PMID:8027331

Quantitative phenomenological model of the BOLD contrast mechanism

NASA Astrophysics Data System (ADS)

Dickson, John D.; Ash, Tom W. J.; Williams, Guy B.; Sukstanskii, Alexander L.; Ansorge, Richard E.; Yablonskiy, Dmitriy A.

2011-09-01

Different theoretical models of the BOLD contrast mechanism are used for many applications including BOLD quantification (qBOLD) and vessel size imaging, both in health and disease. Each model simplifies the system under consideration, making approximations about the structure of the blood vessel network and diffusion of water molecules through inhomogeneities in the magnetic field created by deoxyhemoglobin-containing blood vessels. In this study, Monte-Carlo methods are used to simulate the BOLD MR signal generated by diffusing water molecules in the presence of long, cylindrical blood vessels. Using these simulations we introduce a new, phenomenological model that is far more accurate over a range of blood oxygenation levels and blood vessel radii than existing models. This model could be used to extract physiological parameters of the blood vessel network from experimental data in BOLD-based experiments. We use our model to establish ranges of validity for the existing analytical models of Yablonskiy and Haacke, Kiselev and Posse, Sukstanskii and Yablonskiy (extended to the case of arbitrary time in the spin echo sequence) and Bauer et al. (extended to the case of randomly oriented cylinders). Although these models are shown to be accurate in the limits of diffusion under which they were derived, none of them is accurate for the whole physiological range of blood vessels radii and blood oxygenation levels. We also show the extent of systematic errors that are introduced due to the approximations of these models when used for BOLD signal quantification.

Critical spreading dynamics of parity conserving annihilating random walks with power-law branching

NASA Astrophysics Data System (ADS)

Laise, T.; dos Anjos, F. C.; Argolo, C.; Lyra, M. L.

2018-09-01

We investigate the critical spreading of the parity conserving annihilating random walks model with Lévy-like branching. The random walks are considered to perform normal diffusion with probability p on the sites of a one-dimensional lattice, annihilating in pairs by contact. With probability 1 - p, each particle can also produce two offspring which are placed at a distance r from the original site following a power-law Lévy-like distribution P(r) ∝ 1 /rα. We perform numerical simulations starting from a single particle. A finite-time scaling analysis is employed to locate the critical diffusion probability pc below which a finite density of particles is developed in the long-time limit. Further, we estimate the spreading dynamical exponents related to the increase of the average number of particles at the critical point and its respective fluctuations. The critical exponents deviate from those of the counterpart model with short-range branching for small values of α. The numerical data suggest that continuously varying spreading exponents sets up while the branching process still results in a diffusive-like spreading.

Composition, buoyancy regulation and fate of ice algal aggregates in the Central Arctic Ocean.

PubMed

Fernández-Méndez, Mar; Wenzhöfer, Frank; Peeken, Ilka; Sørensen, Heidi L; Glud, Ronnie N; Boetius, Antje

2014-01-01

Sea-ice diatoms are known to accumulate in large aggregates in and under sea ice and in melt ponds. There is recent evidence from the Arctic that such aggregates can contribute substantially to particle export when sinking from the ice. The role and regulation of microbial aggregation in the highly seasonal, nutrient- and light-limited Arctic sea-ice ecosystem is not well understood. To elucidate the mechanisms controlling the formation and export of algal aggregates from sea ice, we investigated samples taken in late summer 2011 and 2012, during two cruises to the Eurasian Basin of the Central Arctic Ocean. Spherical aggregates densely packed with pennate diatoms, as well as filamentous aggregates formed by Melosira arctica showed sign of different stages of degradation and physiological stoichiometries, with carbon to chlorophyll a ratios ranging from 110 to 66700, and carbon to nitrogen molar ratios of 8-35 and 9-40, respectively. Sub-ice algal aggregate densities ranged between 1 and 17 aggregates m(-2), maintaining an estimated net primary production of 0.4-40 mg C m(-2) d(-1), and accounted for 3-80% of total phototrophic biomass and up to 94% of local net primary production. A potential factor controlling the buoyancy of the aggregates was light intensity, regulating photosynthetic oxygen production and the amount of gas bubbles trapped within the mucous matrix, even at low ambient nutrient concentrations. Our data-set was used to evaluate the distribution and importance of Arctic algal aggregates as carbon source for pelagic and benthic communities.

Composition, Buoyancy Regulation and Fate of Ice Algal Aggregates in the Central Arctic Ocean

PubMed Central

Fernández-Méndez, Mar; Wenzhöfer, Frank; Peeken, Ilka; Sørensen, Heidi L.; Glud, Ronnie N.; Boetius, Antje

2014-01-01

Sea-ice diatoms are known to accumulate in large aggregates in and under sea ice and in melt ponds. There is recent evidence from the Arctic that such aggregates can contribute substantially to particle export when sinking from the ice. The role and regulation of microbial aggregation in the highly seasonal, nutrient- and light-limited Arctic sea-ice ecosystem is not well understood. To elucidate the mechanisms controlling the formation and export of algal aggregates from sea ice, we investigated samples taken in late summer 2011 and 2012, during two cruises to the Eurasian Basin of the Central Arctic Ocean. Spherical aggregates densely packed with pennate diatoms, as well as filamentous aggregates formed by Melosira arctica showed sign of different stages of degradation and physiological stoichiometries, with carbon to chlorophyll a ratios ranging from 110 to 66700, and carbon to nitrogen molar ratios of 8–35 and 9–40, respectively. Sub-ice algal aggregate densities ranged between 1 and 17 aggregates m−2, maintaining an estimated net primary production of 0.4–40 mg C m−2 d−1, and accounted for 3–80% of total phototrophic biomass and up to 94% of local net primary production. A potential factor controlling the buoyancy of the aggregates was light intensity, regulating photosynthetic oxygen production and the amount of gas bubbles trapped within the mucous matrix, even at low ambient nutrient concentrations. Our data-set was used to evaluate the distribution and importance of Arctic algal aggregates as carbon source for pelagic and benthic communities. PMID:25208058

Interactions of lysozyme in concentrated electrolyte solutions from dynamic light-scattering measurements.

PubMed Central

Kuehner, D E; Heyer, C; Rämsch, C; Fornefeld, U M; Blanch, H W; Prausnitz, J M

1997-01-01

The diffusion of hen egg-white lysozyme has been studied by dynamic light scattering in aqueous solutions of ammonium sulfate as a function of protein concentration to 30 g/liter. Experiments were conducted under the following conditions: pH 4-7 and ionic strength 0.05-5.0 M. Diffusivity data for ionic strengths up to 0.5 M were interpreted in the context of a two-body interaction model for monomers. From this analysis, two potential-of-mean-force parameters, the effective monomer charge, and the Hamaker constant were obtained. At higher ionic strength, the data were analyzed using a model that describes the diffusion coefficient of a polydisperse system of interacting protein aggregates in terms of an isodesmic, indefinite aggregation equilibrium constant. Data analysis incorporated multicomponent virial and hydrodynamic effects. The resulting equilibrium constants indicate that lysozyme does not aggregate significantly as ionic strength increases, even at salt concentrations near the point of salting-out precipitation. PMID:9414232

The effect of hardness on the stability of citrate-stabilized gold nanoparticles and their uptake by Daphnia magna.

PubMed

Lee, Byung-Tae; Ranville, James F

2012-04-30

The stability and uptake by Daphnia magna of citrate-stabilized gold nanoparticles (AuNPs) in three different hardness-adjusted synthetic waters were investigated. Negatively charged AuNPs were found to aggregate and settle in synthetic waters within 24 h. Sedimentation rates depended on initial particle concentrations of 0.02, 0.04, and 0.08 nM AuNPs. Hardness of the synthetic waters affected the aggregation of AuNPs and is explained by the compression of diffuse double layer of AuNPs due to the increasing ionic strength. The fractal dimension of AuNPs in the reaction-limited regime of synthetic waters averaged 2.228±0.126 implying the rigid structures of aggregates driven by the collision of small particles with the growing aggregates. Four-day old D. magna accumulated more than 90% of AuNPs in 0.04 nM AuNP suspensions without any observed mortality. Exposure to pre-aggregated AuNP for 48 h in hard water did not show any significant difference in uptake, suggesting D. magna can also ingest settled AuNP aggregates. D. magna exposed to AuNPs shed their exoskeleton whereas the control did not generate any molts over 48 h. This implies that D. magna removed AuNPs on their exoskeleton by producing molts to decrease any adverse effects of adhered AuNPs. Copyright © 2012 Elsevier B.V. All rights reserved.

Historical changes in northeastern US bee pollinators related to shared ecological traits.

PubMed

Bartomeus, Ignasi; Ascher, John S; Gibbs, Jason; Danforth, Bryan N; Wagner, David L; Hedtke, Shannon M; Winfree, Rachael

2013-03-19

Pollinators such as bees are essential to the functioning of terrestrial ecosystems. However, despite concerns about a global pollinator crisis, long-term data on the status of bee species are limited. We present a long-term study of relative rates of change for an entire regional bee fauna in the northeastern United States, based on >30,000 museum records representing 438 species. Over a 140-y period, aggregate native species richness weakly decreased, but richness declines were significant only for the genus Bombus. Of 187 native species analyzed individually, only three declined steeply, all of these in the genus Bombus. However, there were large shifts in community composition, as indicated by 56% of species showing significant changes in relative abundance over time. Traits associated with a declining relative abundance include small dietary and phenological breadth and large body size. In addition, species with lower latitudinal range boundaries are increasing in relative abundance, a finding that may represent a response to climate change. We show that despite marked increases in human population density and large changes in anthropogenic land use, aggregate native species richness declines were modest outside of the genus Bombus. At the same time, we find that certain ecological traits are associated with declines in relative abundance. These results should help target conservation efforts focused on maintaining native bee abundance and diversity and therefore the important ecosystems services that they provide.

The wiper model: avalanche dynamics in an exclusion process

NASA Astrophysics Data System (ADS)

Politi, Antonio; Romano, M. Carmen

2013-10-01

The exclusion-process model (Ciandrini et al 2010 Phys. Rev. E 81 051904) describing traffic of particles with internal stepping dynamics reveals the presence of strong correlations in realistic regimes. Here we study such a model in the limit of an infinitely fast translocation time, where the evolution can be interpreted as a ‘wiper’ that moves to dry neighbouring sites. We trace back the existence of long-range correlations to the existence of avalanches, where many sites are dried at once. At variance with self-organized criticality, in the wiper model avalanches have a typical size equal to the logarithm of the lattice size. In the thermodynamic limit, we find that the hydrodynamic behaviour is a mixture of stochastic (diffusive) fluctuations and increasingly coherent periodic oscillations that are reminiscent of a collective dynamics.

SAVI: Synthetic apertures for long-range, subdiffraction-limited visible imaging using Fourier ptychography

PubMed Central

Holloway, Jason; Wu, Yicheng; Sharma, Manoj K.; Cossairt, Oliver; Veeraraghavan, Ashok

2017-01-01

Synthetic aperture radar is a well-known technique for improving resolution in radio imaging. Extending these synthetic aperture techniques to the visible light domain is not straightforward because optical receivers cannot measure phase information. We propose to use macroscopic Fourier ptychography (FP) as a practical means of creating a synthetic aperture for visible imaging to achieve subdiffraction-limited resolution. We demonstrate the first working prototype for macroscopic FP in a reflection imaging geometry that is capable of imaging optically rough objects. In addition, a novel image space denoising regularization is introduced during phase retrieval to reduce the effects of speckle and improve perceptual quality of the recovered high-resolution image. Our approach is validated experimentally where the resolution of various diffuse objects is improved sixfold. PMID:28439550

Modeling of long range frequency sweeping for energetic particle modes

NASA Astrophysics Data System (ADS)

Nyqvist, R. M.; Breizman, B. N.

2013-04-01

Long range frequency sweeping events are simulated numerically within a one-dimensional, electrostatic bump-on-tail model with fast particle sources and collisions. The numerical solution accounts for fast particle trapping and detrapping in an evolving wave field with a fixed wavelength, and it includes three distinct collisions operators: Drag (dynamical friction on the background electrons), Krook-type collisions, and velocity space diffusion. The effects of particle trapping and diffusion on the evolution of holes and clumps are investigated, and the occurrence of non-monotonic (hooked) frequency sweeping and asymptotically steady holes is discussed. The presented solution constitutes a step towards predictive modeling of frequency sweeping events in more realistic geometries.

Convective flow effects on protein crystal growth

NASA Technical Reports Server (NTRS)

Rosenberger, Franz; Monaco, Lisa A.

1994-01-01

A high-resolution microscopic interferometric setup for the monitoring of protein morphologies has been developed. Growth or dissolution of a crystal can be resolved with a long-term depth resolution of 200 A and a lateral resolution of 2 microns. This capability of simultaneously monitoring the interfacial displacement with high local depth resolution has yielded several novel results. We have found with lysozyme that (1) the normal growth rate is oscillatory, and (2) depending on the impurity content of the solution, the growth step density is either greater or lower at the periphery of a facet than in its center. The repartitioning of Na plus and Cl minus ions between lysozyme solutions and crystals was studied for a wide range of crystallization conditions. A nucleation-growth-repartitioning model was developed, to interpret the large body of data in unified way. The results strongly suggest that (1) the ion to lysozyne ratio in the crystal depends mostly on kinetic rather than crystallographic parameters, and (2) lysozyme crystals possess a salt-rich core with a diameter electron microscopy results appear to confirm this finding, which could have far-reaching consequences for x-ray diffraction studies. A computational model for diffusive-convective transport in protein crystallization has been applied to a realistic growth cell geometry, taking into account the findings of the above repartitioning studies and our kinetics data for the growth of lysozyme. The results show that even in the small cell employed, protein concentration nonuniformities and gravity-driven solutal convection can be significant. The calculated convection velocities are of the same order to magnitude as those found in earlier experiments. As expected, convective transport, i.e., at Og, lysozyme crystal growth remains kinetically limited. The salt distribution in the crystal is predicted to be non-uniform at both 1g and 0g, as a consequence of protein depletion in the solution. Static and dynamic light scattering studies in undersaturated and supersaturated solutions have been performed. Diffusivities in undersaturated solutions, were found to vary with lysozyme concentrations. Depending on the salt concentration, the diffusivities either increase or decrease. Interestingly, the corresponding static scattering intensities behave oppositely, Our current analysis indicates that these changes are inconsistent with aggregation in undersaturated solutions. However, the data are compatible with concentration-dependent changes of the interactions between protein and salt.

Self-organized synthesis of silver dendritic nanostructures via an electroless metal deposition method

NASA Astrophysics Data System (ADS)

Qiu, T.; Wu, X. L.; Mei, Y. F.; Chu, P. K.; Siu, G. G.

2005-09-01

Unique silver dendritic nanostructures, with stems, branches, and leaves, were synthesized with self-organization via a simple electroless metal deposition method in a conventional autoclave containing aqueous HF and AgNO3 solution. Their growth mechanisms are discussed in detail on the basis of a self-assembled localized microscopic electrochemical cell model. A process of diffusion-limited aggregation is suggested for the formation of the silver dendritic nanostructures. This nanostructured material is of great potential to be building blocks for assembling mini-functional devices of the next generation.

Preference limits of the visual dynamic range for ultra high quality and aesthetic conveyance

NASA Astrophysics Data System (ADS)

Daly, Scott; Kunkel, Timo; Sun, Xing; Farrell, Suzanne; Crum, Poppy

2013-03-01

A subjective study was conducted to investigate the preferred maximum and minimum display luminances in order to determine the dynamic ranges for future displays. Two studies address the diffuse reflective regions, and a third study tested preferences of highlight regions. Preferences, as opposed to detection thresholds, were studied to provide results more directly relevant to the viewing of entertainment or art. Test images were specifically designed to test these limits without the perceptual conflicts that usually occur in these types of studies. For the diffuse range, we found a display with a dynamic range having luminances between 0.1 and 650 cd/m2 matches the average preferences. However, to satisfy 90% of the population, a dynamic range from 0.005 and ~3,000 cd/m2 is needed. Since a display should be able to produce values brighter than the diffuse white maximum, as in specular highlights and emissive sources, the highlight study concludes that even the average preferred maximum luminance for highlight reproduction is ~4,000 cd/m2.

Embryonic Mutant Huntingtin Aggregate Formation in Mouse Models of Huntington's Disease.

PubMed

Osmand, Alexander P; Bichell, Terry Jo; Bowman, Aaron B; Bates, Gillian P

2016-12-15

The role of aggregate formation in the pathophysiology of Huntington's disease (HD) remains uncertain. However, the temporal appearance of aggregates tends to correlate with the onset of symptoms and the numbers of neuropil aggregates correlate with the progression of clinical disease. Using highly sensitive immunohistochemical methods we have detected the appearance of diffuse aggregates during embryonic development in the R6/2 and YAC128 mouse models of HD. These are initially seen in developing axonal tracts and appear to spread throughout the cerebrum in the early neonate.

Long-term Culture of Human iPS Cell-derived Telencephalic Neuron Aggregates on Collagen Gel.

PubMed

Oyama, Hiroshi; Takahashi, Koji; Tanaka, Yoshikazu; Takemoto, Hiroshi; Haga, Hisashi

2018-01-01

It takes several months to form the 3-dimensional morphology of the human embryonic brain. Therefore, establishing a long-term culture method for neuronal tissues derived from human induced pluripotent stem (iPS) cells is very important for studying human brain development. However, it is difficult to keep primary neurons alive for more than 3 weeks in culture. Moreover, long-term adherent culture to maintain the morphology of telencephalic neuron aggregates induced from human iPS cells is also difficult. Although collagen gel has been widely used to support long-term culture of cells, it is not clear whether human iPS cell-derived neuron aggregates can be cultured for long periods on this substrate. In the present study, we differentiated human iPS cells to telencephalic neuron aggregates and examined long-term culture of these aggregates on collagen gel. The results indicated that these aggregates could be cultured for over 3 months by adhering tightly onto collagen gel. Furthermore, telencephalic neuronal precursors within these aggregates matured over time and formed layered structures. Thus, long-term culture of telencephalic neuron aggregates derived from human iPS cells on collagen gel would be useful for studying human cerebral cortex development.Key words: Induced pluripotent stem cell, forebrain neuron, collagen gel, long-term culture.

The breakup mechanism of biomolecular and colloidal aggregates in a shear flow

NASA Astrophysics Data System (ADS)

Ó Conchúir, Breanndán; Zaccone, Alessio

2014-03-01

The theory of self-assembly of colloidal particles in shear flow is incomplete. Previous analytical approaches have failed to capture the microscopic interplay between diffusion, shear and intermolecular interactions which controls the aggregates fate in shear. In this work we analytically solved the drift-diffusion equation for the breakup rate of a dimer in flow. Then applying rigidity percolation theory, we found that the lifetime of a generic cluster formed under shear is controlled by the typical lifetime of a single bond in its interior, which in turn depends on the efficiency of the stress transmitted from other bonds in the cluster. We showed that aggregate breakup is a thermally-activated process where the activation energy is controlled by the interplay between intermolecular forces and the shear drift, and where structural parameters determine whether cluster fragmentation or surface erosion prevails. In our latest work, we analyzed floppy modes and nonaffine deformations to derive a lower bound on the fractal dimension df below which aggregates are mechanically unstable, ie. for large aggregates df ~= 2.4. This theoretical framework is in quantitative agreement with experiments and can be used for population balance modeling of colloidal and protein aggregation.

Nonequilibrium forces following quenches in active and thermal matter.

PubMed

Rohwer, Christian M; Solon, Alexandre; Kardar, Mehran; Krüger, Matthias

2018-03-01

Nonequilibrium systems with conserved quantities like density or momentum are known to exhibit long-ranged correlations. This, in turn, leads to long-ranged fluctuation-induced (Casimir) forces, predicted to arise in a variety of nonequilibrium settings. Here, we study such forces, which arise transiently between parallel plates or compact inclusions in a gas of particles, following a change ("quench") in temperature or activity of the medium. Analytical calculations, as well as numerical simulations of passive or active Brownian particles, indicate two distinct forces: (i) The immediate effect of the quench is adsorption or desorption of particles of the medium to the immersed objects, which in turn initiates a front of relaxing (mean) density. This leads to time-dependent density-induced forces. (ii) A long-term effect of the quench is that density fluctuations are modified, manifested as transient (long-ranged) (pair-)correlations that relax diffusively to their (short-ranged) steady-state limit. As a result, transient fluctuation-induced forces emerge. We discuss the properties of fluctuation-induced and density-induced forces as regards universality, relaxation as a function of time, and scaling with distance between objects. Their distinct signatures allow us to distinguish the two types of forces in simulation data. Our simulations also show that a quench of the effective temperature of an active medium gives rise to qualitatively similar effects to a temperature quench in a passive medium. Based on this insight, we propose several scenarios for the experimental observation of the forces described here.

Nonequilibrium forces following quenches in active and thermal matter

NASA Astrophysics Data System (ADS)

Rohwer, Christian M.; Solon, Alexandre; Kardar, Mehran; Krüger, Matthias

2018-03-01

Nonequilibrium systems with conserved quantities like density or momentum are known to exhibit long-ranged correlations. This, in turn, leads to long-ranged fluctuation-induced (Casimir) forces, predicted to arise in a variety of nonequilibrium settings. Here, we study such forces, which arise transiently between parallel plates or compact inclusions in a gas of particles, following a change ("quench") in temperature or activity of the medium. Analytical calculations, as well as numerical simulations of passive or active Brownian particles, indicate two distinct forces: (i) The immediate effect of the quench is adsorption or desorption of particles of the medium to the immersed objects, which in turn initiates a front of relaxing (mean) density. This leads to time-dependent density-induced forces. (ii) A long-term effect of the quench is that density fluctuations are modified, manifested as transient (long-ranged) (pair-)correlations that relax diffusively to their (short-ranged) steady-state limit. As a result, transient fluctuation-induced forces emerge. We discuss the properties of fluctuation-induced and density-induced forces as regards universality, relaxation as a function of time, and scaling with distance between objects. Their distinct signatures allow us to distinguish the two types of forces in simulation data. Our simulations also show that a quench of the effective temperature of an active medium gives rise to qualitatively similar effects to a temperature quench in a passive medium. Based on this insight, we propose several scenarios for the experimental observation of the forces described here.

Size-tunable copper nanocluster aggregates and their application in hydrogen sulfide sensing on paper-based devices

NASA Astrophysics Data System (ADS)

Chen, Po-Cheng; Li, Yu-Chi; Ma, Jia-Yin; Huang, Jia-Yu; Chen, Chien-Fu; Chang, Huan-Tsung

2016-04-01

Polystyrene sulfonate (PSS), a strong polyelectrolyte, was used to prepare red photoluminescent PSS-penicillamine (PA) copper (Cu) nanoclusters (NC) aggregates, which displayed high selectivity and sensitivity to the detection of hydrogen sulfide (H2S). The size of the PSS-PA-Cu NC aggregates could be readily controlled from 5.5 μm to 173 nm using different concentrations of PSS, which enabled better dispersity and higher sensitivity towards H2S. PSS-PA-Cu NC aggregates provided rapid H2S detection by using the strong Cu-S interaction to quench NC photoluminescence as a sensing mechanism. As a result, a detection limit of 650 nM, which is lower than the maximum level permitted in drinking water by the World Health Organization, was achieved for the analysis of H2S in spring-water samples. Moreover, highly dispersed PSS-PA-Cu NC aggregates could be incorporated into a plate-format paper-based analytical device which enables ultra-low sample volumes (5 μL) and feature shorter analysis times (30 min) compared to conventional solution-based methods. The advantages of low reagent consumption, rapid result readout, limited equipment, and long-term storage make this platform sensitive and simple enough to use without specialized training in resource constrained settings.

Retention and effective diffusion of model metabolites on porous graphitic carbon.

PubMed

Lunn, Daniel B; Yun, Young J; Jorgenson, James W

2017-12-29

The study of metabolites in biological samples is of high interest for a wide range of biological and pharmaceutical applications. Reversed phase liquid chromatography is a common technique used for the separation of metabolites, but it provides little retention for polar metabolites. An alternative to C18 bonded phases, porous graphitic carbon has the ability to provide significant retention for both non-polar and polar analytes. The goal of this work is to study the retention and effective diffusion properties of porous graphitic carbon, to see if it is suitable for the wide injection bands and long run times associated with long, packed capillary-scale separations. The retention of a set of standard metabolites was studied for both stationary phases over a wide range of mobile phase conditions. This data showed that porous graphitic carbon benefits from significantly increased retention (often >100 fold) under initial gradient conditions for these metabolites, suggesting much improved ability to focus a wide injection band at the column inlet. The effective diffusion properties of these columns were studied using peak-parking experiments with the standard metabolites under a wide range of retention conditions. Under the high retention conditions, which can be associated with retention after injection loading for gradient separations, D eff /D m ∼0.1 for both the C18-bonded and porous graphitic carbon columns. As C18 bonded particles are widely, and successfully utilized for long gradient separations without issue of increasing peak width from longitudinal diffusion, this suggests that porous graphitic carbon should be amenable for long runtime gradient separations as well. Copyright © 2017 Elsevier B.V. All rights reserved.

Non-Linear Dynamics of Saturn's Rings

NASA Astrophysics Data System (ADS)

Esposito, L. W.

2016-12-01

Non-linear processes can explain why Saturn's rings are so active and dynamic. Ring systems differ from simple linear systems in two significant ways: 1. They are systems of granular material: where particle-to-particle collisions dominate; thus a kinetic, not a fluid description needed. Stresses are strikingly inhomogeneous and fluctuations are large compared to equilibrium. 2. They are strongly forced by resonances: which drive a non-linear response, that push the system across thresholds that lead to persistent states. Some of this non-linearity is captured in a simple Predator-Prey Model: Periodic forcing from the moon causes streamline crowding; This damps the relative velocity. About a quarter phase later, the aggregates stir the system to higher relative velocity and the limit cycle repeats each orbit, with relative velocity ranging from nearly zero to a multiple of the orbit average. Summary of Halo Results: A predator-prey model for ring dynamics produces transient structures like `straw' that can explain the halo morphology and spectroscopy: Cyclic velocity changes cause perturbed regions to reach higher collision speeds at some orbital phases, which preferentially removes small regolith particles; surrounding particles diffuse back too slowly to erase the effect: this gives the halo morphology; this requires energetic collisions (v ≈ 10m/sec, with throw distances about 200km, implying objects of scale R ≈ 20km).Transform to Duffing Eqn : With the coordinate transformation, z = M2/3, the Predator-Prey equations can be combined to form a single second-order differential equation with harmonic resonance forcing.Ring dynamics and history implications: Moon-triggered clumping explains both small and large particles at resonances. We calculate the stationary size distribution using a cell-to-cell mapping procedure that converts the phase-plane trajectories to a Markov chain. Approximating it as an asymmetric random walk with reflecting boundaries determines the power law index, using results of numerical simulations in the tidal environment. Aggregates can explain many dynamic aspects of the rings and can renew rings by shielding and recycling the material within them, depending on how long the mass is sequestered. We can ask: Are Saturn's rings a chaotic non-linear driven system?

Permanganate diffusion and reaction in sedimentary rocks.

PubMed

Huang, Qiuyuan; Dong, Hailiang; Towne, Rachael M; Fischer, Timothy B; Schaefer, Charles E

2014-04-01

In situ chemical oxidation using permanganate has frequently been used to treat chlorinated solvents in fractured bedrock aquifers. However, in systems where matrix back-diffusion is an important process, the ability of the oxidant to migrate and treat target contaminants within the rock matrix will likely determine the overall effectiveness of this remedial approach. In this study, a series of diffusion experiments were performed to measure the permanganate diffusion and reaction in four different types of sedimentary rocks (dark gray mudstone, light gray mudstone, red sandstone, and tan sandstone). Results showed that, within the experimental time frame (~2 months), oxidant migration into the rock was limited to distances less than 500 μm. The observed diffusivities for permanganate into the rock matrices ranged from 5.3 × 10(-13) to 1.3 × 10(-11) cm(2)/s. These values were reasonably predicted by accounting for both the rock oxidant demand and the effective diffusivity of the rock. Various Mn minerals formed as surface coatings from reduction of permanganate coupled with oxidation of total organic carbon (TOC), and the nature of the formed Mn minerals was dependent upon the rock type. Post-treatment tracer testing showed that these Mn mineral coatings had a negligible impact on diffusion through the rock. Overall, our results showed that the extent of permanganate diffusion and reaction depended on rock properties, including porosity, mineralogy, and organic carbon. These results have important implications for our understanding of long-term organic contaminant remediation in sedimentary rocks using permanganate. Copyright © 2014 Elsevier B.V. All rights reserved.

Direct detection constraints on dark photon dark matter

NASA Astrophysics Data System (ADS)

An, Haipeng; Pospelov, Maxim; Pradler, Josef; Ritz, Adam

2015-07-01

Dark matter detectors built primarily to probe elastic scattering of WIMPs on nuclei are also precise probes of light, weakly coupled, particles that may be absorbed by the detector material. In this paper, we derive constraints on the minimal model of dark matter comprised of long-lived vector states V (dark photons) in the 0.01- 100 keV mass range. The absence of an ionization signal in direct detection experiments such as XENON10 and XENON100 places a very strong constraint on the dark photon mixing angle, down to O (10-15), assuming that dark photons comprise the dominant fraction of dark matter. This sensitivity to dark photon dark matter exceeds the indirect bounds derived from stellar energy loss considerations over a significant fraction of the available mass range. We also revisit indirect constraints from V → 3 γ decay and show that limits from modifications to the cosmological ionization history are comparable to the updated limits from the diffuse γ-ray flux.

Direct detection constraints on dark photon dark matter

DOE PAGES

An, Haipeng; Pospelov, Maxim; Pradler, Josef; ...

2015-06-11

Dark matter detectors built primarily to probe elastic scattering of WIMPs on nuclei are also precise probes of light, weakly coupled, particles that may be absorbed by the detector material. In this paper, we derive constraints on the minimal model of dark matter comprised of long-lived vector states V (dark photons) in the 0.01–100KeV mass range. The absence of an ionization signal in direct detection experiments such as XENON10 and XENON100 places a very strong constraint on the dark photon mixing angle, down to Ο(10 –15), assuming that dark photons comprise the dominant fraction of dark matter. This sensitivity tomore » dark photon dark matter exceeds the indirect bounds derived from stellar energy loss considerations over a significant fraction of the available mass range. As a result, we also revisit indirect constraints from V → 3γ decay and show that limits from modifications to the cosmological ionization history are comparable to the updated limits from the diffuse γ-ray flux.« less

Aggregate supply and demand modeling using GIS methods for the front range urban corridor, Colorado

NASA Astrophysics Data System (ADS)

Karakas, Ahmet; Turner, Keith

2004-07-01

The combined use of allocation modeling and geographical information system (GIS) technologies for providing quantitative assessments of aggregate supply and demand is evaluated using representative data for the Front Range Urban Corridor (FRUC) in Colorado. The FRUC extends from the Colorado-Wyoming border to south of Colorado Springs, and includes Denver and the major urban growth regions of Colorado. In this area, aggregate demand is high and is increasing in response to population growth. Neighborhood opposition to the establishment of new pits and quarries and the depletion of many deposits are limiting aggregate supplies. Many sources are already covered by urban development or eliminated from production by zoning. Transport of aggregate by rail from distant resources may be required in the future. Two allocation-modeling procedures are tested in this study. Network analysis procedures provided within the ARC/INFO software, are unsatisfactory. Further aggregate allocation modeling used a model specifically designed for this task; a modified version of an existing Colorado School of Mines allocation model allows for more realistic market analyses. This study evaluated four scenarios. The entire region was evaluated with a scenario reflecting the current market and by a second scenario in which some existing suppliers were closed down and new potential suppliers were activated. The conditions within the Denver metropolitan area were studied before and after the introduction of three possible rail-to-truck aggregate distribution centers. GIS techniques are helpful in developing the required database to describe the Front Range Urban Corridor aggregate market conditions. GIS methods allow the digital representation of the regional road network, and the development of a distance matrix relating all suppliers and purchasers.

Heat transport in oscillator chains with long-range interactions coupled to thermal reservoirs.

PubMed

Iubini, Stefano; Di Cintio, Pierfrancesco; Lepri, Stefano; Livi, Roberto; Casetti, Lapo

2018-03-01

We investigate thermal conduction in arrays of long-range interacting rotors and Fermi-Pasta-Ulam (FPU) oscillators coupled to two reservoirs at different temperatures. The strength of the interaction between two lattice sites decays as a power α of the inverse of their distance. We point out the necessity of distinguishing between energy flows towards or from the reservoirs and those within the system. We show that energy flow between the reservoirs occurs via a direct transfer induced by long-range couplings and a diffusive process through the chain. To this aim, we introduce a decomposition of the steady-state heat current that explicitly accounts for such direct transfer of energy between the reservoir. For 0≤α<1, the direct transfer term dominates, meaning that the system can be effectively described as a set of oscillators each interacting with the thermal baths. Also, the heat current exchanged with the reservoirs depends on the size of the thermalized regions: In the case in which such size is proportional to the system size N, the stationary current is independent on N. For α>1, heat transport mostly occurs through diffusion along the chain: For the rotors transport is normal, while for FPU the data are compatible with an anomalous diffusion, possibly with an α-dependent characteristic exponent.

Heat transport in oscillator chains with long-range interactions coupled to thermal reservoirs

NASA Astrophysics Data System (ADS)

Iubini, Stefano; Di Cintio, Pierfrancesco; Lepri, Stefano; Livi, Roberto; Casetti, Lapo

2018-03-01

We investigate thermal conduction in arrays of long-range interacting rotors and Fermi-Pasta-Ulam (FPU) oscillators coupled to two reservoirs at different temperatures. The strength of the interaction between two lattice sites decays as a power α of the inverse of their distance. We point out the necessity of distinguishing between energy flows towards or from the reservoirs and those within the system. We show that energy flow between the reservoirs occurs via a direct transfer induced by long-range couplings and a diffusive process through the chain. To this aim, we introduce a decomposition of the steady-state heat current that explicitly accounts for such direct transfer of energy between the reservoir. For 0 ≤α <1 , the direct transfer term dominates, meaning that the system can be effectively described as a set of oscillators each interacting with the thermal baths. Also, the heat current exchanged with the reservoirs depends on the size of the thermalized regions: In the case in which such size is proportional to the system size N , the stationary current is independent on N . For α >1 , heat transport mostly occurs through diffusion along the chain: For the rotors transport is normal, while for FPU the data are compatible with an anomalous diffusion, possibly with an α -dependent characteristic exponent.

The role of long-range connectivity for the characterization of the functional-anatomical organization of the cortex.

PubMed

Knösche, Thomas R; Tittgemeyer, Marc

2011-01-01

This review focuses on the role of long-range connectivity as one element of brain structure that is of key importance for the functional-anatomical organization of the cortex. In this context, we discuss the putative guiding principles for mapping brain function and structure onto the cortical surface. Such mappings reveal a high degree of functional-anatomical segregation. Given that brain regions frequently maintain characteristic connectivity profiles and the functional repertoire of a cortical area is closely related to its anatomical connections, long-range connectivity may be used to define segregated cortical areas. This methodology is called connectivity-based parcellation. Within this framework, we investigate different techniques to estimate connectivity profiles with emphasis given to non-invasive methods based on diffusion magnetic resonance imaging (dMRI) and diffusion tractography. Cortical parcellation is then defined based on similarity between diffusion tractograms, and different clustering approaches are discussed. We conclude that the use of non-invasively acquired connectivity estimates to characterize the functional-anatomical organization of the brain is a valid, relevant, and necessary endeavor. Current and future developments in dMRI technology, tractography algorithms, and models of the similarity structure hold great potential for a substantial improvement and enrichment of the results of the technique.

Risk assessment by percolation leaching tests of extensive green roofs with fine fraction of mixed recycled aggregates from construction and demolition waste.

PubMed

López-Uceda, Antonio; Galvín, Adela P; Ayuso, Jesús; Jiménez, José Ramón; Vanwalleghem, Tom; Peña, Adolfo

2018-03-19

Extensive green roofs are urban construction systems that provide thermal regulation and sound proofing for the buildings involved, in addition to providing an urban heat island mitigation or water retention. On the other hand, policies towards reduction of energy consumption, a circular economy and sustainability are core in the European Union. Motivated by this, an experimental study was carried out to evaluate the environmental risk assessment according to release levels of polluting elements on leachates of different green roof substrate mixtures based on recycled aggregates from construction and demolition waste through (i) the performance in laboratory of two procedures: compliance and percolation tests and (ii) an upscaled experimental leaching test for long-term on-site prediction. Four plots were built on a building roof and covered with autochthonous Mediterranean plants in Córdoba, South of Spain. As growing substrate, four mixtures were used of a commercial growing substrate with different proportions of a fine mixed recycled aggregate ranging from 0 to 75% by volume. The results show that these mixtures were classified as non-hazardous materials according to legal limits of the Landfill Directive 2003/33/CE. The release levels registered in extensive green roofs were lower compared to the laboratory test data. This shows how laboratory conditions can overestimate the potential pollutant effect of these materials compared to actual conditions.

The Role of Collateral Paths in Long-Range Diffusion of 3He in Lungs

PubMed Central

Conradi, Mark S.; Yablonskiy, Dmitriy A.; Woods, Jason C.; Gierada, David S.; Bartel, Seth-Emil T.; Haywood, Susan E.; Menard, Christopher

2008-01-01

Rationale and Objectives The hyperpolarized 3He long-range diffusion coefficient (LRDC) in lungs is sensitive to changes in lung structure due to emphysema, reflecting the increase in collateral paths resulting from tissue destruction. However, no clear understanding of LRDC in healthy lungs has emerged. Here we compare LRDC measured in healthy lungs with computer simulations of diffusion along the airway tree with no collateral connections. Materials and Methods Computer simulations of diffusion of spatially modulated spin magnetization were performed in computer generated, symmetric-branching models of lungs and compared with existing LRDC measurements in canine and human lungs. Results The simulations predict LRDC values of order 0.001 cm2/s, approximately 20 times smaller than the measured LRDC. We consider and rule out possible mechanisms for LRDC not included in the simulations: incomplete breath hold, cardiac motion, and passage of dissolved 3He through airway walls. However, a very low density of small (micron) holes in the airways is shown to account for the observed LRDC. Conclusion It is proposed that LRDC in healthy lungs is determined by small collateral pathways. PMID:18486004

Minimal Model of Quantum Kinetic Clusters for the Energy-Transfer Network of a Light-Harvesting Protein Complex.

PubMed

Wu, Jianlan; Tang, Zhoufei; Gong, Zhihao; Cao, Jianshu; Mukamel, Shaul

2015-04-02

The energy absorbed in a light-harvesting protein complex is often transferred collectively through aggregated chromophore clusters. For population evolution of chromophores, the time-integrated effective rate matrix allows us to construct quantum kinetic clusters quantitatively and determine the reduced cluster-cluster transfer rates systematically, thus defining a minimal model of energy-transfer kinetics. For Fenna-Matthews-Olson (FMO) and light-havrvesting complex II (LCHII) monomers, quantum Markovian kinetics of clusters can accurately reproduce the overall energy-transfer process in the long-time scale. The dominant energy-transfer pathways are identified in the picture of aggregated clusters. The chromophores distributed extensively in various clusters can assist a fast and long-range energy transfer.

High-throughput analysis of sub-visible mAb aggregate particles using automated fluorescence microscopy imaging.

PubMed

Paul, Albert Jesuran; Bickel, Fabian; Röhm, Martina; Hospach, Lisa; Halder, Bettina; Rettich, Nina; Handrick, René; Herold, Eva Maria; Kiefer, Hans; Hesse, Friedemann

2017-07-01

Aggregation of therapeutic proteins is a major concern as aggregates lower the yield and can impact the efficacy of the drug as well as the patient's safety. It can occur in all production stages; thus, it is essential to perform a detailed analysis for protein aggregates. Several methods such as size exclusion high-performance liquid chromatography (SE-HPLC), light scattering, turbidity, light obscuration, and microscopy-based approaches are used to analyze aggregates. None of these methods allows determination of all types of higher molecular weight (HMW) species due to a limited size range. Furthermore, quantification and specification of different HMW species are often not possible. Moreover, automation is a perspective challenge coming up with automated robotic laboratory systems. Hence, there is a need for a fast, high-throughput-compatible method, which can detect a broad size range and enable quantification and classification. We describe a novel approach for the detection of aggregates in the size range 1 to 1000 μm combining fluorescent dyes for protein aggregate labelling and automated fluorescence microscope imaging (aFMI). After appropriate selection of the dye and method optimization, our method enabled us to detect various types of HMW species of monoclonal antibodies (mAbs). Using 10 μmol L -1 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonate (Bis-ANS) in combination with aFMI allowed the analysis of mAb aggregates induced by different stresses occurring during downstream processing, storage, and administration. Validation of our results was performed by SE-HPLC, UV-Vis spectroscopy, and dynamic light scattering. With this new approach, we could not only reliably detect different HMW species but also quantify and classify them in an automated approach. Our method achieves high-throughput requirements and the selection of various fluorescent dyes enables a broad range of applications.

Experimental demonstration of multiuser communication in deep water using time reversal.

PubMed

Shimura, T; Ochi, H; Song, H C

2013-10-01

Multiuser communication is demonstrated using experimental data (450-550 Hz) collected in deep water, south of Japan. The multiple users are spatially distributed either in depth or range while a 114-m long, 20-element vertical array (i.e., base station) is deployed to around the sound channel axis (~1000 m). First, signals received separately from ranges of 150 km and 180 km at various depths are combined asynchronously to generate multiuser communication sequences for subsequent processing, achieving an aggregate data rate of 300 bits/s for up to three users. Adaptive time reversal is employed to separate collided packets at the base station, followed by a single channel decision feedback equalizer. Then it is demonstrated that two users separated by 3 km in range at ~1000 m depth can transmit information simultaneously to the base station at ~500 km range with an aggregate data rate of 200 bits/s.

The effects of nutrient chemotaxis on bacterial aggregation patterns with non-linear degenerate cross diffusion

NASA Astrophysics Data System (ADS)

Leyva, J. Francisco; Málaga, Carlos; Plaza, Ramón G.

2013-11-01

This paper studies a reaction-diffusion-chemotaxis model for bacterial aggregation patterns on the surface of thin agar plates. It is based on the non-linear degenerate cross diffusion model proposed by Kawasaki et al. (1997) [5] and it includes a suitable nutrient chemotactic term compatible with such type of diffusion, as suggested by Ben-Jacob et al. (2000) [20]. An asymptotic estimation predicts the growth velocity of the colony envelope as a function of both the nutrient concentration and the chemotactic sensitivity. It is shown that the growth velocity is an increasing function of the chemotactic sensitivity. High resolution numerical simulations using Graphic Processing Units (GPUs), which include noise in the diffusion coefficient for the bacteria, are presented. The numerical results verify that the chemotactic term enhances the velocity of propagation of the colony envelope. In addition, the chemotaxis seems to stabilize the formation of branches in the soft-agar, low-nutrient regime.

Theory and modeling of particles with DNA-mediated interactions

NASA Astrophysics Data System (ADS)

Licata, Nicholas A.

In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors and nanoparticle based drug delivery platforms. In Chapter I we introduce the system, which generically consists of colloidal particles functionalized with specially designed DNA markers. The sequence of bases on the DNA markers determines the particle type. Due to the hybridization between complementary single-stranded DNA, specific, type-dependent interactions can be introduced between particles by choosing the appropriate DNA marker sequences. In Chapter II we develop a statistical mechanical description of the aggregation and melting behavior of particles with DNA-mediated interactions. A quantitative comparison between the theory and experiments is made by calculating the experimentally observed melting profile. In Chapter III a model is proposed to describe the dynamical departure and diffusion of particles which form reversible key-lock connections. The model predicts a crossover from localized to diffusive behavior. The random walk statistics for the particles' in plane diffusion is discussed. The lateral motion is analogous to dispersive transport in disordered semiconductors, ranging from standard diffusion with a renormalized diffusion coefficient to anomalous, subdiffusive behavior. In Chapter IV we propose a method to self-assemble nanoparticle clusters using DNA scaffolds. An optimal concentration ratio is determined for the experimental implementation of our self-assembly proposal. A natural extension is discussed in Chapter V, the programmable self-assembly of nanoparticle clusters where the desired cluster geometry is encoded using DNA-mediated interactions. We determine the probability that the system self-assembles the desired cluster geometry, and discuss the connections to jamming in granular and colloidal systems. In Chapter VI we consider a nanoparticle based drug delivery platform for targeted, cell specific chemotherapy. A key-lock model is proposed to describe the results of in-vitro experiments, and the situation in-vivo is discussed. The cooperative binding, and hence the specificity to cancerous cells, is kinetically limited. The implications for optimizing the design of nanoparticle based drug delivery platforms is discussed. In Chapter VII we present prospects for future research: the connection between DNA-mediated colloidal crystallization and jamming, and the inverse problem in self-assembly.

Signatures of a quantum diffusion limited hydrogen atom tunneling reaction.

PubMed

Balabanoff, Morgan E; Ruzi, Mahmut; Anderson, David T

2017-12-20

We are studying the details of hydrogen atom (H atom) quantum diffusion in highly enriched parahydrogen (pH 2 ) quantum solids doped with chemical species in an effort to better understand H atom transport and reactivity under these conditions. In this work we present kinetic studies of the 193 nm photo-induced chemistry of methanol (CH 3 OH) isolated in solid pH 2 . Short-term irradiation of CH 3 OH at 1.8 K readily produces CH 2 O and CO which we detect using FTIR spectroscopy. The in situ photochemistry also produces CH 3 O and H atoms which we can infer from the post-photolysis reaction kinetics that display significant CH 2 OH growth. The CH 2 OH growth kinetics indicate at least three separate tunneling reactions contribute; (i) reactions of photoproduced CH 3 O with the pH 2 host, (ii) H atom reactions with the CH 2 O photofragment, and (iii) long-range migration of H atoms and reaction with CH 3 OH. We assign the rapid CH 2 OH growth to the following CH 3 O + H 2 → CH 3 OH + H → CH 2 OH + H 2 two-step sequential tunneling mechanism by conducting analogous kinetic measurements using deuterated methanol (CD 3 OD). By performing photolysis experiments at 1.8 and 4.3 K, we show the post-photolysis reaction kinetics change qualitatively over this small temperature range. We use this qualitative change in the reaction kinetics with temperature to identify reactions that are quantum diffusion limited. While these results are specific to the conditions that exist in pH 2 quantum solids, they have direct implications on the analogous low temperature H atom tunneling reactions that occur on metal surfaces and on interstellar grains.

Aggregation and Disaggregation of Senile Plaques in Alzheimer Disease

NASA Astrophysics Data System (ADS)

Cruz, L.; Urbanc, B.; Buldyrev, S. V.; Christie, R.; Gomez-Isla, T.; Havlin, S.; McNamara, M.; Stanley, H. E.; Hyman, B. T.

1997-07-01

We quantitatively analyzed, using laser scanning confocal microscopy, the three-dimensional structure of individual senile plaques in Alzheimer disease. We carried out the quantitative analysis using statistical methods to gain insights about the processes that govern Aβ peptide deposition. Our results show that plaques are complex porous structures with characteristic pore sizes. We interpret plaque morphology in the context of a new dynamical model based on competing aggregation and disaggregation processes in kinetic steady-state equilibrium with an additional diffusion process allowing Aβ deposits to diffuse over the surface of plaques.

Flow Range of Centrifugal Compressor Being Extended

NASA Technical Reports Server (NTRS)

Skoch, Gary J.

2001-01-01

General Aviation will benefit from turbine engines that are both fuel-efficient and reliable. Current engines fall short of their potential to achieve these attributes. The reason is compressor surge, which is a flow stability problem that develops when the compressor is subjected to conditions that are outside of its operating range. Compressor surge can occur when fuel flow to the engine is increased, temporarily back pressuring the compressor and pushing it past its stability limit, or when the compressor is subjected to inlet flow-field distortions that may occur during takeoff and landing. Compressor surge can result in the loss of an aircraft. As a result, engine designers include a margin of safety between the operating line of the engine and the stability limit line of the compressor. Unfortunately, the most efficient operating line for the compressor is usually closer to its stability limit line than it is to the line that provides an adequate margin of safety. A wider stable flow range will permit operation along the most efficient operating line of the compressor, improving the specific fuel consumption of the engine and reducing emissions. The NASA Glenn Research Center is working to extend the stable flow range of the compressor. Significant extension has been achieved in axial compressors by injecting air upstream of the compressor blade rows. Recently, the technique was successfully applied to a 4:1 pressure ratio centrifugal compressor by injecting streams of air into the diffuser. Both steady and controlled unsteady injection were used to inject air through the diffuser shroud surface and extend the range. Future work will evaluate the effect of air injection through the diffuser hub surface and diffuser vanes with the goal of maximizing the range extension while minimizing the amount of injected air that is required.

Creep of quartz by dislocation and grain boundary processes

NASA Astrophysics Data System (ADS)

Fukuda, J. I.; Holyoke, C. W., III; Kronenberg, A. K.

2015-12-01

Wet polycrystalline quartz aggregates deformed at temperatures T of 600°-900°C and strain rates of 10-4-10-6 s-1 at a confining pressure Pc of 1.5 GPa exhibit plasticity at low T, governed by dislocation glide and limited recovery, and grain size-sensitive creep at high T, governed by diffusion and sliding at grain boundaries. Quartz aggregates were HIP-synthesized, subjecting natural milky quartz powder to T=900°C and Pc=1.5 GPa, and grain sizes (2 to 25 mm) were varied by annealing at these conditions for up to 10 days. Infrared absorption spectra exhibit a broad OH band at 3400 cm-1 due to molecular water inclusions with a calculated OH content (~4000 ppm, H/106Si) that is unchanged by deformation. Rate-stepping experiments reveal different stress-strain rate functions at different temperatures and grain sizes, which correspond to differing stress-temperature sensitivities. At 600-700°C and grain sizes of 5-10 mm, flow law parameters compare favorably with those for basal plasticity and dislocation creep of wet quartzites (effective stress exponents n of 3 to 6 and activation enthalpy H* ~150 kJ/mol). Deformed samples show undulatory extinction, limited recrystallization, and c-axis maxima parallel to the shortening direction. Similarly fine-grained samples deformed at 800°-900°C exhibit flow parameters n=1.3-2.0 and H*=135-200 kJ/mol corresponding to grain size-sensitive Newtonian creep. Deformed samples show some undulatory extinction and grain sizes change by recrystallization; however, grain boundary deformation processes are indicated by the low value of n. Our experimental results for grain size-sensitive creep can be compared with models of grain boundary diffusion and grain boundary sliding using measured rates of silicon grain boundary diffusion. While many quartz mylonites show microstructural and textural evidence for dislocation creep, results for grain size-sensitive creep may apply to very fine-grained (<10 mm) quartz mylonites.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makhnovskii, Yurii A.; Berezhkovskii, Alexander M.; Antipov, Anatoly E.

This paper is devoted to particle transport in a tube formed by alternating wide and narrow sections, in the presence of an external biasing force. The focus is on the effective transport coefficients—mobility and diffusivity, as functions of the biasing force and the geometric parameters of the tube. Dependences of the effective mobility and diffusivity on the tube geometric parameters are known in the limiting cases of no bias and strong bias. The approximations used to obtain these results are inapplicable at intermediate values of the biasing force. To bridge the two limits Brownian dynamics simulations were run to determinemore » the transport coefficients at intermediate values of the force. The simulations were performed for a representative set of tube geometries over a wide range of the biasing force. They revealed that there is a range of the narrow section length, where the force dependence of the mobility has a maximum. In contrast, the diffusivity is a monotonically increasing function of the force. A simple formula is proposed, which reduces to the known dependences of the diffusivity on the tube geometric parameters in both limits of zero and strong bias. At intermediate values of the biasing force, the formula catches the diffusivity dependence on the narrow section length, if the radius of these sections is not too small.« less

A diffusion model for solute atoms diffusing and aggregating in nuclear structural materials

NASA Astrophysics Data System (ADS)

Song, Quan; Meng, Fan-Xin; Ning, Bo-Yuan; Zhuang, Jun; Ning, Xi-Jing

2017-12-01

Not Available Project supported by the Specialized Research Fund for the Doctoral Program of Higher Education, China (Grant No. 20130071110018) and the National Natural Science Foundation of China (Grant No. 11274073).

Impact of Microcystis aeruginosa Exudate on the Formation and Reactivity of Iron Oxide Particles Following Fe(II) and Fe(III) Addition.

PubMed

Garg, Shikha; Wang, Kai; Waite, T David

2017-05-16

Impact of the organic exudate secreted by a toxic strain of Microcystis aeruginosa on the formation, aggregation, and reactivity of iron oxides that are formed on addition of Fe(II) and Fe(III) salts to a solution of the exudate is investigated in this study. The exudate has a stabilizing effect on the particles formed with decreased aggregation rate and increased critical coagulant concentration required for diffusion-limited aggregation to occur. These results suggest that the presence of algal exudates from Microcystis aeruginosa may significantly influence particle aggregation both in natural water bodies where Fe(II) oxidation results in oxide formation and in water treatment where Fe(III) salts are commonly added to aid particle growth and contaminant capture. The exudate also affects the reactivity of iron oxide particles formed with exudate coated particles undergoing faster dissolution than bare iron oxide particles. This has implications to iron availability, especially where algae procure iron via dissolution of iron oxide particles as a result of either reaction with reducing moieties, light-mediated ligand to metal charge transfer and/or reaction with siderophores. The increased reactivity of exudate coated particles is attributed, for the most part, to the smaller size of these particles, higher surface area and increased accessibility of surface sites.

Real-time measurement of size-resolved elemental composition ratio for flame synthesized composite nanoparticle aggregates using a tandem SMPS-ICP-OES

PubMed Central

Reed, Nathan; Fang, Jiaxi; Chavalmane, Sanmathi; Biswas, Pratim

2017-01-01

Composite nanoparticles find application in catalysis, drug delivery, and energy storage and require increasingly fine control of their physical properties and composition. While composite nanoparticles have been widely synthesized and characterized, little work has systematically correlated the initial concentration of precursors and the final composition of flame synthesized composite nanoparticles. This relationship is explored in a diffusion flame aerosol reactor by coupling a scanning mobility particle sizer (SMPS) with an inductively coupled plasma optical emission spectrometer (ICP-OES). A framework for studying the relationship between the initial precursor concentrations of different elements and the final nanoparticle composition is explored. The size-resolved elemental composition was measured by directly injecting size-selected fractions of aggregated magnetite and silicon dioxide composite nanoparticles into the ICP-OES plasma. This work showed a correlation between precursor molar ratio and the measured elemental ratio in the mobility size range of 50 to 140 nm. Building on previous work studying size resolved elemental composition of engineered nanoparticles, the analysis is extended to flame synthesized composite nanoparticle aggregates in this work. PMID:28435179

Real-time measurement of size-resolved elemental composition ratio for flame synthesized composite nanoparticle aggregates using a tandem SMPS-ICP-OES.

PubMed

Reed, Nathan; Fang, Jiaxi; Chavalmane, Sanmathi; Biswas, Pratim

2017-01-01

Composite nanoparticles find application in catalysis, drug delivery, and energy storage and require increasingly fine control of their physical properties and composition. While composite nanoparticles have been widely synthesized and characterized, little work has systematically correlated the initial concentration of precursors and the final composition of flame synthesized composite nanoparticles. This relationship is explored in a diffusion flame aerosol reactor by coupling a scanning mobility particle sizer (SMPS) with an inductively coupled plasma optical emission spectrometer (ICP-OES). A framework for studying the relationship between the initial precursor concentrations of different elements and the final nanoparticle composition is explored. The size-resolved elemental composition was measured by directly injecting size-selected fractions of aggregated magnetite and silicon dioxide composite nanoparticles into the ICP-OES plasma. This work showed a correlation between precursor molar ratio and the measured elemental ratio in the mobility size range of 50 to 140 nm. Building on previous work studying size resolved elemental composition of engineered nanoparticles, the analysis is extended to flame synthesized composite nanoparticle aggregates in this work.

The relevance of light diffusion profiles for interstitial PDT using light-diffusing optical fibers

NASA Astrophysics Data System (ADS)

Stringasci, Mirian D.; Fortunato, Thereza C.; Moriyama, Lilian T.; Vollet Filho, José Dirceu; Bagnato, Vanderlei S.; Kurachi, Cristina

2017-02-01

Photodynamic therapy (PDT) is a technique used for several tumor types treatment. Light penetration on biological tissue is one limiting factor for PDT applied to large tumors. An alternative is using interstitial PDT, in which optical fibers are inserted into tumors. Cylindrical diffusers have been used in interstitial PDT. Light emission of different diffusers depends on the manufacturing process, size and optical properties of fibers, which make difficult to establish an adequate light dosimetry, since usually light profile is not designed for direct tissue-fiber contact. This study discusses the relevance of light distribution by a cylindrical diffuser into a turbid lipid emulsion solution, and how parts of a single diffuser contribute to illumination. A 2 cm-long cylindrical diffuser optical fiber was connected to a diode laser (630 nm), and the light spatial distribution was measured by scanning the solution with a collection probe. From the light field profile generated by a 1 mm-long intermediary element of a 20 mm-long cylindrical diffuser, recovery of light distribution for the entire diffuser was obtained. PDT was performed in rat healthy liver for a real treatment outcome analysis. By using computational tools, a typical necrosis profile generated by the irradiation with such a diffuser fiber was reconstructed. The results showed that it was possible predicting theoretically the shape of a necrosis profile in a healthy, homogeneous tissue with reasonable accuracy. The ability to predict the necrosis profile obtained from an interstitial illumination by optical diffusers has the potential improve light dosimetry for interstitial PDT.

Patterns of [PSI+] aggregation allow insights into cellular organization of yeast prion aggregates

PubMed Central

Tyedmers, Jens

2012-01-01

The yeast prion phenomenon is very widespread and mounting evidence suggests that it has an impact on cellular regulatory mechanisms related to phenotypic responses to changing environments. Studying the aggregation patterns of prion amyloids during different stages of the prion life cycle is a first key step to understand major principles of how and where cells generate, organize and turn-over prion aggregates. The induction of the [PSI+] state involves the actin cytoskeleton and quality control compartments such as the Insoluble Protein Deposit (IPOD). An initially unstable transitional induction state can be visualized by overexpression of the prion determinant and displays characteristic large ring- and ribbon-shaped aggregates consisting of poorly fragmented bundles of very long prion fibrils. In the mature prion state, the aggregation pattern is characterized by highly fragmented, shorter prion fibrils that form aggregates, which can be visualized through tagging with fluorescent proteins. The number of aggregates formed varies, ranging from a single large aggregate at the IPOD to multiple smaller ones, depending on several parameters discussed. Aggregate units below the resolution of light microscopy that are detectable by fluorescence correlation spectroscopy are in equilibrium with larger aggregates in this stage and can mediate faithful inheritance of the prion state. Loss of the prion state is often characterized by reduced fragmentation of prion fibrils and fewer, larger aggregates. PMID:22449721

Mechanistic modeling of thermo-hydrological processes and microbial interactions at pore to profile scales resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-04-01

The sensitivity of the Earth's polar regions to raising global temperatures is reflected in rapidly changing hydrological processes with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and the stimulation of other soil-borne GHG emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and a host of other environmental factors. Soil structural elements such as aggregates and layering and hydration status affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hotspots or hot-layers). We developed a mechanistic individual based model to quantify microbial activity dynamics within soil pore networks considering, hydration, temperature, transport processes and enzymatic activity associated with methane production in soil. The model was the upscaled from single aggregates (or hotspots) to quantifying emissions from soil profiles in which freezing/thawing processes provide macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged parts of the profile) for resolving methane production and oxidation rates. Methane transport pathways through soil by diffusion and ebullition of bubbles vary with hydration dynamics and affect emission patterns. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability, enzyme activity, PH) on long term methane emissions and carbon decomposition rates in the rapidly changing polar regions.

Model of turnover kinetics in the lamellipodium: implications of slow- and fast- diffusing capping protein and Arp2/3 complex

NASA Astrophysics Data System (ADS)

McMillen, Laura M.; Vavylonis, Dimitrios

2016-12-01

Cell protrusion through polymerization of actin filaments at the leading edge of motile cells may be influenced by spatial gradients of diffuse actin and regulators. Here we study the distribution of two of the most important regulators, capping protein and Arp2/3 complex, which regulate actin polymerization in the lamellipodium through capping and nucleation of free barbed ends. We modeled their kinetics using data from prior single molecule microscopy experiments on XTC cells. These experiments have provided evidence for a broad distribution of diffusion coefficients of both capping protein and Arp2/3 complex. The slowly diffusing proteins appear as extended ‘clouds’ while proteins bound to the actin filament network appear as speckles that undergo retrograde flow. Speckle appearance and disappearance events correspond to assembly and dissociation from the actin filament network and speckle lifetimes correspond to the dissociation rate. The slowly diffusing capping protein could represent severed capped actin filament fragments or membrane-bound capping protein. Prior evidence suggests that slowly diffusing Apr2/3 complex associates with the membrane. We use the measured rates and estimates of diffusion coefficients of capping protein and Arp2/3 complex in a Monte Carlo simulation that includes particles in association with a filament network and diffuse in the cytoplasm. We consider two separate pools of diffuse proteins, representing fast and slowly diffusing species. We find a steady state with concentration gradients involving a balance of diffusive flow of fast and slow species with retrograde flow. We show that simulations of FRAP are consistent with prior experiments performed on different cell types. We provide estimates for the ratio of bound to diffuse complexes and calculate conditions where Arp2/3 complex recycling by diffusion may become limiting. We discuss the implications of slowly diffusing populations and suggest experiments to distinguish among mechanisms that influence long range transport.

Data-Driven Diffusion Of Innovations: Successes And Challenges In 3 Large-Scale Innovative Delivery Models

PubMed Central

Dorr, David A.; Cohen, Deborah J.; Adler-Milstein, Julia

2018-01-01

Failed diffusion of innovations may be linked to an inability to use and apply data, information, and knowledge to change perceptions of current practice and motivate change. Using qualitative and quantitative data from three large-scale health care delivery innovations—accountable care organizations, advanced primary care practice, and EvidenceNOW—we assessed where data-driven innovation is occurring and where challenges lie. We found that implementation of some technological components of innovation (for example, electronic health records) has occurred among health care organizations, but core functions needed to use data to drive innovation are lacking. Deficits include the inability to extract and aggregate data from the records; gaps in sharing data; and challenges in adopting advanced data functions, particularly those related to timely reporting of performance data. The unexpectedly high costs and burden incurred during implementation of the innovations have limited organizations’ ability to address these and other deficits. Solutions that could help speed progress in data-driven innovation include facilitating peer-to-peer technical assistance, providing tailored feedback reports to providers from data aggregators, and using practice facilitators skilled in using data technology for quality improvement to help practices transform. Policy efforts that promote these solutions may enable more rapid uptake of and successful participation in innovative delivery system reforms. PMID:29401031

Data-Driven Diffusion Of Innovations: Successes And Challenges In 3 Large-Scale Innovative Delivery Models.

PubMed

Dorr, David A; Cohen, Deborah J; Adler-Milstein, Julia

2018-02-01

Failed diffusion of innovations may be linked to an inability to use and apply data, information, and knowledge to change perceptions of current practice and motivate change. Using qualitative and quantitative data from three large-scale health care delivery innovations-accountable care organizations, advanced primary care practice, and EvidenceNOW-we assessed where data-driven innovation is occurring and where challenges lie. We found that implementation of some technological components of innovation (for example, electronic health records) has occurred among health care organizations, but core functions needed to use data to drive innovation are lacking. Deficits include the inability to extract and aggregate data from the records; gaps in sharing data; and challenges in adopting advanced data functions, particularly those related to timely reporting of performance data. The unexpectedly high costs and burden incurred during implementation of the innovations have limited organizations' ability to address these and other deficits. Solutions that could help speed progress in data-driven innovation include facilitating peer-to-peer technical assistance, providing tailored feedback reports to providers from data aggregators, and using practice facilitators skilled in using data technology for quality improvement to help practices transform. Policy efforts that promote these solutions may enable more rapid uptake of and successful participation in innovative delivery system reforms.

Dynamics and mechanisms of asbestos-fiber aggregate growth in water

NASA Astrophysics Data System (ADS)

Wu, L.; Ortiz, C. P.; Jerolmack, D. J.

2015-12-01

Most colloidal particles including asbestos fibers form aggregates in water, when solution chemistry provides favorable conditions. To date, the growth of colloidal aggregates has been observed in many model systems under optical and scanning electron microscopy; however, all of these studies have used near-spherical particles. The highly elongated nature of asbestos fibers may cause anomalous aggregate growth and morphology, but this has never been examined. Although the exposure pathway of concern for asbestos is through the air, asbestos particles typically reside in soil that is at least partially saturated, and aggregates formed in the aqueous phase may influence the mobility of particles in the environment. Here we study solution-phase aggregation kinetics of asbestos fibers using a liquid-cell by in situ microscopy, over micron to centimeter length scales and from a tenth of a second to hours. We employ an elliptical particle tracking technique to determine particle trajectories and to quantify diffusivity. Experiments reveal that diffusing fibers join by cross linking, but that such linking is sometimes reversible. The resulting aggregates are very sparse and non-compact, with a fractal dimension that is lower than any previously reported value. Their morphology, growth rate and particle size distribution exhibit non-classical behavior that deviates significantly from observations of aggregates composed of near-spherical particles. We also perform experiments using synthetic colloidal particles, and compare these to asbestos in order to separate the controls of particle shape vs. material properties. This direct method for quantitatively observing aggregate growth is a first step toward predicting asbestos fiber aggregate size distributions in the environment. Moreover, many emerging environmental contaminants - such as carbon nanotubes - are elongated colloids, and our work suggests that theories for aggregate growth may need to be modified in order to model these particles.

Influence of structure of iron nanoparticles in aggregates on their magnetic properties

PubMed Central

2011-01-01

Zero-valent iron nanoparticles rapidly aggregate. One of the reasons is magnetic forces among the nanoparticles. Magnetic field around particles is caused by composition of the particles. Their core is formed from zero-valent iron, and shell is a layer of magnetite. The magnetic forces contribute to attractive forces among the nanoparticles and that leads to increasing of aggregation of the nanoparticles. This effect is undesirable for decreasing of remediation properties of iron particles and limited transport possibilities. The aggregation of iron nanoparticles was established for consequent processes: Brownian motion, sedimentation, velocity gradient of fluid around particles and electrostatic forces. In our previous work, an introduction of influence of magnetic forces among particles on the aggregation was presented. These forces have significant impact on the rate of aggregation. In this article, a numerical computation of magnetic forces between an aggregate and a nanoparticle and between two aggregates is shown. It is done for random position of nanoparticles in an aggregate and random or arranged directions of magnetic polarizations and for structured aggregates with arranged vectors of polarizations. Statistical computation by Monte Carlo is done, and range of dominant area of magnetic forces around particles is assessed. PMID:21917152

Simple and efficient LCAO basis sets for the diffuse states in carbon nanostructures.

PubMed

Papior, Nick R; Calogero, Gaetano; Brandbyge, Mads

2018-06-27

We present a simple way to describe the lowest unoccupied diffuse states in carbon nanostructures in density functional theory calculations using a minimal LCAO (linear combination of atomic orbitals) basis set. By comparing plane wave basis calculations, we show how these states can be captured by adding long-range orbitals to the standard LCAO basis sets for the extreme cases of planar sp 2 (graphene) and curved carbon (C 60 ). In particular, using Bessel functions with a long range as additional basis functions retain a minimal basis size. This provides a smaller and simpler atom-centered basis set compared to the standard pseudo-atomic orbitals (PAOs) with multiple polarization orbitals or by adding non-atom-centered states to the basis.

Simple and efficient LCAO basis sets for the diffuse states in carbon nanostructures

NASA Astrophysics Data System (ADS)

Papior, Nick R.; Calogero, Gaetano; Brandbyge, Mads

2018-06-01

We present a simple way to describe the lowest unoccupied diffuse states in carbon nanostructures in density functional theory calculations using a minimal LCAO (linear combination of atomic orbitals) basis set. By comparing plane wave basis calculations, we show how these states can be captured by adding long-range orbitals to the standard LCAO basis sets for the extreme cases of planar sp 2 (graphene) and curved carbon (C60). In particular, using Bessel functions with a long range as additional basis functions retain a minimal basis size. This provides a smaller and simpler atom-centered basis set compared to the standard pseudo-atomic orbitals (PAOs) with multiple polarization orbitals or by adding non-atom-centered states to the basis.

Highly elevated serum lactate dehydrogenase is associated with central nervous system relapse in patients with diffuse large B-cell lymphoma: Results of a multicenter prospective cohort study.

PubMed

Kim, Seok Jin; Hong, Jun Sik; Chang, Myung Hee; Kim, Jeong-A; Kwak, Jae-Yong; Kim, Jin Seok; Yoon, Dok Hyun; Lee, Won Sik; Do, Young Rok; Kang, Hye Jin; Eom, Hyeon-Seok; Park, Yong; Won, Jong-Ho; Mun, Yeung-Chul; Kim, Hyo Jung; Kwon, Jung Hye; Kong, Jee Hyun; Oh, Sung Yong; Lee, Sunah; Bae, Sung Hwa; Yang, Deok-Hwan; Jun, Hyun Jung; Kim, Yang Soo; Yun, Hwan Jung; Lee, Soon Il; Kim, Min Kyoung; Park, Eun Kyung; Kim, Won Seog; Suh, Cheolwon

2016-11-01

Central nervous system involvement remains a challenging issue in the treatment of patients with diffuse large B-cell lymphoma. We conducted a prospective cohort study with newly diagnosed diffuse large B-cell lymphoma patients receiving rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone to identify incidence and risk factors for central nervous system involvement. Among 595 patients, 279 patients received pre-treatment central nervous system evaluation, and 14 patients had central nervous system involvement at diagnosis (2.3% out of entire patients and 5.0% out of the 279 patients). For those patients, median follow-up duration was 38.2 months and some of them achieved long-term survival. Out of 581 patients who did not have central nervous system involvement at diagnosis, 26 patients underwent secondary central nervous system relapse with a median follow-up of 35 months, and the median time to central nervous system involvement was 10.4 months (range: 3.4-29.2). Serum lactate dehydrogenase > ×3 upper limit of normal range, the Eastern Cooperative Oncology Group performance status ≥ 2, and involvement of sinonasal tract or testis, were independent risk factors for central nervous system relapse in multivariate analysis. Our study suggests that enhanced stratification of serum lactate dehydrogenase according to the National Comprehensive Cancer Network-International Prognostic Index may contribute to better prediction for central nervous system relapse in patients with diffuse large B-cell lymphoma. This trial was registered at clinicaltrials.gov identifier: 01202448.

Highly elevated serum lactate dehydrogenase is associated with central nervous system relapse in patients with diffuse large B-cell lymphoma: Results of a multicenter prospective cohort study

PubMed Central

Kim, Seok Jin; Hong, Jun Sik; Chang, Myung Hee; Kim, Jeong-A; Kwak, Jae-Yong; Kim, Jin Seok; Yoon, Dok Hyun; Lee, Won Sik; Do, Young Rok; Kang, Hye Jin; Eom, Hyeon-Seok; Park, Yong; Won, Jong-Ho; Mun, Yeung-Chul; Kim, Hyo Jung; Kwon, Jung Hye; Kong, Jee Hyun; Oh, Sung Yong; Lee, Sunah; Bae, Sung Hwa; Yang, Deok-Hwan; Jun, Hyun Jung; Kim, Yang Soo; Yun, Hwan Jung; Il Lee, Soon; Kim, Min Kyoung; Park, Eun Kyung; Kim, Won Seog; Suh, Cheolwon

2016-01-01

Central nervous system involvement remains a challenging issue in the treatment of patients with diffuse large B-cell lymphoma. We conducted a prospective cohort study with newly diagnosed diffuse large B-cell lymphoma patients receiving rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone to identify incidence and risk factors for central nervous system involvement. Among 595 patients, 279 patients received pre-treatment central nervous system evaluation, and 14 patients had central nervous system involvement at diagnosis (2.3% out of entire patients and 5.0% out of the 279 patients). For those patients, median follow-up duration was 38.2 months and some of them achieved long-term survival. Out of 581 patients who did not have central nervous system involvement at diagnosis, 26 patients underwent secondary central nervous system relapse with a median follow-up of 35 months, and the median time to central nervous system involvement was 10.4 months (range: 3.4–29.2). Serum lactate dehydrogenase > ×3 upper limit of normal range, the Eastern Cooperative Oncology Group performance status ≥ 2, and involvement of sinonasal tract or testis, were independent risk factors for central nervous system relapse in multivariate analysis. Our study suggests that enhanced stratification of serum lactate dehydrogenase according to the National Comprehensive Cancer Network-International Prognostic Index may contribute to better prediction for central nervous system relapse in patients with diffuse large B-cell lymphoma. This trial was registered at clinicaltrials.gov identifier: 01202448. PMID:27713132

Aggregating QECB Allocations & Using QECBs to Support the Private Sector. A Case Study on Massachusetts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zimring, Mark; Borgeson, Merrian

2012-08-01

Qualified Energy Conservation Bonds (QECBs) are federally-subsidized bonds that enable state, tribal, and local government issuers to borrow money to fund a range of energy conservation projects at very attractive interest rates and long terms. While small allocation sizes have deterred some local governments from pursuing issuances, state agencies in Massachusetts have partnered with local governments to aggregate QECBs to support a range of public and private projects. In most states, QECBs have been utilized primarily to fund energy conservation projects for public entities, but Massachusetts has facilitated over $10 million of private activity QECB issuances to support three privately-ownedmore » renewable energy projects—with more projects in the pipeline.« less

Epizootic podoknemidokoptiasis in American robins

USGS Publications Warehouse

Pence, Danny B.; Cole, Rebecca A.; Brugger, Kristin E.; Fischer, John R.

1999-01-01

Epizootics of scaly leg disease caused by infection with the submacroscopic mite Knemidokoptes jamaicensis (Acari: Knemidokoptidae) in migratory American robins (Turdus migratorius) from a residential area of Tulsa (Oklahoma, USA) are documented during the winters (December through February) of 1993–94 and 1994–95. Estimates of 60 to >80% of the birds in several different flights arriving in the area had lesions consistent with knemidokoptic mange. Epizootic occurrence of K. jamaicensis also is confirmed incidentally in American robins from Georgia (USA) in 1995 and 1998 and in Florida (USA) in 1991. These are the first confirmed epizootics of scaly leg attributed to infections with mites specifically identified as K. jamaicensis in North America. Severity of observed lesions in American robins ranged from scaly hyperkeratosis of the feet and legs to extensive proliferative lesions with loss of digits or the entire foot in some birds. Histologically, there was severe diffuse hyperkeratosis of the epidermis which contained numerous mites and multifocal aggregates of degranulating to degenerating eosinophilic heterophils; there was mild to severe superficial dermatitis with aggregates of eosinophilic heterophils and some mononuclear cells. Based on limited data from affected captive birds in Florida, we questioned the efficacy of ivermectin as an effective acaricide for knemidokoptiasis and propose that conditions associated with captivity may exacerbate transmission of this mite among caged birds. While knemidokoptic mange apparently can result in substantial host morbidity and possibly mortality, the ultimate impact of these epizootics on American robin populations presently is unknown.

Role of collateral paths in long-range diffusion in lungs

PubMed Central

Bartel, Seth-Emil T.; Haywood, Susan E.; Woods, Jason C.; Chang, Yulin V.; Menard, Christopher; Yablonskiy, Dmitriy A.; Gierada, David S.; Conradi, Mark S.

2010-01-01

The long-range apparent diffusion coefficient (LRADC) of 3He gas in lungs, measured over times of several seconds and distances of 1–3 cm, probes the connections between the airways. Previous work has shown the LRADC to be small in health and substantially elevated in emphysema, reflecting tissue destruction, which is known to create collateral pathways. To better understand what controls LRADC, we report computer simulations and measurements of 3He gas diffusion in healthy lungs. The lung is generated with a random algorithm using well-defined rules, yielding a three-dimensional set of nodes or junctions, each connected by airways to one parent node and two daughters; airway dimensions are taken from published values. Spin magnetization in the simulated lung is modulated sinusoidally, and the diffusion equation is solved to 1,000 s. The modulated magnetization decays with a time constant corresponding to an LRADC of ~0.001 cm2/s, which is smaller by a factor of ~20 than the values in healthy lungs measured here and previously in vivo and in explanted lungs. It appears that collateral gas pathways, not present in the simulations, are functional in healthy lungs; they provide additional and more direct routes for long-range motion than the canonical airway tree. This is surprising, inasmuch as collateral ventilation is believed to be physiologically insignificant in healthy lungs. We discuss the effect on LRADC of small collateral connections through airway walls and rule out other possible mechanisms. The role of collateral paths is supported by measurements of smaller LRADC in pigs, where collateral ventilation is known to be smaller. PMID:18292298

Short- and long-time diffusion and dynamic scaling in suspensions of charged colloidal particles

NASA Astrophysics Data System (ADS)

Banchio, Adolfo J.; Heinen, Marco; Holmqvist, Peter; Nägele, Gerhard

2018-04-01

We report on a comprehensive theory-simulation-experimental study of collective and self-diffusion in concentrated suspensions of charge-stabilized colloidal spheres. In theory and simulation, the spheres are assumed to interact directly by a hard-core plus screened Coulomb effective pair potential. The intermediate scattering function, fc(q, t), is calculated by elaborate accelerated Stokesian dynamics (ASD) simulations for Brownian systems where many-particle hydrodynamic interactions (HIs) are fully accounted for, using a novel extrapolation scheme to a macroscopically large system size valid for all correlation times. The study spans the correlation time range from the colloidal short-time to the long-time regime. Additionally, Brownian Dynamics (BD) simulation and mode-coupling theory (MCT) results of fc(q, t) are generated where HIs are neglected. Using these results, the influence of HIs on collective and self-diffusion and the accuracy of the MCT method are quantified. It is shown that HIs enhance collective and self-diffusion at intermediate and long times. At short times self-diffusion, and for wavenumbers outside the structure factor peak region also collective diffusion, are slowed down by HIs. MCT significantly overestimates the slowing influence of dynamic particle caging. The dynamic scattering functions obtained in the ASD simulations are in overall good agreement with our dynamic light scattering (DLS) results for a concentration series of charged silica spheres in an organic solvent mixture, in the experimental time window and wavenumber range. From the simulation data for the time derivative of the width function associated with fc(q, t), there is indication of long-time exponential decay of fc(q, t), for wavenumbers around the location of the static structure factor principal peak. The experimental scattering functions in the probed time range are consistent with a time-wavenumber factorization scaling behavior of fc(q, t) that was first reported by Segrè and Pusey [Phys. Rev. Lett. 77, 771 (1996)] for suspensions of hard spheres. Our BD simulation and MCT results predict a significant violation of exact factorization scaling which, however, is approximately restored according to the ASD results when HIs are accounted for, consistent with the experimental findings for fc(q, t). Our study of collective diffusion is amended by simulation and theoretical results for the self-intermediate scattering function, fs(q, t), and its non-Gaussian parameter α2(t) and for the particle mean squared displacement W(t) and its time derivative. Since self-diffusion properties are not assessed in standard DLS measurements, a method to deduce W(t) approximately from fc(q, t) is theoretically validated.

Calculating Mass Diffusion in High-Pressure Binary Fluids

NASA Technical Reports Server (NTRS)

Bellan, Josette; Harstad, Kenneth

2004-01-01

A comprehensive mathematical model of mass diffusion has been developed for binary fluids at high pressures, including critical and supercritical pressures. Heretofore, diverse expressions, valid for limited parameter ranges, have been used to correlate high-pressure binary mass-diffusion-coefficient data. This model will likely be especially useful in the computational simulation and analysis of combustion phenomena in diesel engines, gas turbines, and liquid rocket engines, wherein mass diffusion at high pressure plays a major role.

Multiple echo multi-shot diffusion sequence.

PubMed

Chabert, Steren; Galindo, César; Tejos, Cristian; Uribe, Sergio A

2014-04-01

To measure both transversal relaxation time (T2 ) and diffusion coefficients within a single scan using a multi-shot approach. Both measurements have drawn interest in many applications, especially in skeletal muscle studies, which have short T2 values. Multiple echo single-shot schemes have been proposed to obtain those variables simultaneously within a single scan, resulting in a reduction of the scanning time. However, one problem with those approaches is the associated long echo read-out. Consequently, the minimum achievable echo time tends to be long, limiting the application of these sequences to tissues with relatively long T2 . To address this problem, we propose to extend the multi-echo sequences using a multi-shot approach, so that to allow shorter echo times. A multi-shot dual-echo EPI sequence with diffusion gradients and echo navigators was modified to include independent diffusion gradients in any of the two echoes. The multi-shot approach allows us to drastically reduce echo times. Results showed a good agreement for the T2 and mean diffusivity measurements with gold standard sequences in phantoms and in vivo data of calf muscles from healthy volunteers. A fast and accurate method is proposed to measure T2 and diffusion coefficients simultaneously, tested in vitro and in healthy volunteers. Copyright © 2013 Wiley Periodicals, Inc.

Brownian aggregation rate of colloid particles with several active sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nekrasov, Vyacheslav M.; Yurkin, Maxim A.; Chernyshev, Andrei V., E-mail: chern@ns.kinetics.nsc.ru

2014-08-14

We theoretically analyze the aggregation kinetics of colloid particles with several active sites. Such particles (so-called “patchy particles”) are well known as chemically anisotropic reactants, but the corresponding rate constant of their aggregation has not yet been established in a convenient analytical form. Using kinematic approximation for the diffusion problem, we derived an analytical formula for the diffusion-controlled reaction rate constant between two colloid particles (or clusters) with several small active sites under the following assumptions: the relative translational motion is Brownian diffusion, and the isotropic stochastic reorientation of each particle is Markovian and arbitrarily correlated. This formula was shownmore » to produce accurate results in comparison with more sophisticated approaches. Also, to account for the case of a low number of active sites per particle we used Monte Carlo stochastic algorithm based on Gillespie method. Simulations showed that such discrete model is required when this number is less than 10. Finally, we applied the developed approach to the simulation of immunoagglutination, assuming that the formed clusters have fractal structure.« less

Clustering and heterogeneous dynamics in a kinetic Monte Carlo model of self-propelled hard disks

NASA Astrophysics Data System (ADS)

Levis, Demian; Berthier, Ludovic

2014-06-01

We introduce a kinetic Monte Carlo model for self-propelled hard disks to capture with minimal ingredients the interplay between thermal fluctuations, excluded volume, and self-propulsion in large assemblies of active particles. We analyze in detail the resulting (density, self-propulsion) nonequilibrium phase diagram over a broad range of parameters. We find that purely repulsive hard disks spontaneously aggregate into fractal clusters as self-propulsion is increased and rationalize the evolution of the average cluster size by developing a kinetic model of reversible aggregation. As density is increased, the nonequilibrium clusters percolate to form a ramified structure reminiscent of a physical gel. We show that the addition of a finite amount of noise is needed to trigger a nonequilibrium phase separation, showing that demixing in active Brownian particles results from a delicate balance between noise, interparticle interactions, and self-propulsion. We show that self-propulsion has a profound influence on the dynamics of the active fluid. We find that the diffusion constant has a nonmonotonic behavior as self-propulsion is increased at finite density and that activity produces strong deviations from Fickian diffusion that persist over large time scales and length scales, suggesting that systems of active particles generically behave as dynamically heterogeneous systems.

A new model to study the phase transition from microstructures to nanostructures in ionic/ionic surfactants mixture.

PubMed

Sohrabi, Beheshteh; Gharibi, Hussein; Javadian, Soheila; Hashemianzadeh, Majid

2007-08-30

The phase behavior and aggregate structures of mixtures of the oppositely charged surfactants cetyltrimethyl ammonium bromide (CTAB) and sodium dodecyl sulfate (SDS) are explored at high dilution by pulsed field gradient stimulated echo (PFG-STE) NMR. The aggregation numbers and hydrodynamic radii of vesicles and mixed micelles were determined by a combination of viscosity and self-diffusion coefficient measurements. The average size of the mixed micelles was larger than that of micelles containing uniformly charged head groups. Analysis of the variations of the self-diffusion coefficient and viscosity with changing concentration of CTAB or SDS in the cationic-rich and anionic-rich regions revealed a phase transition from vesicles to mixed micelles. Differences in the lengths of the CTAB and SDS hydrophobic chains stabilize vesicles relative to other microstructures (e.g., liquid crystalline and precipitate phase), and vesicles form spontaneously over a wide range of compositions in both cationic-rich and anionic-rich solutions. The results obtained from conductometry measurements confirmed this transition. Finally, according to the capacitor model, a new model was developed for estimating the surface potentials and electrostatic free energy (g(elec)). Then we investigated the variations of electrostatic and transfer free energy in phase transition between mixed micelle and vesicle.

Liquid crystals from mesogens containing gold nanoparticles

NASA Astrophysics Data System (ADS)

Lewandowski, Wiktor; Gorecka, Ewa

Long-range ordered structures made of nanoparticles are perspective materials for future optical, electronic and sensing technologies. Conspicuous physicochemical features of nanoparticle aggregates originate from distant-dependent collective interactions, therefore lately a lot of attention was put to the development of assembly strategies allowing control over nanoparticle spatial distribution. In this chapter we will focus on the assembly process based on using thermotropic liquid-crystalline molecules as surface nanoparticle ligands. First, we discuss architectural parameters that inuence structure and thermal properties of the aggregates. Then, we show that this approach enables formation of assemblies with metamaterial characteristic, gives access to dynamic materials with light-, magneto- and thermo-responsive behavior and allows formation of aggregates with unique structures, which all make this strategy an attractive object of research.

Water Use in the US Electric Power Sector: Energy Systems ...

EPA Pesticide Factsheets

This presentation reviews the water demands of long-range electricity scenarios. It addresses questions such as: What are the aggregate water requirements of the U.S. electric power sector? How could water requirements evolve under different long-range regional generation mixes? It also looks at research addressing the electricity generation water demand from a life cycle perspective, such as water use for the fuel cycle (natural gas, coal, uranium, etc.) and water use for the materials/equipment/manufacturing of new power plants. The presentation is part of panel session on the Water-Energy Nexus at the World Energy Engineering Congress

Optimization of the diffusive gradients in thin films (DGT) method for simultaneous assay of potassium and plant-available phosphorus in soils.

PubMed

Zhang, Yulin; Mason, Sean; McNeill, Ann; McLaughlin, Michael J

2013-09-15

Potassium (K) and phosphorus (P) are two important macronutrients for crops, and are usually applied to soils as granular fertilizer before seeding. Therefore, accurate soil tests prior to planting to predict crop response to fertilizers are important in optimizing crop yields. Traditional methods used for testing both available K and P in soils, which are based on chemical extraction procedures, are to be soil-type dependent, and the predictive relationships across a broad range of soils are generally poor. The diffusive gradients in thin films (DGT) technique, based on diffusion theory, is extensively used to measure the diffusive supply of trace elements, metals and some nutrients in soils and water. When DGT is used to assess plant-available P in soils, a good relationship is found between crop response to P fertilizer and concentrations of P in soil measured by DGT, and therefore the DGT method provides a more precise recommendation of P fertilizer requirements. Adaptation of the DGT method to measure plant-available K in soils has already been attempted [1], but limitations were reported due to the non-uniform size of the resin gel, decreased K binding rate of the gel at long deployment times and a limited ability to measure a wide range of K concentrations. To eliminate these problems, a new resin gel has been developed by combining Amberlite and ferrihydrite. This mixed Amberlite and ferrihydrite (MAF) gel has improved properties in terms of handling and even distribution of Amberlite in the gel. The elution efficiencies of the MAF gel for K and P were 90% and 96%, respectively. The diffusion coefficient of K through the diffusive gel was 1.30 × 10(-5)cm(2)s(-1) at 22 ± 1°C and was stable through time. Since ferrihydrite is already used in DGT P testing, the ability of the MAF gel to assess available P simultaneously was also assessed. The MAF gel performed the same as the traditional ferrihydrite gel for available P assessment in a wide variety of agricultural soils. This means that the newly developed gel has the potential to measure K and plant-available P in soils simultaneously. Copyright © 2013 Elsevier B.V. All rights reserved.

A thermal after-effect of UV irradiation of muscle glycogen phosphorylase b

PubMed Central

Eronina, Tatiana B.; Chebotareva, Natalia A.; Kleymenov, Sergey Yu.; Shubin, Vladimir V.; Kurganov, Boris I.

2017-01-01

Different test systems are used to characterize the anti-aggregation efficiency of molecular chaperone proteins and of low-molecular-weight chemical chaperones. Test systems based on aggregation of UV-irradiated protein are of special interest because they allow studying the protective action of different agents at physiological temperatures. The kinetics of UV-irradiated glycogen phosphorylase b (UV-Phb) from rabbit skeletal muscle was studied at 37°C using dynamic light scattering in a wide range of protein concentrations. It has been shown that the order of aggregation with respect to the protein is equal to unity. A conclusion has been made that the rate-limiting stage of the overall process of aggregation is heat-induced structural reorganization of a UV-Phb molecule, which contains concealed damage. PMID:29216272

Mesoscopic structure of neuronal tracts from time-dependent diffusion

PubMed Central

Burcaw, Lauren M.; Fieremans, Els; Novikov, Dmitry S.

2015-01-01

Interpreting brain diffusion MRI measurements in terms of neuronal structure at a micrometer level is an exciting unresolved problem. Here we consider diffusion transverse to a bundle of fibers, and show theoretically, as well as using Monte Carlo simulations and measurements in a phantom made of parallel fibers mimicking axons, that the time dependent diffusion coefficient approaches its macroscopic limit slowly, in a (lnt)/t fashion. The logarithmic singularity arises due to short range disorder in the fiber packing. We identify short range disorder in axonal fibers based on histological data from the splenium, and argue that the time dependent contribution to the overall diffusion coefficient from the extra-axonal water dominates that of the intra-axonal water. This dominance may explain the bias in measuring axon diameters in clinical settings. The short range disorder is also reflected in the linear frequency dependence of the diffusion coefficient measured with oscillating gradients, in agreement with recent experiments. Our results relate the measured diffusion to the mesoscopic structure of neuronal tissue, uncovering the sensitivity of diffusion metrics to axonal arrangement within a fiber tract, and providing an alternative interpretation of axonal diameter mapping techniques. PMID:25837598

Mesoscopic structure of neuronal tracts from time-dependent diffusion.

PubMed

Burcaw, Lauren M; Fieremans, Els; Novikov, Dmitry S

2015-07-01

Interpreting brain diffusion MRI measurements in terms of neuronal structure at a micrometer level is an exciting unresolved problem. Here we consider diffusion transverse to a bundle of fibers, and show theoretically, as well as using Monte Carlo simulations and measurements in a phantom made of parallel fibers mimicking axons, that the time dependent diffusion coefficient approaches its macroscopic limit slowly, in a (ln t)/t fashion. The logarithmic singularity arises due to short range disorder in the fiber packing. We identify short range disorder in axonal fibers based on histological data from the splenium, and argue that the time dependent contribution to the overall diffusion coefficient from the extra-axonal water dominates that of the intra-axonal water. This dominance may explain the bias in measuring axon diameters in clinical settings. The short range disorder is also reflected in the asymptotically linear frequency dependence of the diffusion coefficient measured with oscillating gradients, in agreement with recent experiments. Our results relate the measured diffusion to the mesoscopic structure of neuronal tissue, uncovering the sensitivity of diffusion metrics to axonal arrangement within a fiber tract, and providing an alternative interpretation of axonal diameter mapping techniques. Copyright © 2015 Elsevier Inc. All rights reserved.

Molecular Dynamics Study of the Solution Structure, Clustering, and Diffusion of Four Aqueous Alkanolamines.

PubMed

Melnikov, Sergey M; Stein, Matthias

2018-03-15

CO 2 sequestration from anthropogenic resources is a challenge to the design of environmental processes at a large scale. Reversible chemical absorption by amine-based solvents is one of the most efficient methods of CO 2 removal. Molecular simulation techniques are very useful tools to investigate CO 2 binding by aqueous alkanolamine molecules for further technological application. In the present work, we have performed detailed atomistic molecular dynamics simulations of aqueous solutions of three prototype amines: monoethanolamine (MEA) as a standard, 3-aminopropanol (MPA), 2-methylaminoethanol (MMEA), and 4-diethylamino-2-butanol (DEAB) as potential novel CO 2 absorptive solvents. Solvent densities, radial distribution functions, cluster size distributions, hydrogen-bonding statistics, and diffusion coefficients for a full range of mixture compositions have been obtained. The solvent densities and diffusion coefficients from simulations are in good agreement with those in the experiment. In aqueous solution, MEA, MPA, and MMEA molecules prefer to be fully solvated by water molecules, whereas DEAB molecules tend to self-aggregate. In a range from 30/70-50/50 (w/w) alkanolamine/water mixtures, they form a bicontinuous phase (both alkanolamine and water are organized in two mutually percolating clusters). Among the studied aqueous alkanolamine solutions, the diffusion coefficients decrease in the following order MEA > MPA = MMEA > DEAB. With an increase of water content, the diffusion coefficients increase for all studied alkanolamines. The presented results are a first step for process-scale simulation and provide important qualitative and quantitative information for the design and engineering of efficient new CO 2 removal processes.

Bacterial Inclusion Bodies Contain Amyloid-Like Structure

PubMed Central

Wang, Lei; Maji, Samir K; Sawaya, Michael R; Eisenberg, David; Riek, Roland

2008-01-01

Protein aggregation is a process in which identical proteins self-associate into imperfectly ordered macroscopic entities. Such aggregates are generally classified as amorphous, lacking any long-range order, or highly ordered fibrils. Protein fibrils can be composed of native globular molecules, such as the hemoglobin molecules in sickle-cell fibrils, or can be reorganized β-sheet–rich aggregates, termed amyloid-like fibrils. Amyloid fibrils are associated with several pathological conditions in humans, including Alzheimer disease and diabetes type II. We studied the structure of bacterial inclusion bodies, which have been believed to belong to the amorphous class of aggregates. We demonstrate that all three in vivo-derived inclusion bodies studied are amyloid-like and comprised of amino-acid sequence-specific cross-β structure. These findings suggest that inclusion bodies are structured, that amyloid formation is an omnipresent process both in eukaryotes and prokaryotes, and that amino acid sequences evolve to avoid the amyloid conformation. PMID:18684013

Time-Dependent Influence of Cell Membrane Permeability on MR Diffusion Measurements

PubMed Central

Li, Hua; Jiang, Xiaoyu; Xie, Jingping; McIntyre, J. Oliver; Gore, John C.; Xu, Junzhong

2015-01-01

Purpose To investigate the influence of cell membrane permeability on diffusion measurements over a broad range of diffusion times. Methods Human myelogenous leukemia K562 cells were cultured and treated with saponin to selectively alter cell membrane permeability, resulting in a broad physiologically relevant range from 0.011 μm/ms to 0.044 μm/ms. Apparent diffusion coefficient (ADC) values were acquired with the effective diffusion time (Δeff) ranging from 0.42 to 3000 ms. Cosine-modulated oscillating gradient spin echo (OGSE) measurements were performed to achieve short Δeff from 0.42 to 5 ms, while stimulated echo acquisitions (STEAM) were used to achieve long Δeff from 11 to 2999 ms. Computer simulations were also performed to support the experimental results. Results Both computer simulations and experiments in vitro showed that the influence of membrane permeability on diffusion MR measurements is highly dependent on the choice of diffusion time, and it is negligible only when the diffusion time is at least one order of magnitude smaller than the intracellular exchange lifetime. Conclusion The influence of cell membrane permeability on the measured ADCs is negligible in OGSE measurements at moderately high frequencies. By contrast, cell membrane permeability has a significant influence on ADC and quantitative diffusion measurements at low frequencies such as those sampled using conventional pulsed gradient methods. PMID:26096552

Noah, Joseph and Convex Hulls

NASA Astrophysics Data System (ADS)

Watkins, N. W.; Chau, Y.; Chapman, S. C.

2010-12-01

The idea of describing animal movement by mathematical models based on diffusion and Brownian motion has a long heritage. It has thus been natural to account for those aspects of motion that depart from the Brownian by the use of models incorporating long memory & subdiffusion (“the Joseph effect”) and/or heavy tails & superdiffusion (“the Noah effect”). My own interest in this problem was originally from a geoscience perspective, and was triggered by the need to model time series in space physics where both effects coincide. Subsequently I have been involved in animal foraging studies [e.g. Edwards et al, Nature, 2007]. I will describe some recent work [Watkins et al, PRE, 2009] which studies how fixed-timestep and variable-timestep formulations of anomalous diffusion are related in the presence of heavy tails and long range memory (stable processes versus the CTRW). Quantities for which different scaling relations are predicted between the two approaches are of particular interest, to aid testability. I will also present some of work in progress on the convex hull of anomalously diffusing walkers, inspired by its possible relevance to the idea of home range in biology, and by Randon-Furling et al’s recent analytical results in the Brownian case [PRL, 2009].

Optical diffuse reflectance accessory for measurements of skin tissue by near-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Marbach, R.; Heise, H. M.

1995-02-01

An optimized accessory for measuring the diffuse reflectance spectra of human skin tissue in the near-infrared spectral range is presented. The device includes an on-axis ellipsoidal collecting mirror with efficient illumination optics for small sampling areas of bulky body specimens. The optical design is supported by the results of a Monte Carlo simulation study of the reflectance characteristics of skin tissue. Because the results evolved from efforts to measure blood glucose noninvasively, the main emphasis is placed on the long-wavelength near-infrared range where sufficient penetration depth for radiation into tissue is still available. The accessory is applied for in vivo diffuse reflectance measurements.

Interplay between Long-Range Crystal Order and Short-Range Molecular Interactions Tunes Carrier Mobility in Liquid Crystal Dyes

PubMed Central

2017-01-01

We investigated the influence of molecular packing on the optical and electrical properties of the liquid crystalline dye 4,7-bis[5-(2-fluoro-4-pentyl-phenyl)-2-thienyl]-2,1,3-benzothiadiazole (FPPTB). FPPTB is crystalline at room temperature, exhibits a nematic phase at temperatures above 149 °C and is in an isotropic melt at temperatures above 230 °C. Solution processed FPPTB films were subject to thermal annealing through these phase transition temperatures and characterized with X-ray diffraction and polarized optical microscopy. Cooling FPPTB films from the nematic and isotropic phases increased crystal domain size, but also induced local structural variations in the molecular packing of crystalline FPPTB. The decrease in long-range order was correlated with an increase in short-range π–π interactions, leading to changes in molecular aggregation which persisted even when the FPPTB films were cooled to room temperature. Annealing-induced changes in molecular aggregation were confirmed with optical spectroscopy. The carrier mobility in FPPTB films increased over 2 orders of magnitude from (2.2 ± 0.4) × 10–5 cm2 V–1 s–1 in as-spun films to μ = (5.0 ± 0.8) × 10–3 cm2 V–1 s–1 in films cooled from the isotropic melt. We discuss the relationship between thermal stability and high carrier mobility values in terms of the interplay between long-range molecular order and increased π–π interactions between molecular pairs in the FPPTB film. PMID:28139915

Long term management practices influenced soil aggregation and carbon dynamics

USDA-ARS?s Scientific Manuscript database

Soil aggregation protects soil organic C (SOC) against rapid decomposition, improves soil quality, and reduces soil erosion potential. The objectives of this study are to evaluate the effects of long-term (21 yrs.) management practices on SOC, water stable aggregate (WSA), and aggregate-associated ...

Size-tunable copper nanocluster aggregates and their application in hydrogen sulfide sensing on paper-based devices

PubMed Central

Chen, Po-Cheng; Li, Yu-Chi; Ma, Jia-Yin; Huang, Jia-Yu; Chen, Chien-Fu; Chang, Huan-Tsung

2016-01-01

Polystyrene sulfonate (PSS), a strong polyelectrolyte, was used to prepare red photoluminescent PSS-penicillamine (PA) copper (Cu) nanoclusters (NC) aggregates, which displayed high selectivity and sensitivity to the detection of hydrogen sulfide (H2S). The size of the PSS-PA-Cu NC aggregates could be readily controlled from 5.5 μm to 173 nm using different concentrations of PSS, which enabled better dispersity and higher sensitivity towards H2S. PSS-PA-Cu NC aggregates provided rapid H2S detection by using the strong Cu-S interaction to quench NC photoluminescence as a sensing mechanism. As a result, a detection limit of 650 nM, which is lower than the maximum level permitted in drinking water by the World Health Organization, was achieved for the analysis of H2S in spring-water samples. Moreover, highly dispersed PSS-PA-Cu NC aggregates could be incorporated into a plate-format paper-based analytical device which enables ultra-low sample volumes (5 μL) and feature shorter analysis times (30 min) compared to conventional solution-based methods. The advantages of low reagent consumption, rapid result readout, limited equipment, and long-term storage make this platform sensitive and simple enough to use without specialized training in resource constrained settings. PMID:27113330

A Device for Long-Term Perfusion, Imaging, and Electrical Interfacing of Brain Tissue In vitro

PubMed Central

Killian, Nathaniel J.; Vernekar, Varadraj N.; Potter, Steve M.; Vukasinovic, Jelena

2016-01-01

Distributed microelectrode array (MEA) recordings from consistent, viable, ≥500 μm thick tissue preparations over time periods from days to weeks may aid in studying a wide range of problems in neurobiology that require in vivo-like organotypic morphology. Existing tools for electrically interfacing with organotypic slices do not address necrosis that inevitably occurs within thick slices with limited diffusion of nutrients and gas, and limited removal of waste. We developed an integrated device that enables long-term maintenance of thick, functionally active, brain tissue models using interstitial perfusion and distributed recordings from thick sections of explanted tissue on a perforated multi-electrode array. This novel device allows for automated culturing, in situ imaging, and extracellular multi-electrode interfacing with brain slices, 3-D cell cultures, and potentially other tissue culture models. The device is economical, easy to assemble, and integrable with standard electrophysiology tools. We found that convective perfusion through the culture thickness provided a functional benefit to the preparations as firing rates were generally higher in perfused cultures compared to their respective unperfused controls. This work is a step toward the development of integrated tools for days-long experiments with more consistent, healthier, thicker, and functionally more active tissue cultures with built-in distributed electrophysiological recording and stimulation functionality. The results may be useful for the study of normal processes, pathological conditions, and drug screening strategies currently hindered by the limitations of acute (a few hours long) brain slice preparations. PMID:27065793

NMR investigation of water diffusion in different biofilm structures.

PubMed

Herrling, Maria P; Weisbrodt, Jessica; Kirkland, Catherine M; Williamson, Nathan H; Lackner, Susanne; Codd, Sarah L; Seymour, Joseph D; Guthausen, Gisela; Horn, Harald

2017-12-01

Mass transfer in biofilms is determined by diffusion. Different mostly invasive approaches have been used to measure diffusion coefficients in biofilms, however, data on heterogeneous biomass under realistic conditions is still missing. To non-invasively elucidate fluid-structure interactions in complex multispecies biofilms pulsed field gradient-nuclear magnetic resonance (PFG-NMR) was applied to measure the water diffusion in five different types of biomass aggregates: one type of sludge flocs, two types of biofilm, and two types of granules. Data analysis is an important issue when measuring heterogeneous systems and is shown to significantly influence the interpretation and understanding of water diffusion. With respect to numerical reproducibility and physico-chemical interpretation, different data processing methods were explored: (bi)-exponential data analysis and the Γ distribution model. Furthermore, the diffusion coefficient distribution in relation to relaxation was studied by D-T 2 maps obtained by 2D inverse Laplace transform (2D ILT). The results show that the effective diffusion coefficients for all biofilm samples ranged from 0.36 to 0.96 relative to that of water. NMR diffusion was linked to biofilm structure (e.g., biomass density, organic and inorganic matter) as observed by magnetic resonance imaging and to traditional biofilm parameters: diffusion was most restricted in granules with compact structures, and fast diffusion was found in heterotrophic biofilms with fluffy structures. The effective diffusion coefficients in the biomass were found to be broadly distributed because of internal biomass heterogeneities, such as gas bubbles, precipitates, and locally changing biofilm densities. Thus, estimations based on biofilm bulk properties in multispecies systems can be overestimated and mean diffusion coefficients might not be sufficiently informative to describe mass transport in biofilms and the near bulk. © 2017 Wiley Periodicals, Inc.

Fractal Electronic Circuits Assembled From Nanoclusters

NASA Astrophysics Data System (ADS)

Fairbanks, M. S.; McCarthy, D.; Taylor, R. P.; Brown, S. A.

2009-07-01

Many patterns in nature can be described using fractal geometry. The effect of this fractal character is an array of properties that can include high internal connectivity, high dispersivity, and enhanced surface area to volume ratios. These properties are often desirable in applications and, consequently, fractal geometry is increasingly employed in technologies ranging from antenna to storm barriers. In this paper, we explore the application of fractal geometry to electrical circuits, inspired by the pervasive fractal structure of neurons in the brain. We show that, under appropriate growth conditions, nanoclusters of Sb form into islands on atomically flat substrates via a process close to diffusion-limited aggregation (DLA), establishing fractal islands that will form the basis of our fractal circuits. We perform fractal analysis of the islands to determine the spatial scaling properties (characterized by the fractal dimension, D) of the proposed circuits and demonstrate how varying growth conditions can affect D. We discuss fabrication approaches for establishing electrical contact to the fractal islands. Finally, we present fractal circuit simulations, which show that the fractal character of the circuit translates into novel, non-linear conduction properties determined by the circuit's D value.

Identifying the limitations of conventional biofiltration of diffuse methane emissions at long-term operation.

PubMed

Gómez-Cuervo, S; Hernández, J; Omil, F

2016-08-01

There is growing international concern about the increasing levels of greenhouse gases in the atmosphere, particularly CO2 and methane. The emissions of methane derived from human activities are associated with large flows and very low concentrations, such as those emitted from landfills and wastewater treatment plants, among others. The present work was focused on the biological methane degradation at diffuse concentrations (0.2% vv(-1)) in a conventional biofilter using a mixture of compost, perlite and bark chips as carrier. An extensive characterization of the process was carried out at long-term operation (250 days) in a fully monitored pilot plant, achieving stable conditions during the entire period. Operational parameters such as waterings, nitrogen addition and inlet loads and contact time influences were evaluated. Obtained results indicate that empty bed residence times within 4-8 min are crucial to maximize elimination rates. Waterings and the type of nitrogen supplied in the nutrient solution (ammonia or nitrate) have a strong impact on the biofilter performance. The better results compatible with a stable operation were achieved using nitrate, with elimination capacities up to 7.6 ± 1.1 g CH4 m(-3 )h(-1). The operation at low inlet concentrations (IC) implied that removal rates obtained were quite limited (ranging 3-8 g CH4 m(-3 )h(-1)); however, these results could be significantly increased (up to 20.6 g CH4 m(-3) h(-1)) at higher IC, which indicates that the mass transfer from the gas to the liquid layer surrounding the biofilm is a key limitation of the process.

The cmc-value of a bolalipid with two phosphocholine headgroups and a C24 alkyl chain: Unusual binding properties of fluorescence probes to bolalipid aggregates.

PubMed

Kordts, Martin; Kerth, Andreas; Drescher, Simon; Ott, Maria; Blume, Alfred

2017-09-01

Bolalipids with a long alkyl chain and two phosphocholine polar groups self-assemble in water into two different types of aggregate structures, namely helical nanofibers at low temperature and two types of micellar aggregates at higher temperature. We tried to determine the critical aggregation concentration (cac) or critical micellar concentration (cmc) of the bolalipid tetracosane-1,24-bis(phosphocholine) (PC-C24-PC) by using different fluorescent probes. The use of pyrene or pyrene derivatives as fluorophores failed, whereas the probes 1,8-ANS and particularly bis-ANS gave consistent results. The structure of the bolalipid aggregates obviously hinders partitioning or binding of pyrene derivatives into the micellar interior, whereas 1,8-ANS and bis-ANS can bind to the surface of the aggregate structures. The observed large increase in fluorescence intensity of bis-ANS indicates that binding to the hydrophobic surface of the aggregates leads to a reduction of the dye mobility. However, binding of bis-ANS is relatively weak, so that the determination of a cac/cmc-value is difficult. Simulations of the intensity curves for PC-C24-PC lead to estimates of the cac/cmc-value of 0.3-1.0×10 -6 M, depending on the structure of the aggregates. Single molecule fluorescence correlation spectroscopy was used to determine the mobility of bis-ANS as a function of concentration of PC-C24-PC. The dye diffusion time and the molecular brightness are lower at low bolalipid concentration, when only free dye is present, and increase at higher concentration when bis-ANS is bound to the aggregates. The experimental cac/cmc-values are higher than those estimated, using an incremental method for the change in Gibbs free energy for micellization with n-alkyl-phosphocholines with only one polar group as a comparison. Apparently, for PC-C24-PC in micellar or fibrous aggregates, more CH 2 groups are exposed to water than in a conventional micelle of an n-alkyl-phosphocholine. Copyright © 2017 Elsevier Inc. All rights reserved.

Unimodal primary sensory cortices are directly connected by long-range horizontal projections in the rat sensory cortex.

PubMed

Stehberg, Jimmy; Dang, Phat T; Frostig, Ron D

2014-01-01

Research based on functional imaging and neuronal recordings in the barrel cortex subdivision of primary somatosensory cortex (SI) of the adult rat has revealed novel aspects of structure-function relationships in this cortex. Specifically, it has demonstrated that single whisker stimulation evokes subthreshold neuronal activity that spreads symmetrically within gray matter from the appropriate barrel area, crosses cytoarchitectural borders of SI and reaches deeply into other unimodal primary cortices such as primary auditory (AI) and primary visual (VI). It was further demonstrated that this spread is supported by a spatially matching underlying diffuse network of border-crossing, long-range projections that could also reach deeply into AI and VI. Here we seek to determine whether such a network of border-crossing, long-range projections is unique to barrel cortex or characterizes also other primary, unimodal sensory cortices and therefore could directly connect them. Using anterograde (BDA) and retrograde (CTb) tract-tracing techniques, we demonstrate that such diffuse horizontal networks directly and mutually connect VI, AI and SI. These findings suggest that diffuse, border-crossing axonal projections connecting directly primary cortices are an important organizational motif common to all major primary sensory cortices in the rat. Potential implications of these findings for topics including cortical structure-function relationships, multisensory integration, functional imaging, and cortical parcellation are discussed.

Unimodal primary sensory cortices are directly connected by long-range horizontal projections in the rat sensory cortex

PubMed Central

Stehberg, Jimmy; Dang, Phat T.; Frostig, Ron D.

2014-01-01

Research based on functional imaging and neuronal recordings in the barrel cortex subdivision of primary somatosensory cortex (SI) of the adult rat has revealed novel aspects of structure-function relationships in this cortex. Specifically, it has demonstrated that single whisker stimulation evokes subthreshold neuronal activity that spreads symmetrically within gray matter from the appropriate barrel area, crosses cytoarchitectural borders of SI and reaches deeply into other unimodal primary cortices such as primary auditory (AI) and primary visual (VI). It was further demonstrated that this spread is supported by a spatially matching underlying diffuse network of border-crossing, long-range projections that could also reach deeply into AI and VI. Here we seek to determine whether such a network of border-crossing, long-range projections is unique to barrel cortex or characterizes also other primary, unimodal sensory cortices and therefore could directly connect them. Using anterograde (BDA) and retrograde (CTb) tract-tracing techniques, we demonstrate that such diffuse horizontal networks directly and mutually connect VI, AI and SI. These findings suggest that diffuse, border-crossing axonal projections connecting directly primary cortices are an important organizational motif common to all major primary sensory cortices in the rat. Potential implications of these findings for topics including cortical structure-function relationships, multisensory integration, functional imaging, and cortical parcellation are discussed. PMID:25309339

The optimization of concrete mixtures for use in highway applications

NASA Astrophysics Data System (ADS)

Moini, Mohamadreza

Portland cement concrete is most used commodity in the world after water. Major part of civil and transportation infrastructure including bridges, roadway pavements, dams, and buildings is made of concrete. In addition to this, concrete durability is often of major concerns. In 2013 American Society of Civil Engineers (ASCE) estimated that an annual investment of 170 billion on roads and 20.5 billion for bridges is needed on an annual basis to substantially improve the condition of infrastructure. Same article reports that one-third of America's major roads are in poor or mediocre condition [1]. However, portland cement production is recognized with approximately one cubic meter of carbon dioxide emission. Indeed, the proper and systematic design of concrete mixtures for highway applications is essential as concrete pavements represent up to 60% of interstate highway systems with heavier traffic loads. Combined principles of material science and engineering can provide adequate methods and tools to facilitate the concrete design and improve the existing specifications. In the same manner, the durability must be addressed in the design and enhancement of long-term performance. Concrete used for highway pavement applications has low cement content and can be placed at low slump. However, further reduction of cement content (e.g., versus current specifications of Wisconsin Department of Transportation to 315-338 kg/m 3 (530-570 lb/yd3) for mainstream concrete pavements and 335 kg/m3 (565 lb/yd3) for bridge substructure and superstructures) requires delicate design of the mixture to maintain the expected workability, overall performance, and long-term durability in the field. The design includes, but not limited to optimization of aggregates, supplementary cementitious materials (SCMs), chemical and air-entraining admixtures. This research investigated various theoretical and experimental methods of aggregate optimization applicable for the reduction of cement content. Conducted research enabled further reduction of cement contents to 250 kg/m3 (420 lb/yd3) as required for the design of sustainable concrete pavements. This research demonstrated that aggregate packing can be used in multiple ways as a tool to optimize the aggregates assemblies and achieve the optimal particle size distribution of aggregate blends. The SCMs, and air-entraining admixtures were selected to comply with existing WisDOT performance requirements and chemical admixtures were selected using the separate optimization study excluded from this thesis. The performance of different concrete mixtures was evaluated for fresh properties, strength development, and compressive and flexural strength ranging from 1 to 360 days. The methods and tools discussed in this research are applicable, but not limited to concrete pavement applications. The current concrete proportioning standards such as ACI 211 or current WisDOT roadway standard specifications (Part 5: Structures, Section 501: Concrete) for concrete have limited or no recommendations, methods or guidelines on aggregate optimization, the use of ternary aggregate blends (e.g., such as those used in asphalt industry), the optimization of SCMs (e.g., class F and C fly ash, slag, metakaolin, silica fume), modern superplasticizers (such as polycarboxylate ether, PCE) and air-entraining admixtures. This research has demonstrated that the optimization of concrete mixture proportions can be achieved by the use and proper selection of optimal aggregate blends and result in 12% to 35% reduction of cement content and also more than 50% enhancement of performance. To prove the proposed concrete proportioning method the following steps were performed: • The experimental aggregate packing was investigated using northern and southern source of aggregates from Wisconsin; • The theoretical aggregate packing models were utilized and results were compared with experiments; • Multiple aggregate optimization methods (e.g., optimal grading, coarseness chart) were studied and compared to aggregate packing results and performance of experimented concrete mixtures; • Optimal aggregate blends were selected and used for concrete mixtures; • The optimal dosage of admixtures were selected for three types of plasticizing and superplasticizing admixtures based on a separately conducted study; • The SCM dosages were selected based on current WisDOT specifications; • The optimal air-entraining admixture dosage was investigated based on performance of preliminary concrete mixtures; • Finally, optimal concrete mixtures were tested for fresh properties, compressive strength development, modulus of rupture, at early ages (1day) and ultimate ages (360 days). • Durability performance indicators for optimal concrete mixtures were also tested for resistance of concrete to rapid chloride permeability (RCP) at 30 days and 90 days and resistance to rapid freezing and thawing at 56 days.

DLA based compressed sensing for high resolution MR microscopy of neuronal tissue

NASA Astrophysics Data System (ADS)

Nguyen, Khieu-Van; Li, Jing-Rebecca; Radecki, Guillaume; Ciobanu, Luisa

2015-10-01

In this work we present the implementation of compressed sensing (CS) on a high field preclinical scanner (17.2 T) using an undersampling trajectory based on the diffusion limited aggregation (DLA) random growth model. When applied to a library of images this approach performs better than the traditional undersampling based on the polynomial probability density function. In addition, we show that the method is applicable to imaging live neuronal tissues, allowing significantly shorter acquisition times while maintaining the image quality necessary for identifying the majority of neurons via an automatic cell segmentation algorithm.

Quantitative assessment of the degradation of aggregated TDP-43 mediated by the ubiquitin proteasome system and macroautophagy.

PubMed

Cascella, Roberta; Fani, Giulia; Capitini, Claudia; Rusmini, Paola; Poletti, Angelo; Cecchi, Cristina; Chiti, Fabrizio

2017-12-01

Amyotrophic lateral sclerosis and frontotemporal lobar degeneration with ubiquitin-positive inclusions are neurodegenerative disorders that share the cytosolic deposition of TDP-43 (TAR DNA-binding protein 43) in the CNS. TDP-43 is well known as being actively degraded by both the proteasome and macroautophagy. The well-documented decrease in the efficiency of these clearance systems in aging and neurodegeneration, as well as the genetic evidence that many of the familial forms of TDP-43 proteinopathies involve genes that are associated with them, suggest that a failure of these protein degradation systems is a major factor that contributes to the onset of TDP-43-associated disorders. Here, we inserted preformed human TDP-43 aggregates in the cytosol of murine NSC34 and N2a cells in diffuse form and observed their degradation under conditions in which exogenous TDP-43 is not expressed and endogenous nuclear TDP-43 is not recruited, thereby allowing a time zero to be established in TDP-43 degradation and to observe its disposal kinetically and analytically. TDP-43 degradation was observed in the absence and presence of selective inhibitors and small interfering RNAs against the proteasome and autophagy. We found that cytosolic diffuse aggregates of TDP-43 can be distinguished in 3 different classes on the basis of their vulnerability to degradation, which contributed to the definition-with previous reports-of a total of 6 distinct classes of misfolded TDP-43 species that range from soluble monomer to undegradable macroaggregates. We also found that the proteasome and macroautophagy-degradable pools of TDP-43 are fully distinguishable, rather than in equilibrium between them on the time scale required for degradation, and that a significant crosstalk exists between the 2 degradation processes.-Cascella, R., Fani, G., Capitini, C., Rusmini, P., Poletti, A., Cecchi, C., Chiti, F. Quantitative assessment of the degradation of aggregated TDP-43 mediated by the ubiquitin proteasome system and macroautophagy. © FASEB.

77 FR 36251 - Intermountain Region, Boise National Forest; Emmett Ranger District, Idaho; Scriver Creek...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-18

... relocated segment of NFS Road 696D would be decommissioned); and (4) road maintenance activities would occur... maintenance activities may include but are not limited to road prism blading, spot aggregate placement...) Permanent national forest system (NFS) roads can increase long term resource impacts and road maintenance...

Patchy reaction-diffusion and population abundance: the relative importance of habitat amount and arrangement

Treesearch

Curtis H. Flather; Michael Bevers

2002-01-01

A discrete reaction-diffusion model was used to estimate long-term equilibrium populations of a hypothetical species inhabiting patchy landscapes to examine the relative importance of habitat amount and arrangement in explaining population size. When examined over a broad range of habitat amounts and arrangements, population size was largely determined by a pure amount...

Improvement of the trace metal composition of medium for nitrite-dependent anaerobic methane oxidation bacteria: Iron (II) and copper (II) make a difference.

PubMed

He, Zhanfei; Geng, Sha; Pan, Yawei; Cai, Chaoyang; Wang, Jiaqi; Wang, Liqiao; Liu, Shuai; Zheng, Ping; Xu, Xinhua; Hu, Baolan

2015-11-15

Nitrite-dependent anaerobic methane oxidation (n-damo) is a potential bioprocess for treating nitrogen-containing wastewater. This process uses methane, an inexpensive and nontoxic end-product of anaerobic digestion, as an external electron donor. However, the low turnover rate and slow growth rate of n-damo functional bacteria limit the practical application of this process. In the present study, the short- and long-term effects of variations in trace metal concentrations on n-damo bacteria were investigated, and the concentrations of trace metal elements of medium were improved. The results were subsequently verified by a group of long-term inoculations (90 days) and were applied in a sequencing batch reactor (SBR) (84 days). The results indicated that iron (Fe(II)) and copper (Cu(II)) (20 and 10 μmol L(-1), respectively) significantly stimulated the activity and the growth of n-damo bacteria, whereas other trace metal elements, including zinc (Zn), molybdenum (Mo), cobalt (Co), manganese (Mn), and nickel (Ni), had no significant effect on n-damo bacteria in the tested concentration ranges. Interestingly, fluorescence in situ hybridization (FISH) showed that a large number of dense, large aggregates (10-50 μm) of n-damo bacteria were formed by cell adhesion in the SBR reactor after using the improved medium, and to our knowledge this is the first discovery of large aggregates of n-damo bacteria. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microscopic theory of topologically entangled fluids of rigid macromolecules

NASA Astrophysics Data System (ADS)

Sussman, Daniel M.; Schweizer, Kenneth S.

2011-06-01

We present a first-principles theory for the slow dynamics of a fluid of entangling rigid crosses of zero excluded volume based on a generalization of the dynamic mean-field approach of Szamel for infinitely thin nonrotating rods. The latter theory exactly includes topological constraints at the two-body collision level and self-consistently renormalizes an effective diffusion tensor to account for many-body effects. Remarkably, it predicts scaling laws consistent with the phenomenological reptation-tube predictions of Doi and Edwards for the long-time diffusion and the localization length in the heavily entangled limit. We generalize this approach to a different macromolecular architecture, infinitely thin three-dimensional crosses, and also extend the range of densities over which a dynamic localization length can be calculated for rods. Ideal gases of nonrotating crosses have recently received attention in computer simulations and are relevant as a simple model of both a strong-glass former and entangling star-branched polymers. Comparisons of our theory with these simulations reveal reasonable agreement for the magnitude and reduced density dependence of the localization length and also the self-diffusion constant if the consequences of local density fluctuations are taken into account.

O'Connell's process as a vicious Brownian motion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Katori, Makoto

Vicious Brownian motion is a diffusion scaling limit of Fisher's vicious walk model, which is a system of Brownian particles in one dimension such that if two motions meet they kill each other. We consider the vicious Brownian motions conditioned never to collide with each other and call it noncolliding Brownian motion. This conditional diffusion process is equivalent to the eigenvalue process of the Hermitian-matrix-valued Brownian motion studied by Dyson [J. Math. Phys. 3, 1191 (1962)]. Recently, O'Connell [Ann. Probab. (to be published)] introduced a generalization of the noncolliding Brownian motion by using the eigenfunctions (the Whittaker functions) of themore » quantum Toda lattice in order to analyze a directed polymer model in 1 + 1 dimensions. We consider a system of one-dimensional Brownian motions with a long-ranged killing term as a generalization of the vicious Brownian motion and construct the O'Connell process as a conditional process of the killing Brownian motions to survive forever.« less

Conceptual models governing leaching behavior and their long-term predictive capability

USGS Publications Warehouse

Claassen, Hans C.

1981-01-01

Six models that may be used to describe the interaction of radioactive waste solids with aqueous solutions are as follows:Simple linear mass transfer;Simple parabolic mass transfer;Parabolic mass transfer with the formation of a diffusion-limiting surface layer at an arbitrary time;Initial parabolic mass transfer followed by linear mass transfer at an arbitrary time;Parabolic (or linear) mass transfer and concomitant surface sorption; andParabolic (or linear) mass transfer and concomitant chemical precipitation.Some of these models lead to either illogical or unrealistic predictions when published data are extrapolated to long times. These predictions result because most data result from short-term experimentation. Probably for longer times, processes will occur that have not been observed in the shorter experiments. This hypothesis has been verified by mass-transfer data from laboratory experiments using natural volcanic glass to predict the composition of groundwater. That such rate-limiting mechanisms do occur is reassuring, although now it is not possible to deduce a single mass-transfer limiting mechanism that could control the solution concentration of all components of all waste forms being investigated. Probably the most reasonable mechanisms are surface sorption and chemical precipitation of the species of interest. Another is limiting of mass transfer by chemical precipitation on the waste form surface of a substance not containing the species of interest, that is, presence of a diffusion-limiting layer. The presence of sorption and chemical precipitation as factors limiting mass transfer has been verified in natural groundwater systems, whereas the diffusion-limiting mechanism has not been verified yet.

Phase diagram for a two-dimensional, two-temperature, diffusive XY model.

PubMed

Reichl, Matthew D; Del Genio, Charo I; Bassler, Kevin E

2010-10-01

Using Monte Carlo simulations, we determine the phase diagram of a diffusive two-temperature conserved order parameter XY model. When the two temperatures are equal the system becomes the equilibrium XY model with the continuous Kosterlitz-Thouless (KT) vortex-antivortex unbinding phase transition. When the two temperatures are unequal the system is driven by an energy flow from the higher temperature heat-bath to the lower temperature one and reaches a far-from-equilibrium steady state. We show that the nonequilibrium phase diagram contains three phases: A homogenous disordered phase and two phases with long range, spin texture order. Two critical lines, representing continuous phase transitions from a homogenous disordered phase to two phases of long range order, meet at the equilibrium KT point. The shape of the nonequilibrium critical lines as they approach the KT point is described by a crossover exponent φ=2.52±0.05. Finally, we suggest that the transition between the two phases with long-range order is first-order, making the KT-point where all three phases meet a bicritical point.

Social aggregation in the pelagic zone with special reference to fish and invertebrates.

PubMed

Ritz, David A; Hobday, Alistair J; Montgomery, John C; Ward, Ashley J W

2011-01-01

Aggregations of organisms, ranging from zooplankton to whales, are an extremely common phenomenon in the pelagic zone; perhaps the best known are fish schools. Social aggregation is a special category that refers to groups that self-organize and maintain cohesion to exploit benefits such as protection from predators, and location and capture of resources more effectively and with greater energy efficiency than could a solitary individual. In this review we explore general aggregation principles, with specific reference to pelagic organisms; describe a range of new technologies either designed for studying aggregations or that could potentially be exploited for this purpose; report on the insights gained from theoretical modelling; discuss the relationship between social aggregation and ocean management; and speculate on the impact of climate change. Examples of aggregation occur in all animal phyla. Among pelagic organisms, it is possible that repeated co-occurrence of stable pairs of individuals, which has been established for some schooling fish, is the likely precursor leading to networks of social interaction and more complex social behaviour. Social network analysis has added new insights into social behaviour and allows us to dissect aggregations and to examine how the constituent individuals interact with each other. This type of analysis is well advanced in pinnipeds and cetaceans, and work on fish is progressing. Detailed three-dimensional analysis of schools has proved to be difficult, especially at sea, but there has been some progress recently. The technological aids for studying social aggregation include video and acoustics, and have benefited from advances in digitization, miniaturization, motion analysis and computing power. New techniques permit three-dimensional tracking of thousands of individual animals within a single group which has allowed novel insights to within-group interactions. Approaches using theoretical modelling of aggregations have a long history but only recently have hypotheses been tested empirically. The lack of synchrony between models and empirical data, and lack of a common framework to schooling models have hitherto hampered progress; however, recent developments in this field offer considerable promise. Further, we speculate that climate change, already having effects on ecosystems, could have dramatic effects on aggregations through its influence on species composition by altering distribution ranges, migration patterns, vertical migration, and oceanic acidity. Because most major commercial fishing targets schooling species, these changes could have important consequences for the dependent businesses. 2011 Elsevier Ltd. All rights reserved.

Effects of inlet flow field conditions on the performance of centrifugal compressor diffusers: Part 2 -- Straight-channel diffuser

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deniz, S.; Greitzer, E.M.; Cumpsty, N.A.

2000-01-01

This is Part 2 of an examination of the influence of inlet flow conditions on the performance and operating range of centrifugal compressor vaned diffusers. The paper describes tests of a straight-channel type diffuser, sometimes called a wedge-vane diffuser, and compares the results with those from the discrete-passage diffusers described in Part 1. Effects of diffuser inlet Mach number, flow angle, blockage, and axial flow nonuniformity on diffuser pressure recovery and operating range are addressed. The straight-channel diffuser investigated has 30 vanes and was designed for the same aerodynamic duty as the discrete-passage diffuser described in Part 1. The rangesmore » of the overall pressure recovery coefficients were 0.50--0.78 for the straight-channel diffuser and 0.50--0.70 for the discrete-passage diffuser, except when the diffuser was choked. In other words, the maximum pressure recovery of the straight-channel diffuser was found to be roughly 10% higher than that of the discrete-passage diffuser investigated. The two types of diffuser showed similar behavior regarding the dependence of pressure recovery on diffuser inlet flow angle and the insensitivity of the performance to inlet flow field axial distortion and Mach number. The operating range of the straight-channel diffuser, as for the discrete-passage diffusers, was limited by the onset of rotating stall at a fixed momentum-averaged flow angle into the diffuser, which was for the straight-channel diffuser, {alpha}{sub crit} = 70 {+-} 0.5 deg. The background, nomenclature, and description of the facility and method are all given in Part 1.« less

Frontier mutualism: coevolutionary patterns at the northern range limit of the leaf-cutter ant–fungus symbiosis

PubMed Central

Mueller, Ulrich G.; Mikheyev, Alexander S.; Solomon, Scott E.; Cooper, Michael

2011-01-01

Tropical leaf-cutter ants cultivate the fungus Attamyces bromatificus in a many-to-one, diffuse coevolutionary relationship where ant and fungal partners re-associate frequently over time. To evaluate whether ant–Attamyces coevolution is more specific (tighter) in peripheral populations, we characterized the host-specificities of Attamyces genotypes at their northern, subtropical range limits (southern USA, Mexico and Cuba). Population-genetic patterns of northern Attamyces reveal features that have so far not been observed in the diffusely coevolving, tropical ant–Attamyces associations. These unique features include (i) cases of one-to-one ant–Attamyces specialization that tighten coevolution at the northern frontier; (ii) distributions of genetically identical Attamyces clones over large areas (up to 81 000 km2, approx. the area of Ireland, Austria or Panama); (iii) admixture rates between Attamyces lineages that appear lower in northern than in tropical populations; and (iv) long-distance gene flow of Attamyces across a dispersal barrier for leaf-cutter ants (ocean between mainland North America and Cuba). The latter suggests that Attamyces fungi may occasionally disperse independently of the ants, contrary to the traditional assumption that Attamyces fungi depend entirely on leaf-cutter queens for dispersal. Peripheral populations in Argentina or at mid-elevation sites in the Andes may reveal additional regional variants in ant–Attamyces coevolution. Studies of such populations are most likely to inform models of coextinctions of obligate mutualistic partners that are doubly stressed by habitat marginality and by environmental change. PMID:21389026

Experimental detection of long-distance interactions between biomolecules through their diffusion behavior: numerical study.

PubMed

Nardecchia, Ilaria; Spinelli, Lionel; Preto, Jordane; Gori, Matteo; Floriani, Elena; Jaeger, Sebastien; Ferrier, Pierre; Pettini, Marco

2014-08-01

The dynamical properties and diffusive behavior of a collection of mutually interacting particles are numerically investigated for two types of long-range interparticle interactions: Coulomb-electrostatic and dipole-electrodynamic. It is shown that when the particles are uniformly distributed throughout the accessible space, the self-diffusion coefficient is always lowered by the considered interparticle interactions, irrespective of their attractive or repulsive character. This fact is also confirmed by a simple model to compute the correction to the Brownian diffusion coefficient due to the interactions among the particles. These interactions are also responsible for the onset of dynamical chaos and an associated chaotic diffusion which still follows an Einstein-Fick-like law for the mean-square displacement as a function of time. Transitional phenomena are observed for Coulomb-electrostatic (repulsive) and dipole-electrodynamic (attractive) interactions considered both separately and in competition. The outcomes reported in this paper clearly indicate a feasible experimental method to probe the activation of resonant electrodynamic interactions among biomolecules.

Rugate filter for light-trapping in solar cells.

PubMed

Fahr, Stephan; Ulbrich, Carolin; Kirchartz, Thomas; Rau, Uwe; Rockstuhl, Carsten; Lederer, Falk

2008-06-23

We suggest a design for a coating that could be applied on top of any solar cell having at least one diffusing surface. This coating acts as an angle and wavelength selective filter, which increases the average path length and absorptance at long wavelengths without altering the solar cell performance at short wavelengths. The filter design is based on a continuous variation of the refractive index in order to minimize undesired reflection losses. Numerical procedures are used to optimize the filter for a 10 microm thick monocrystalline silicon solar cell, which lifts the efficiency above the Auger limit for unconcentrated illumination. The feasibility to fabricate such filters is also discussed, considering a finite available refractive index range.

Long-range exciton transport in conjugated polymer nanofibers prepared by seeded growth

NASA Astrophysics Data System (ADS)

Jin, Xu-Hui; Price, Michael B.; Finnegan, John R.; Boott, Charlotte E.; Richter, Johannes M.; Rao, Akshay; Menke, S. Matthew; Friend, Richard H.; Whittell, George R.; Manners, Ian

2018-05-01

Easily processed materials with the ability to transport excitons over length scales of more than 100 nanometers are highly desirable for a range of light-harvesting and optoelectronic devices. We describe the preparation of organic semiconducting nanofibers comprising a crystalline poly(di-n-hexylfluorene) core and a solvated, segmented corona consisting of polyethylene glycol in the center and polythiophene at the ends. These nanofibers exhibit exciton transfer from the core to the lower-energy polythiophene coronas in the end blocks, which occurs in the direction of the interchain π-π stacking with very long diffusion lengths (>200 nanometers) and a large diffusion coefficient (0.5 square centimeters per second). This is made possible by the uniform exciton energetic landscape created by the well-ordered, crystalline nanofiber core.

Detection of Diffusion Heterogeneity in Single Particle Tracking Trajectories Using a Hidden Markov Model with Measurement Noise Propagation

PubMed Central

Slator, Paddy J.; Cairo, Christopher W.; Burroughs, Nigel J.

2015-01-01

We develop a Bayesian analysis framework to detect heterogeneity in the diffusive behaviour of single particle trajectories on cells, implementing model selection to classify trajectories as either consistent with Brownian motion or with a two-state (diffusion coefficient) switching model. The incorporation of localisation accuracy is essential, as otherwise false detection of switching within a trajectory was observed and diffusion coefficient estimates were inflated. Since our analysis is on a single trajectory basis, we are able to examine heterogeneity between trajectories in a quantitative manner. Applying our method to the lymphocyte function-associated antigen 1 (LFA-1) receptor tagged with latex beads (4 s trajectories at 1000 frames s−1), both intra- and inter-trajectory heterogeneity were detected; 12–26% of trajectories display clear switching between diffusive states dependent on condition, whilst the inter-trajectory variability is highly structured with the diffusion coefficients being related by D 1 = 0.68D 0 − 1.5 × 104 nm2 s−1, suggestive that on these time scales we are detecting switching due to a single process. Further, the inter-trajectory variability of the diffusion coefficient estimates (1.6 × 102 − 2.6 × 105 nm2 s−1) is very much larger than the measurement uncertainty within trajectories, suggesting that LFA-1 aggregation and cytoskeletal interactions are significantly affecting mobility, whilst the timescales of these processes are distinctly different giving rise to inter- and intra-trajectory variability. There is also an ‘immobile’ state (defined as D < 3.0 × 103 nm2 s−1) that is rarely involved in switching, immobility occurring with the highest frequency (47%) under T cell activation (phorbol-12-myristate-13-acetate (PMA) treatment) with enhanced cytoskeletal attachment (calpain inhibition). Such ‘immobile’ states frequently display slow linear drift, potentially reflecting binding to a dynamic actin cortex. Our methods allow significantly more information to be extracted from individual trajectories (ultimately limited by time resolution and time-series length), and allow statistical comparisons between trajectories thereby quantifying inter-trajectory heterogeneity. Such methods will be highly informative for the construction and fitting of molecule mobility models within membranes incorporating aggregation, binding to the cytoskeleton, or traversing membrane microdomains. PMID:26473352

Individual differences in long-range time representation.

PubMed

Agostino, Camila S; Caetano, Marcelo S; Balci, Fuat; Claessens, Peter M E; Zana, Yossi

2017-04-01

On the basis of experimental data, long-range time representation has been proposed to follow a highly compressed power function, which has been hypothesized to explain the time inconsistency found in financial discount rate preferences. The aim of this study was to evaluate how well linear and power function models explain empirical data from individual participants tested in different procedural settings. The line paradigm was used in five different procedural variations with 35 adult participants. Data aggregated over the participants showed that fitted linear functions explained more than 98% of the variance in all procedures. A linear regression fit also outperformed a power model fit for the aggregated data. An individual-participant-based analysis showed better fits of a linear model to the data of 14 participants; better fits of a power function with an exponent β > 1 to the data of 12 participants; and better fits of a power function with β < 1 to the data of the remaining nine participants. Of the 35 volunteers, the null hypothesis β = 1 was rejected for 20. The dispersion of the individual β values was approximated well by a normal distribution. These results suggest that, on average, humans perceive long-range time intervals not in a highly compressed, biased manner, but rather in a linear pattern. However, individuals differ considerably in their subjective time scales. This contribution sheds new light on the average and individual psychophysical functions of long-range time representation, and suggests that any attribution of deviation from exponential discount rates in intertemporal choice to the compressed nature of subjective time must entail the characterization of subjective time on an individual-participant basis.

Maximizing Aggregation of Organic Fluorophores to Prolong Fluorescence Lifetime for Two-Photon Fluorescence Lifetime Imaging.

PubMed

Hu, Wenbo; Guo, Lihong; Bai, Lei; Miao, Xiaofei; Ni, Yun; Wang, Qi; Zhao, Hui; Xie, Meng; Li, Lin; Lu, Xiaomei; Huang, Wei; Fan, Quli

2018-05-28

Two-photon fluorescence lifetime imaging (TP-FLIM) not only permits imaging deep inside the tissues with precise spatial manipulation but also circumvents tissue autofluorescence, holding tremendous promise in molecular imaging. However, the serious lack of suitable contrast agents with long fluorescence lifetime and efficient two-photon absorption (TPA) greatly limits the advance of TP-FLIM. This study reports a simple approach to fabricate water-soluble organic semiconducting nanoparticles [thioxanthone (TXO) NPs] with ultralong fluorescence lifetime and efficient TPA for in vivo TP-FLIM. The approach utilizes the aggregation of a specifically selected thermally activated delayed fluorescence (TADF) fluorophore to prolong its fluorescence lifetime. Encapsulating the TADF fluorophore within an amphiphilic copolymer not only maximizes its aggregation but also obtains TXO NPs with efficient TPA. Importantly, as-prepared TXO NPs exhibit a considerably long fluorescence lifetime at a magnitude of 4.2 µs, which is almost 1000 times larger than that of existing organic contrast agents. Moreover, such long fluorescence lifetime is almost oxygen-inert, readily realizing both in vitro and in vivo TP-FLIM. This work may set valuable guidance for designing organic semiconducting materials with ultralong fluorescence lifetimes to fulfill the potential of FLIM. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Long-term transport behavior of psychoactive compounds in sewage-affected groundwater

NASA Astrophysics Data System (ADS)

Nham, Hang Thuy Thi; Greskowiak, Janek; Hamann, Enrico; Meffe, Raffaella; Hass, Ulrike; Massmann, Gudrun

2016-11-01

The present study provides a model-based characterization of the long-term transport behavior of five psychoactive compounds (meprobamate, pyrithyldione, primidone, phenobarbital and phenylethylmalonamide) introduced into groundwater via sewage irrigation in Berlin, Germany. Compounds are still present in the groundwater despite the sewage farm closure in the year 1980. Due to the limited information on (i) compound concentrations in the source water and (ii) substance properties, a total of 180 cross-sectional model realizations for each compound were carried out, covering a large range of possible parameter combinations. Results were compared with the present-day contamination patterns in the aquifer and the most likely scenarios were identified based on a number of model performance criteria. The simulation results show that (i) compounds are highly persistent under the present field conditions, and (ii) sorption is insignificant. Thus, back-diffusion from low permeability zones appears as the main reason for the compound retardation.

A morphogram for silica-witherite biomorphs and its application to microfossil identification in the early earth rock record.

PubMed

Rouillard, J; García-Ruiz, J-M; Gong, J; van Zuilen, M A

2018-05-01

Archean hydrothermal environments formed a likely site for the origin and early evolution of life. These are also the settings, however, were complex abiologic structures can form. Low-temperature serpentinization of ultramafic crust can generate alkaline, silica-saturated fluids in which carbonate-silica crystalline aggregates with life-like morphologies can self-assemble. These "biomorphs" could have adsorbed hydrocarbons from Fischer-Tropsch type synthesis processes, leading to metamorphosed structures that resemble carbonaceous microfossils. Although this abiogenic process has been extensively cited in the literature and has generated important controversy, so far only one specific biomorph type with a filamentous shape has been discussed for the interpretation of Archean microfossils. It is therefore critical to precisely determine the full distribution in morphology and size of these biomorphs, and to study the range of plausible geochemical conditions under which these microstructures can form. Here, a set of witherite-silica biomorph synthesis experiments in silica-saturated solutions is presented, for a range of pH values (from 9 to 11.5) and barium ion concentrations (from 0.6 to 40 mmol/L BaCl 2 ). Under these varying conditions, a wide range of life-like structures is found, from fractal dendrites to complex shapes with continuous curvature. The size, spatial concentration, and morphology of the biomorphs are strongly controlled by environmental parameters, among which pH is the most important. This potentially limits the diversity of environments in which the growth of biomorphs could have occurred on Early Earth. Given the variety of the observed biomorph morphologies, our results show that the morphology of an individual microstructure is a poor criterion for biogenicity. However, biomorphs may be distinguished from actual populations of cellular microfossils by their wide, unimodal size distribution. Biomorphs grown by diffusion in silica gel can be differentiated by their continuous gradient in size, spatial density, and morphology along the direction of diffusion. © 2018 The Authors. Geobiology Published by John Wiley & Sons Ltd.

On the formation and early evolution of soot in turbulent nonpremixed flames

NASA Astrophysics Data System (ADS)

Bisetti, F.; Blanquart, G.; Mueller, M. E.; Pitsch, H.

2010-11-01

A direct numerical simulation of soot formation in a turbulent nonpremixed flame has been performed to investigate unsteady hydrodynamic strain effects on soot growth processes and transport immediately following nucleation. For the first time in a DNS, polycyclic aromatic hydrocarbon (PAH) species are included in the chemical kinetics mechanism to describe soot inception. A novel statistical representation of soot aggregates based on the Hybrid Method of Moments (HMOM) is employed. In agreement with previous experimental studies in laminar flames, Damköhler number effects are significant, and soot nucleation and growth are locally inhibited by high scalar dissipation rate. Upon formation on the rich side of the flame, soot is displaced relative to curved mixture fraction iso-surfaces due to differential diffusion effects. Soot traveling towards the flame is oxidized, and aggregates displaced away from the flame grow by condensation of PAH species on the surface of soot aggregates. In contrast to previous DNS studies employing simplified models, we find that soot-flame interaction plays a limited role in soot growth. Nucleation and condensation processes occurring in the fuel stream are responsible for the greatest generation of soot mass.

Comparison of GEOS-5 AGCM planetary boundary layer depths computed with various definitions

NASA Astrophysics Data System (ADS)

McGrath-Spangler, E. L.; Molod, A.

2014-07-01

Accurate models of planetary boundary layer (PBL) processes are important for forecasting weather and climate. The present study compares seven methods of calculating PBL depth in the GEOS-5 atmospheric general circulation model (AGCM) over land. These methods depend on the eddy diffusion coefficients, bulk and local Richardson numbers, and the turbulent kinetic energy. The computed PBL depths are aggregated to the Köppen-Geiger climate classes, and some limited comparisons are made using radiosonde profiles. Most methods produce similar midday PBL depths, although in the warm, moist climate classes the bulk Richardson number method gives midday results that are lower than those given by the eddy diffusion coefficient methods. Additional analysis revealed that methods sensitive to turbulence driven by radiative cooling produce greater PBL depths, this effect being most significant during the evening transition. Nocturnal PBLs based on Richardson number methods are generally shallower than eddy diffusion coefficient based estimates. The bulk Richardson number estimate is recommended as the PBL height to inform the choice of the turbulent length scale, based on the similarity to other methods during the day, and the improved nighttime behavior.

Characterization of the motion of membrane proteins using high-speed atomic force microscopy

NASA Astrophysics Data System (ADS)

Casuso, Ignacio; Khao, Jonathan; Chami, Mohamed; Paul-Gilloteaux, Perrine; Husain, Mohamed; Duneau, Jean-Pierre; Stahlberg, Henning; Sturgis, James N.; Scheuring, Simon

2012-08-01

For cells to function properly, membrane proteins must be able to diffuse within biological membranes. The functions of these membrane proteins depend on their position and also on protein-protein and protein-lipid interactions. However, so far, it has not been possible to study simultaneously the structure and dynamics of biological membranes. Here, we show that the motion of unlabelled membrane proteins can be characterized using high-speed atomic force microscopy. We find that the molecules of outer membrane protein F (OmpF) are widely distributed in the membrane as a result of diffusion-limited aggregation, and while the overall protein motion scales roughly with the local density of proteins in the membrane, individual protein molecules can also diffuse freely or become trapped by protein-protein interactions. Using these measurements, and the results of molecular dynamics simulations, we determine an interaction potential map and an interaction pathway for a membrane protein, which should provide new insights into the connection between the structures of individual proteins and the structures and dynamics of supramolecular membranes.

Comparison of GEOS-5 AGCM Planetary Boundary Layer Depths Computed with Various Definitions

NASA Technical Reports Server (NTRS)

Mcgrath-Spangler, E. L.; Molod, A.

2014-01-01

Accurate models of planetary boundary layer (PBL) processes are important for forecasting weather and climate. The present study compares seven methods of calculating PBL depth in the GEOS-5 atmospheric general circulation model (AGCM) over land. These methods depend on the eddy diffusion coefficients, bulk and local Richardson numbers, and the turbulent kinetic energy. The computed PBL depths are aggregated to the Koppen climate classes, and some limited comparisons are made using radiosonde profiles. Most methods produce similar midday PBL depths, although in the warm, moist climate classes, the bulk Richardson number method gives midday results that are lower than those given by the eddy diffusion coefficient methods. Additional analysis revealed that methods sensitive to turbulence driven by radiative cooling produce greater PBL depths, this effect being most significant during the evening transition. Nocturnal PBLs based on Richardson number are generally shallower than eddy diffusion coefficient based estimates. The bulk Richardson number estimate is recommended as the PBL height to inform the choice of the turbulent length scale, based on the similarity to other methods during the day, and the improved nighttime behavior.

Comparison of GEOS-5 AGCM planetary boundary layer depths computed with various definitions

NASA Astrophysics Data System (ADS)

McGrath-Spangler, E. L.; Molod, A.

2014-03-01

Accurate models of planetary boundary layer (PBL) processes are important for forecasting weather and climate. The present study compares seven methods of calculating PBL depth in the GEOS-5 atmospheric general circulation model (AGCM) over land. These methods depend on the eddy diffusion coefficients, bulk and local Richardson numbers, and the turbulent kinetic energy. The computed PBL depths are aggregated to the Köppen climate classes, and some limited comparisons are made using radiosonde profiles. Most methods produce similar midday PBL depths, although in the warm, moist climate classes, the bulk Richardson number method gives midday results that are lower than those given by the eddy diffusion coefficient methods. Additional analysis revealed that methods sensitive to turbulence driven by radiative cooling produce greater PBL depths, this effect being most significant during the evening transition. Nocturnal PBLs based on Richardson number are generally shallower than eddy diffusion coefficient based estimates. The bulk Richardson number estimate is recommended as the PBL height to inform the choice of the turbulent length scale, based on the similarity to other methods during the day, and the improved nighttime behavior.

Nonmonotonic diffusion in crowded environments

PubMed Central

Putzel, Gregory Garbès; Tagliazucchi, Mario; Szleifer, Igal

2015-01-01

We study the diffusive motion of particles among fixed spherical crowders. The diffusers interact with the crowders through a combination of a hard-core repulsion and a short-range attraction. The long-time effective diffusion coefficient of the diffusers is found to depend non-monotonically on the strength of their attraction to the crowders. That is, for a given concentration of crowders, a weak attraction to the crowders enhances diffusion. We show that this counterintuitive fact can be understood in terms of the mesoscopic excess chemical potential landscape experienced by the diffuser. The roughness of this excess chemical potential landscape quantitatively captures the nonmonotonic dependence of the diffusion rate on the strength of crowder-diffuser attraction; thus it is a purely static predictor of dynamic behavior. The mesoscopic view given here provides a unified explanation for enhanced diffusion effects that have been found in various systems of technological and biological interest. PMID:25302920

Short-Path Statistics and the Diffusion Approximation

NASA Astrophysics Data System (ADS)

Blanco, Stéphane; Fournier, Richard

2006-12-01

In the field of first return time statistics in bounded domains, short paths may be defined as those paths for which the diffusion approximation is inappropriate. This is at the origin of numerous open questions concerning the characterization of residence time distributions. We show here how general integral constraints can be derived that make it possible to address short-path statistics indirectly by application of the diffusion approximation to long paths. Application to the moments of the distribution at the low-Knudsen limit leads to simple practical results and novel physical pictures.

Exact calculations of survival probability for diffusion on growing lines, disks, and spheres: The role of dimension.

PubMed

Simpson, Matthew J; Baker, Ruth E

2015-09-07

Unlike standard applications of transport theory, the transport of molecules and cells during embryonic development often takes place within growing multidimensional tissues. In this work, we consider a model of diffusion on uniformly growing lines, disks, and spheres. An exact solution of the partial differential equation governing the diffusion of a population of individuals on the growing domain is derived. Using this solution, we study the survival probability, S(t). For the standard non-growing case with an absorbing boundary, we observe that S(t) decays to zero in the long time limit. In contrast, when the domain grows linearly or exponentially with time, we show that S(t) decays to a constant, positive value, indicating that a proportion of the diffusing substance remains on the growing domain indefinitely. Comparing S(t) for diffusion on lines, disks, and spheres indicates that there are minimal differences in S(t) in the limit of zero growth and minimal differences in S(t) in the limit of fast growth. In contrast, for intermediate growth rates, we observe modest differences in S(t) between different geometries. These differences can be quantified by evaluating the exact expressions derived and presented here.

Influence of water-insoluble nonionic copolymer E(6)P(39)E(6) on the microstructure and self-aggregation dynamics of aqueous SDS solution-NMR and SANS investigations.

PubMed

Prameela, G K S; Phani Kumar, B V N; Aswal, V K; Mandal, Asit Baran

2013-10-28

The influence of water-insoluble nonionic triblock copolymer PEO-PPO-PEO [poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide)] i.e., E6P39E6 with molecular weight 2800, on the microstructure and self-aggregation dynamics of anionic surfactant sodium dodecylsulfate (SDS) in aqueous solution (D2O) were investigated using high resolution nuclear magnetic resonance (NMR) and small-angle neutron scattering (SANS) measurements. Variable concentration and temperature proton ((1)H), carbon ((13)C) NMR chemical shifts, (1)H self-diffusion coefficients, (1)H spin-lattice and spin-spin relaxation rates data indicate that the higher hydrophobic nature of copolymer significantly influenced aggregation characteristics of SDS. The salient features of the NMR investigations include (i) the onset of mixed micelles at lower SDS concentrations (<3 mM) relative to the copolymer-free case and their evolution into SDS free micelles at higher SDS concentrations (~30 mM), (ii) disintegration of copolymer-SDS mixed aggregate at moderate SDS concentrations (~10 mM) and still binding of a copolymer with SDS and (iii) preferential localization of the copolymer occurred at the SDS micelle surface. SANS investigations indicate prolate ellipsoidal shaped mixed aggregates with an increase in SDS aggregation number, while a contrasting behavior in the copolymer aggregation is observed. The aggregation features of SDS and the copolymer, the sizes of mixed aggregates and the degree of counterion dissociation (α) extracted from SANS data analysis corroborate reasonably well with those of (1)H NMR self-diffusion and sodium ((23)Na) spin-lattice relaxation data.

β-sheet propensity controls the kinetic pathways and morphologies of seeded peptide aggregation

NASA Astrophysics Data System (ADS)

Morriss-Andrews, Alex; Bellesia, Giovanni; Shea, Joan-Emma

2012-10-01

The effect of seeds in templating the morphology of peptide aggregates is examined using molecular dynamics simulations and a coarse-grained peptide representation. Varying the nature of the aggregate seed between β-sheet, amorphous, and β-barrel seeds leads to different aggregation pathways and to morphologically different aggregates. Similar effects are seen by varying the β-sheet propensity of the free peptides. For a fibrillar seed and free peptides of high β-sheet propensity, fibrillar growth occurred by means of direct attachment (without structural rearrangement) of free individual peptides and small ordered oligomers onto the seed. For a fibrillar seed and free peptides of low β-sheet propensity, fibrillar growth occurred through a dock-lock mechanism, in which the free peptides first docked onto the seed, and then locked on, extending and aligning to join the fibril. Amorphous seeds absorbed free peptides into themselves indiscriminately, with any fibrillar rearrangement subsequent to this absorption by means of a condensation-ordering transition. Although the mechanisms observed by varying peptide β-sheet propensity are diverse, the initial pathways can always be broken down into the following steps: (i) the free peptides diffuse in the bulk and attach individually to the seed; (ii) the free peptides diffuse and aggregate among themselves; (iii) the free peptide oligomers collide with the seed; and (iv) the free oligomers merge with the seed and rearrange in a manner dependent on the backbone flexibility of both the free and seed peptides. Our simulations indicate that it is possible to sequester peptides from amorphous aggregates into fibrils, and also that aggregate morphology (and thus cytoxicity) can be controlled by introducing seeds of aggregate-compatible peptides with differing β-sheet propensities into the system.

Flow and diffusion in channel-guided cell migration.

PubMed

Marel, Anna-Kristina; Zorn, Matthias; Klingner, Christoph; Wedlich-Söldner, Roland; Frey, Erwin; Rädler, Joachim O

2014-09-02

Collective migration of mechanically coupled cell layers is a notable feature of wound healing, embryonic development, and cancer progression. In confluent epithelial sheets, the dynamics have been found to be highly heterogeneous, exhibiting spontaneous formation of swirls, long-range correlations, and glass-like dynamic arrest as a function of cell density. In contrast, the flow-like properties of one-sided cell-sheet expansion in confining geometries are not well understood. Here, we studied the short- and long-term flow of Madin-Darby canine kidney (MDCK) cells as they moved through microchannels. Using single-cell tracking and particle image velocimetry (PIV), we found that a defined averaged stationary cell current emerged that exhibited a velocity gradient in the direction of migration and a plug-flow-like profile across the advancing sheet. The observed flow velocity can be decomposed into a constant term of directed cell migration and a diffusion-like contribution that increases with density gradient. The diffusive component is consistent with the cell-density profile and front propagation speed predicted by the Fisher-Kolmogorov equation. To connect diffusion-mediated transport to underlying cellular motility, we studied single-cell trajectories and occurrence of vorticity. We discovered that the directed large-scale cell flow altered fluctuations in cellular motion at short length scales: vorticity maps showed a reduced frequency of swirl formation in channel flow compared with resting sheets of equal cell density. Furthermore, under flow, single-cell trajectories showed persistent long-range, random-walk behavior superimposed on drift, whereas cells in resting tissue did not show significant displacements with respect to neighboring cells. Our work thus suggests that active cell migration manifests itself in an underlying, spatially uniform drift as well as in randomized bursts of short-range correlated motion that lead to a diffusion-mediated transport. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Anatomical accuracy of brain connections derived from diffusion MRI tractography is inherently limited.

PubMed

Thomas, Cibu; Ye, Frank Q; Irfanoglu, M Okan; Modi, Pooja; Saleem, Kadharbatcha S; Leopold, David A; Pierpaoli, Carlo

2014-11-18

Tractography based on diffusion-weighted MRI (DWI) is widely used for mapping the structural connections of the human brain. Its accuracy is known to be limited by technical factors affecting in vivo data acquisition, such as noise, artifacts, and data undersampling resulting from scan time constraints. It generally is assumed that improvements in data quality and implementation of sophisticated tractography methods will lead to increasingly accurate maps of human anatomical connections. However, assessing the anatomical accuracy of DWI tractography is difficult because of the lack of independent knowledge of the true anatomical connections in humans. Here we investigate the future prospects of DWI-based connectional imaging by applying advanced tractography methods to an ex vivo DWI dataset of the macaque brain. The results of different tractography methods were compared with maps of known axonal projections from previous tracer studies in the macaque. Despite the exceptional quality of the DWI data, none of the methods demonstrated high anatomical accuracy. The methods that showed the highest sensitivity showed the lowest specificity, and vice versa. Additionally, anatomical accuracy was highly dependent upon parameters of the tractography algorithm, with different optimal values for mapping different pathways. These results suggest that there is an inherent limitation in determining long-range anatomical projections based on voxel-averaged estimates of local fiber orientation obtained from DWI data that is unlikely to be overcome by improvements in data acquisition and analysis alone.

Theory and Experiment of Binary Diffusion Coefficient of n-Alkanes in Dilute Gases.

PubMed

Liu, Changran; McGivern, W Sean; Manion, Jeffrey A; Wang, Hai

2016-10-10

Binary diffusion coefficients were measured for n-pentane, n-hexane, and n-octane in helium and of n-pentane in nitrogen over the temperature range of 300 to 600 K, using reversed-flow gas chromatography. A generalized, analytical theory is proposed for the binary diffusion coefficients of long-chain molecules in simple diluent gases, taking advantage of a recently developed gas-kinetic theory of the transport properties of nanoslender bodies in dilute free-molecular flows. The theory addresses the long-standing question about the applicability of the Chapman-Enskog theory in describing the transport properties of nonspherical molecular structures, or equivalently, the use of isotropic potentials of interaction for a roughly cylindrical molecular structure such as large normal alkanes. An approximate potential energy function is proposed for the intermolecular interaction of long-chain n-alkane with typical bath gases. Using this potential and the analytical theory for nanoslender bodies, we show that the diffusion coefficients of n-alkanes in typical bath gases can be treated by the resulting analytical model accurately, especially for compounds larger than n-butane.

MD simulations of the formation of stable clusters in mixtures of alkaline salts and imidazolium-based ionic liquids.

PubMed

Méndez-Morales, Trinidad; Carrete, Jesús; Bouzón-Capelo, Silvia; Pérez-Rodríguez, Martín; Cabeza, Óscar; Gallego, Luis J; Varela, Luis M

2013-03-21

Structural and dynamical properties of room-temperature ionic liquids containing the cation 1-butyl-3-methylimidazolium ([BMIM](+)) and three different anions (hexafluorophosphate, [PF6](-), tetrafluoroborate, [BF4](-), and bis(trifluoromethylsulfonyl)imide, [NTf2](-)) doped with several molar fractions of lithium salts with a common anion at 298.15 K and 1 atm were investigated by means of molecular dynamics simulations. The effect of the size of the salt cation was also analyzed by comparing these results with those for mixtures of [BMIM][PF6] with NaPF6. Lithium/sodium solvation and ionic mobilities were analyzed via the study of radial distribution functions, coordination numbers, cage autocorrelation functions, mean-square displacements (including the analysis of both ballistic and diffusive regimes), self-diffusion coefficients of all the ionic species, velocity and current autocorrelation functions, and ionic conductivity in all the ionic liquid/salt systems. We found that lithium and sodium cations are strongly coordinated in two different positions with the anion present in the mixture. Moreover, [Li](+) and [Na](+) cations were found to form bonded-like, long-lived aggregates with the anions in their first solvation shell, which act as very stable kinetic entities within which a marked rattling motion of salt ions takes place. With very long MD simulation runs, this phenomenon is proved to be on the basis of the decrease of self-diffusion coefficients and ionic conductivities previously reported in experimental and computational results.

Alpha-helix to beta-sheet transition in long-chain poly-l-lysine: Formation of alpha-helical fibrils by poly-l-lysine.

PubMed

Cieślik-Boczula, Katarzyna

2017-06-01

The temperature-induced α-helix to β-sheet transition in long-chain poly-l-lysine (PLL), accompanied by the gauche-to-trans isomerization of CH 2 groups in the hydrocarbon side chains of Lys amino acid residues, and formation of β-sheet as well as α-helix fibrillar aggregates of PLL have been studied using Fourier-transform infrared (FT-IR) and vibrational circular dichroism (VCD) spectroscopy, and transmission electron microscopy (TEM). In a low-temperature alkaline water solution or in a methanol-rich water mixture, the secondary structure of PLL is represented by α-helical conformations with unordered and gauche-rich hydrocarbon side chains. Under these conditions, PLL molecules aggregate into α-helical fibrils. PLLs dominated by extended antiparallel β-sheet structures with highly ordered trans-rich hydrocarbon side chains are formed in a high-temperature range at alkaline pD and aggregate into fibrillar, protofibrillar, and spherical forms. Presented data support the idea that fibrillar aggregation is a varied phenomenon possible in repetitive structural elements with not only a β-sheet-rich conformation, but also an α-helical-rich conformation. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Diffusion-controlled formation and collapse of a d-dimensional A-particle island in the B-particle sea.

PubMed

Shipilevsky, Boris M

2017-06-01

We consider diffusion-controlled evolution of a d-dimensional A-particle island in the B-particle sea at propagation of the sharp reaction front A+B→0 at equal species diffusivities. The A-particle island is formed by a localized (point) A-source with a strength λ that acts for a finite time T. We reveal the conditions under which the island collapse time t_{c} becomes much longer than the injection period T (long-living island) and demonstrate that regardless of d the evolution of the long-living island radius r_{f}(t) is described by the universal law ζ_{f}=r_{f}/r_{f}^{M}=sqrt[eτ|lnτ|], where τ=t/t_{c} and r_{f}^{M} is the maximal island expansion radius at the front turning point t_{M}=t_{c}/e. We find that in the long-living island regime the ratio t_{c}/T changes with the increase of the injection period T by the law ∝(λ^{2}T^{2-d})^{1/d}, i.e., increases with the increase of T in the one-dimensional (1D) case, does not change with the increase of T in the 2D case and decreases with the increase of T in the 3D case. We derive the scaling laws for particles death in the long-living island and determine the limits of their applicability. We demonstrate also that these laws describe asymptotically the evolution of the d-dimensional spherical island with a uniform initial particle distribution generalizing the results obtained earlier for the quasi-one-dimensional geometry. As striking results, we present a systematic analysis of the front relative width evolution for fluctuation, logarithmically modified, and mean-field regimes, and we demonstrate that in a wide range of parameters the front remains sharp up to a narrow vicinity of the collapse point.

SeaWiFS long-term solar diffuser reflectance trend analysis

NASA Astrophysics Data System (ADS)

Eplee, Robert E., Jr.; Patt, Frederick S.; Barnes, Robert A.; McClain, Charles R.

2006-08-01

The NASA Ocean Biology Processing Group's Calibration and Validation (Cal/Val) Team implemented daily solar calibrations of SeaWiFS to look for step-function changes in the instrument response and has used these calibrations to supplement the monthly lunar calibrations in monitoring the radiometric stability of SeaWiFS during its first year of on-orbit operations. The Team has undertaken an analysis of the mission-long solar calibration time series, with the lunar-derived radiometric corrections over time applied, to assess the long-term degradation of the solar diffuser reflectance over nine years on orbit. The SeaWiFS diffuser is an aluminum plate coated with YB71 paint. The bidirectional reflectance distribution function of the diffuser was not fully characterized before launch, so the Cal/Val Team has implemented a regression of the solar incidence angles and the drift in the node of the satellite's orbit against the diffuser time series to correct for solar incidence angle effects. An exponential function with a time constant of 200 days yields the best fit to the diffuser time series. The decrease in diffuser reflectance over the mission is wavelength-dependent, ranging from 9% in the blue (412 nm) to 5% in the red and near infrared (670-865 nm). The degradation of diffuser reflctance is similar to that observed for SeaWiFS radiometric response itself from lunar calibration time series for bands 1-5 (412-555 nm), though the magnitude of the change is four times larger for the diffuser. Evidently, the same optical degradation process has affected both the telescope optics and the solar diffuser in the blue and green. The Cal/Val Team has developed a methodology for computing the signal-to-noise ratio (SNR) for SeaWiFS on orbit from the diffuser time series. The on-orbit change in the SNR for each band over the nine-year mission is less than 7%. The on-orbit performance of the SeaWiFS solar diffuser should offer insight into the long-term on-orbit performance of solar diffusers on other instruments, such as MODIS, VIIRS, and ABI.

Charge collection and pore filling in solid-state dye-sensitized solar cells.

PubMed

Snaith, Henry J; Humphry-Baker, Robin; Chen, Peter; Cesar, Ilkay; Zakeeruddin, Shaik M; Grätzel, Michael

2008-10-22

The solar to electrical power conversion efficiency for dye-sensitized solar cells (DSCs) incorporating a solid-state organic hole-transporter can be over 5%. However, this is for devices significantly thinner than the optical depth of the active composites and by comparison to the liquid electrolyte based DSCs, which exhibit efficiencies in excess of 10%, more than doubling of this efficiency is clearly attainable if all the steps in the photovoltaic process can be optimized. Two issues are currently being addressed by the field. The first aims at enhancing the electron diffusion length by either reducing the charge recombination or enhancing the charge transport rates. This should enable a larger fraction of photogenerated charges to be collected. The second, though less actively investigated, aims to improve the physical composite formation, which in this instance is the infiltration of mesoporous TiO(2) with the organic hole-transporter 2,2',7,7'-tetrakis(N,N-di-p-methoxypheny-amine)-9,9'-spirobifluorene (spiro-MeOTAD). Here, we perform a broad experimental study to elucidate the limiting factors to the solar cell performance. We first investigate the charge transport and recombination in the solid-state dye-sensitized solar cell under realistic working conditions via small perturbation photovoltage and photocurrent decay measurements. From these measurements we deduce that the electron diffusion length near short-circuit is as long as 20 µm. However, at applied biases approaching open-circuit potential under realistic solar conditions, the diffusion length becomes comparable with the film thickness, ∼2 µm, illustrating that real losses to open-circuit voltage, fill factor and hence efficiency are occurring due to ineffective charge collection. The long diffusion length near short-circuit, on the other hand, illustrates that another process, separate from ineffective charge collection, is rendering the solar cell less than ideal. We investigate the process of TiO(2) mesopore infiltration with spiro-MeOTAD by examining the cross-sectional images of and performing photo-induced absorption spectroscopy on devices with a range of thickness, infiltrated with spiro-MeOTAD with a range of concentrations. We present our interpretation of the mechanism for material infiltration, and by improving the casting conditions demonstrate efficient charge collection through devices of over 7 µm in thickness. This investigation represents an improvement in our understanding of the limiting factors to the dye-sensitized solar cell. However, much work, focused on composite formation and improved kinetic competition, is required to realize the true potential of this concept.

Anomalous versus Slowed-Down Brownian Diffusion in the Ligand-Binding Equilibrium

PubMed Central

Soula, Hédi; Caré, Bertrand; Beslon, Guillaume; Berry, Hugues

2013-01-01

Measurements of protein motion in living cells and membranes consistently report transient anomalous diffusion (subdiffusion) that converges back to a Brownian motion with reduced diffusion coefficient at long times after the anomalous diffusion regime. Therefore, slowed-down Brownian motion could be considered the macroscopic limit of transient anomalous diffusion. On the other hand, membranes are also heterogeneous media in which Brownian motion may be locally slowed down due to variations in lipid composition. Here, we investigate whether both situations lead to a similar behavior for the reversible ligand-binding reaction in two dimensions. We compare the (long-time) equilibrium properties obtained with transient anomalous diffusion due to obstacle hindrance or power-law-distributed residence times (continuous-time random walks) to those obtained with space-dependent slowed-down Brownian motion. Using theoretical arguments and Monte Carlo simulations, we show that these three scenarios have distinctive effects on the apparent affinity of the reaction. Whereas continuous-time random walks decrease the apparent affinity of the reaction, locally slowed-down Brownian motion and local hindrance by obstacles both improve it. However, only in the case of slowed-down Brownian motion is the affinity maximal when the slowdown is restricted to a subregion of the available space. Hence, even at long times (equilibrium), these processes are different and exhibit irreconcilable behaviors when the area fraction of reduced mobility changes. PMID:24209851

Present and future CCDs for UV and X-ray scientific measurements

NASA Technical Reports Server (NTRS)

Janesick, J. R.; Elliott, S. T.; Mccarthy, J. K.; Marsh, H. H.; Collins, S. A.; Blouke, M. M.

1985-01-01

Interacting quantum efficiencies in excess of 50 percent have been demonstrated with CCDs throughout the spectral range 600-9,00 A, and comparable sensitivity is expected to continue to wavelengths as short as a few Angstroms. Nondispersive X-ray spectra throughout the 250-8000 V range have been obtained with an FWHM spectral resolution of 200-250 eV. At present, however, both spectral and spatial resolution is limited at some energies by the diffusion of photogenerated charge into more than one picture element. Progress in reducing charge diffusion is reported, with particular attention given to a theoretical diffusion model and its implications for further improvement.

Liquid Chromatography Applications to Determination of Sorption on Aquifer Materials

DTIC Science & Technology

1989-11-01

and D. R. Nielsen. Modeling tritium and chloride 36 transport through an aggregated oxisol . Water Resources Res. 19 691-700 (1983). P. Nkedi-Kizza, J. W...describing ion exchange during transport through an aggregated oxisol . Water Resources Res. 20 1123-1130 (1984). P. Nkedi-Kizza, P. S. C. Rao, R. E. Jessup...and J. M. Davidson. Ion exchange and diffusive mass transfer during miscible displacement through an aggregated oxisol . Soil Sci. Soc. Am. J. 46 471

Role of short-range correlation in facilitation of wave propagation in a long-range ladder chain

NASA Astrophysics Data System (ADS)

Farzadian, O.; Niry, M. D.

2018-09-01

We extend a new method for generating a random chain, which has a kind of short-range correlation induced by a repeated sequence while retaining long-range correlation. Three distinct methods are considered to study the localization-delocalization transition of mechanical waves in one-dimensional disordered media with simultaneous existence of short and long-range correlation. First, a transfer-matrix method was used to calculate numerically the localization length of a wave in a binary chain. We found that the existence of short-range correlation in a long-range correlated chain can increase the localization length at the resonance frequency Ωc. Then, we carried out an analytical study of the delocalization properties of the waves in correlated disordered media around Ωc. Finally, we apply a dynamical method based on the direct numerical simulation of the wave equation to study the propagation of waves in the correlated chain. Imposing short-range correlation on the long-range background will lead the propagation to super-diffusive transport. The results obtained with all three methods are in agreement with each other.

Latent heat induced rotation limited aggregation in 2D ice nanocrystals.

PubMed

Bampoulis, Pantelis; Siekman, Martin H; Kooij, E Stefan; Lohse, Detlef; Zandvliet, Harold J W; Poelsema, Bene

2015-07-21

The basic science responsible for the fascinating shapes of ice crystals and snowflakes is still not understood. Insufficient knowledge of the interaction potentials and the lack of relevant experimental access to the growth process are to blame for this failure. Here, we study the growth of fractal nanostructures in a two-dimensional (2D) system, intercalated between mica and graphene. Based on our scanning tunneling spectroscopy data, we provide compelling evidence that these fractals are 2D ice. They grow while they are in material contact with the atmosphere at 20 °C and without significant thermal contact to the ambient. The growth is studied in situ, in real time and space at the nanoscale. We find that the growing 2D ice nanocrystals assume a fractal shape, which is conventionally attributed to Diffusion Limited Aggregation (DLA). However, DLA requires a low mass density mother phase, in contrast to the actual currently present high mass density mother phase. Latent heat effects and consequent transport of heat and molecules are found to be key ingredients for understanding the evolution of the snow (ice) flakes. We conclude that not the local availability of water molecules (DLA), but rather them having the locally required orientation is the key factor for incorporation into the 2D ice nanocrystal. In combination with the transport of latent heat, we attribute the evolution of fractal 2D ice nanocrystals to local temperature dependent rotation limited aggregation. The ice growth occurs under extreme supersaturation, i.e., the conditions closely resemble the natural ones for the growth of complex 2D snow (ice) flakes and we consider our findings crucial for solving the "perennial" snow (ice) flake enigma.

Latent heat induced rotation limited aggregation in 2D ice nanocrystals

NASA Astrophysics Data System (ADS)

Bampoulis, Pantelis; Siekman, Martin H.; Kooij, E. Stefan; Lohse, Detlef; Zandvliet, Harold J. W.; Poelsema, Bene

2015-07-01

The basic science responsible for the fascinating shapes of ice crystals and snowflakes is still not understood. Insufficient knowledge of the interaction potentials and the lack of relevant experimental access to the growth process are to blame for this failure. Here, we study the growth of fractal nanostructures in a two-dimensional (2D) system, intercalated between mica and graphene. Based on our scanning tunneling spectroscopy data, we provide compelling evidence that these fractals are 2D ice. They grow while they are in material contact with the atmosphere at 20 °C and without significant thermal contact to the ambient. The growth is studied in situ, in real time and space at the nanoscale. We find that the growing 2D ice nanocrystals assume a fractal shape, which is conventionally attributed to Diffusion Limited Aggregation (DLA). However, DLA requires a low mass density mother phase, in contrast to the actual currently present high mass density mother phase. Latent heat effects and consequent transport of heat and molecules are found to be key ingredients for understanding the evolution of the snow (ice) flakes. We conclude that not the local availability of water molecules (DLA), but rather them having the locally required orientation is the key factor for incorporation into the 2D ice nanocrystal. In combination with the transport of latent heat, we attribute the evolution of fractal 2D ice nanocrystals to local temperature dependent rotation limited aggregation. The ice growth occurs under extreme supersaturation, i.e., the conditions closely resemble the natural ones for the growth of complex 2D snow (ice) flakes and we consider our findings crucial for solving the "perennial" snow (ice) flake enigma.

Passive phloem loading and long-distance transport in a synthetic tree-on-a-chip.

PubMed

Comtet, Jean; Jensen, Kaare H; Turgeon, Robert; Stroock, Abraham D; Hosoi, A E

2017-03-20

Vascular plants rely on differences in osmotic pressure to export sugars from regions of synthesis (mature leaves) to sugar sinks (roots, fruits). In this process, known as Münch pressure flow, the loading of sugars from photosynthetic cells to the export conduit (the phloem) is crucial, as it sets the pressure head necessary to power long-distance transport. Whereas most herbaceous plants use active mechanisms to increase phloem sugar concentration above that of the photosynthetic cells, in most tree species, for which transport distances are largest, loading seems, counterintuitively, to occur by means of passive symplastic diffusion from the mesophyll to the phloem. Here, we use a synthetic microfluidic model of a passive loader to explore the non-linear dynamics that arise during export and determine the ability of passive loading to drive long-distance transport. We first demonstrate that in our device, the phloem concentration is set by the balance between the resistances to diffusive loading from the source and convective export through the phloem. Convection-limited export corresponds to classical models of Münch transport, where the phloem concentration is close to that of the source; in contrast, diffusion-limited export leads to small phloem concentrations and weak scaling of flow rates with hydraulic resistance. We then show that the effective regime of convection-limited export is predominant in plants with large transport resistances and low xylem pressures. Moreover, hydrostatic pressures developed in our synthetic passive loader can reach botanically relevant values as high as 10 bars. We conclude that passive loading is sufficient to drive long-distance transport in large plants, and that trees are well suited to take full advantage of passive phloem loading strategies.

Time-dependent diffusion MRI in cancer: tissue modeling and applications

NASA Astrophysics Data System (ADS)

Reynaud, Olivier

2017-11-01

In diffusion weighted imaging (DWI), the apparent diffusion coefficient has been recognized as a useful and sensitive surrogate for cell density, paving the way for non-invasive tumor staging, and characterization of treatment efficacy in cancer. However, microstructural parameters, such as cell size, density and/or compartmental diffusivities affect diffusion in various fashions, making of conventional DWI a sensitive but non-specific probe into changes happening at cellular level. Alternatively, tissue complexity can be probed and quantified using the time dependence of diffusion metrics, sometimes also referred to as temporal diffusion spectroscopy when only using oscillating diffusion gradients. Time-dependent diffusion (TDD) is emerging as a strong candidate for specific and non-invasive tumor characterization. Despite the lack of a general analytical solution for all diffusion times / frequencies, TDD can be probed in various regimes where systems simplify in order to extract relevant information about tissue microstructure. The fundamentals of TDD are first reviewed (a) in the short time regime, disentangling structural and diffusive tissue properties, and (b) near the tortuosity limit, assuming weakly heterogeneous media near infinitely long diffusion times. Focusing on cell bodies (as opposed to neuronal tracts), a simple but realistic model for intracellular diffusion can offer precious insight on diffusion inside biological systems, at all times. Based on this approach, the main three geometrical models implemented so far (IMPULSED, POMACE, VERDICT) are reviewed. Their suitability to quantify cell size, intra- and extracellular spaces (ICS and ECS) and diffusivities are assessed. The proper modeling of tissue membrane permeability – hardly a newcomer in the field, but lacking applications - and its impact on microstructural estimates are also considered. After discussing general issues with tissue modeling and microstructural parameter estimation (i.e. fitting), potential solutions are detailed. The in vivo applications of this new, non-invasive, specific approach in cancer are reviewed, ranging from the characterization of gliomas in rodent brains and observation of time-dependence in breast tissue lesions and prostate cancer, to the recent preclinical evaluation of new treatments efficacy. It is expected that clinical applications of TDD will strongly benefit the community in terms of non-invasive cancer screening.

Mean first-passage times of non-Markovian random walkers in confinement.

PubMed

Guérin, T; Levernier, N; Bénichou, O; Voituriez, R

2016-06-16

The first-passage time, defined as the time a random walker takes to reach a target point in a confining domain, is a key quantity in the theory of stochastic processes. Its importance comes from its crucial role in quantifying the efficiency of processes as varied as diffusion-limited reactions, target search processes or the spread of diseases. Most methods of determining the properties of first-passage time in confined domains have been limited to Markovian (memoryless) processes. However, as soon as the random walker interacts with its environment, memory effects cannot be neglected: that is, the future motion of the random walker does not depend only on its current position, but also on its past trajectory. Examples of non-Markovian dynamics include single-file diffusion in narrow channels, or the motion of a tracer particle either attached to a polymeric chain or diffusing in simple or complex fluids such as nematics, dense soft colloids or viscoelastic solutions. Here we introduce an analytical approach to calculate, in the limit of a large confining volume, the mean first-passage time of a Gaussian non-Markovian random walker to a target. The non-Markovian features of the dynamics are encompassed by determining the statistical properties of the fictitious trajectory that the random walker would follow after the first-passage event takes place, which are shown to govern the first-passage time kinetics. This analysis is applicable to a broad range of stochastic processes, which may be correlated at long times. Our theoretical predictions are confirmed by numerical simulations for several examples of non-Markovian processes, including the case of fractional Brownian motion in one and higher dimensions. These results reveal, on the basis of Gaussian processes, the importance of memory effects in first-passage statistics of non-Markovian random walkers in confinement.

Mean first-passage times of non-Markovian random walkers in confinement

NASA Astrophysics Data System (ADS)

Guérin, T.; Levernier, N.; Bénichou, O.; Voituriez, R.

2016-06-01

The first-passage time, defined as the time a random walker takes to reach a target point in a confining domain, is a key quantity in the theory of stochastic processes. Its importance comes from its crucial role in quantifying the efficiency of processes as varied as diffusion-limited reactions, target search processes or the spread of diseases. Most methods of determining the properties of first-passage time in confined domains have been limited to Markovian (memoryless) processes. However, as soon as the random walker interacts with its environment, memory effects cannot be neglected: that is, the future motion of the random walker does not depend only on its current position, but also on its past trajectory. Examples of non-Markovian dynamics include single-file diffusion in narrow channels, or the motion of a tracer particle either attached to a polymeric chain or diffusing in simple or complex fluids such as nematics, dense soft colloids or viscoelastic solutions. Here we introduce an analytical approach to calculate, in the limit of a large confining volume, the mean first-passage time of a Gaussian non-Markovian random walker to a target. The non-Markovian features of the dynamics are encompassed by determining the statistical properties of the fictitious trajectory that the random walker would follow after the first-passage event takes place, which are shown to govern the first-passage time kinetics. This analysis is applicable to a broad range of stochastic processes, which may be correlated at long times. Our theoretical predictions are confirmed by numerical simulations for several examples of non-Markovian processes, including the case of fractional Brownian motion in one and higher dimensions. These results reveal, on the basis of Gaussian processes, the importance of memory effects in first-passage statistics of non-Markovian random walkers in confinement.

Turbulent eddy diffusion models in exposure assessment - Determination of the eddy diffusion coefficient.

PubMed

Shao, Yuan; Ramachandran, Sandhya; Arnold, Susan; Ramachandran, Gurumurthy

2017-03-01

The use of the turbulent eddy diffusion model and its variants in exposure assessment is limited due to the lack of knowledge regarding the isotropic eddy diffusion coefficient, D T . But some studies have suggested a possible relationship between D T and the air changes per hour (ACH) through a room. The main goal of this study was to accurately estimate D T for a range of ACH values by minimizing the difference between the concentrations measured and predicted by eddy diffusion model. We constructed an experimental chamber with a spatial concentration gradient away from the contaminant source, and conducted 27 3-hr long experiments using toluene and acetone under different air flow conditions (0.43-2.89 ACHs). An eddy diffusion model accounting for chamber boundary, general ventilation, and advection was developed. A mathematical expression for the slope based on the geometrical parameters of the ventilation system was also derived. There is a strong linear relationship between D T and ACH, providing a surrogate parameter for estimating D T in real-life settings. For the first time, a mathematical expression for the relationship between D T and ACH has been derived that also corrects for non-ideal conditions, and the calculated value of the slope between these two parameters is very close to the experimentally determined value. The values of D T obtained from the experiments are generally consistent with values reported in the literature. They are also independent of averaging time of measurements, allowing for comparison of values obtained from different measurement settings. These findings make the use of turbulent eddy diffusion models for exposure assessment in workplace/indoor environments more practical.

Edible oil structures at low and intermediate concentrations. I. Modeling, computer simulation, and predictions for X ray scattering

NASA Astrophysics Data System (ADS)

Pink, David A.; Quinn, Bonnie; Peyronel, Fernanda; Marangoni, Alejandro G.

2013-12-01

Triacylglycerols (TAGs) are biologically important molecules which form the recently discovered highly anisotropic crystalline nanoplatelets (CNPs) and, ultimately, the large-scale fat crystal networks in edible oils. Identifying the hierarchies of these networks and how they spontaneously self-assemble is important to understanding their functionality and oil binding capacity. We have modelled CNPs and studied how they aggregate under the assumption that all CNPs are present before aggregation begins and that their solubility in the liquid oil is very low. We represented CNPs as rigid planar arrays of spheres with diameter ≈50 nm and defined the interaction between spheres in terms of a Hamaker coefficient, A, and a binding energy, VB. We studied three cases: weak binding, |VB|/kBT ≪ 1, physically realistic binding, VB = Vd(R, Δ), so that |VB|/kBT ≈ 1, and Strong binding with |VB|/kBT ≫ 1. We divided the concentration of CNPs, ϕ, with 0≤ϕ= 10-2 (solid fat content) ≤1, into two regions: Low and intermediate concentrations with 0<ϕ<0.25 and high concentrations with 0.25 < ϕ and considered only the first case. We employed Monte Carlo computer simulation to model CNP aggregation and analyzed them using static structure functions, S(q). We found that strong binding cases formed aggregates with fractal dimension, D, 1.7≤D ≤1.8, in accord with diffusion limited cluster-cluster aggregation (DLCA) and weak binding formed aggregates with D =3, indicating a random distribution of CNPs. We found that models with physically realistic intermediate binding energies formed linear multilayer stacks of CNPs (TAGwoods) with fractal dimension D =1 for ϕ =0.06,0.13, and 0.22. TAGwood lengths were greater at lower ϕ than at higher ϕ, where some of the aggregates appeared as thick CNPs. We increased the spatial scale and modelled the TAGwoods as rigid linear arrays of spheres of diameter ≈500 nm, interacting via the attractive van der Waals interaction. We found that TAGwoods aggregated via DLCA into clusters with fractal dimension D =1.7-1.8. As the simulations were run further, TAGwoods relaxed their positions in order to maximize the attractive interaction making the process look like reaction limited cluster-cluster aggregation with the fractal dimension increasing to D =2.0-2.1. For higher concentrations of CNPs, many TAGwood clusters were formed and, because of their weak interactions, were distributed randomly with D =3.0. We summarize the hierarchy of structures and make predictions for X-ray scattering.

Microscopic origin and macroscopic implications of lane formation in mixtures of oppositely driven particles

NASA Astrophysics Data System (ADS)

Klymko, Katherine; Geissler, Phillip L.; Whitelam, Stephen

2016-08-01

Colloidal particles of two types, driven in opposite directions, can segregate into lanes [Vissers et al., Soft Matter 7, 2352 (2011), 10.1039/c0sm01343a]. This phenomenon can be reproduced by two-dimensional Brownian dynamics simulations of model particles [Dzubiella et al., Phys. Rev. E 65, 021402 (2002), 10.1103/PhysRevE.65.021402]. Here we use computer simulation to assess the generality of lane formation with respect to variation of particle type and dynamical protocol. We find that laning results from rectification of diffusion on the scale of a particle diameter: oppositely driven particles must, in the time taken to encounter each other in the direction of the drive, diffuse in the perpendicular direction by about one particle diameter. This geometric constraint implies that the diffusion constant of a particle, in the presence of those of the opposite type, grows approximately linearly with the Péclet number, a prediction confirmed by our numerics over a range of model parameters. Such environment-dependent diffusion is statistically similar to an effective interparticle attraction; consistent with this observation, we find that oppositely driven nonattractive colloids display features characteristic of the simplest model system possessing both interparticle attractions and persistent motion, the driven Ising lattice gas [Katz, Leibowitz, and Spohn, J. Stat. Phys. 34, 497 (1984), 10.1007/BF01018556]. These features include long-ranged correlations in the disordered regime, a critical regime characterized by a change in slope of the particle current with the Péclet number, and fluctuations that grow with system size. By analogy, we suggest that lane formation in the driven colloid system is a phase transition in the macroscopic limit, but that macroscopic phase separation would not occur in finite time upon starting from disordered initial conditions.

A Study to Analyze the Permeation of High Density Gases and Propellant Vapors Through Single Layer Teflon or Teflon Structure Materials and Laminations. Volume 1

NASA Technical Reports Server (NTRS)

Johnson, R. L.; Young, Donald L. (Technical Monitor)

1967-01-01

This report contains the results of a fifteen month analytical and experimental study of the leakage rate of the pressurant gases (N2, He) and the propellant vapors (N2O4,N2H4) through bladder structures consisting of two layers of Teflon separated by a metallic foil diffusion barrier containing microscopic or larger holes. Results were obtained for the steady state leakage rate through circular holes and long rectangular openings in the barrier for arbitrary thicknesses of the two Teflon layers. The effect of hole shape and relative hole position on the leakage rate were studied. The transient problem was analyzed and it was shown that steady state calculations are adequate for estimating the leakage rate. A computer program entitled "Diffusion Analyzer Program" was developed to calculate the leakage rate, both transient and steady state. Finally, the analytical results were compared to experimentally determined values of the leakage rate through a model laminated bladder structure. The results of the analysis are in good agreement with experiment. The experimental effort (Part II of the Bladder Permeation Program) measured the solubility, diffusion coefficient and permeability of helium, nitrogen and nitrogen tetroxide vapor through Teflon TFE and FEP membranes. Data were obtained in the temperature range of 25 to 100 C at pressures ranging from near vacuum to about 20 atmospheres. Results of the experimental effort were compared with the limited data previously reported. As a verification to the applicability of results to actual bladder systems, counter diffusion tests were performed with a laminated sample containing aluminum foil with a selected group of holes.

Neuroimaging in Pediatric Traumatic Brain Injury: Current and Future Predictors of Functional Outcome

ERIC Educational Resources Information Center

Suskauer, Stacy J.; Huisman, Thierry A. G. M.

2009-01-01

Although neuroimaging has long played a role in the acute management of pediatric traumatic brain injury (TBI), until recently, its use as a tool for understanding and predicting long-term brain-behavior relationships after TBI has been limited by the relatively poor sensitivity of routine clinical imaging for detecting diffuse axonal injury…

Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape

PubMed Central

Yu, Hao; Dee, Derek R.; Liu, Xia; Brigley, Angela M.; Sosova, Iveta; Woodside, Michael T.

2015-01-01

The timescale for the microscopic dynamics of proteins during conformational transitions is set by the intrachain diffusion coefficient, D. Despite the central role of protein misfolding and aggregation in many diseases, it has proven challenging to measure D for these processes because of their heterogeneity. We used single-molecule force spectroscopy to overcome these challenges and determine D for misfolding of the prion protein PrP. Observing directly the misfolding of individual dimers into minimal aggregates, we reconstructed the energy landscape governing nonnative structure formation. Remarkably, rather than displaying multiple pathways, as typically expected for aggregation, PrP dimers were funneled into a thermodynamically stable misfolded state along a single pathway containing several intermediates, one of which blocked native folding. Using Kramers’ rate theory, D was found to be 1,000-fold slower for misfolding than for native folding, reflecting local roughening of the misfolding landscape, likely due to increased internal friction. The slow diffusion also led to much longer transit times for barrier crossing, allowing transition paths to be observed directly for the first time to our knowledge. These results open a new window onto the microscopic mechanisms governing protein misfolding. PMID:26109573

Applying Nanoscale Kirkendall Diffusion for Template-Free, Kilogram-Scale Production of SnO2 Hollow Nanospheres via Spray Drying System

PubMed Central

Cho, Jung Sang; Ju, Hyeon Seok; Kang, Yun Chan

2016-01-01

A commercially applicable and simple process for the preparation of aggregation-free metal oxide hollow nanospheres is developed by applying nanoscale Kirkendall diffusion to a large-scale spray drying process. The precursor powders prepared by spray drying are transformed into homogeneous metal oxide hollow nanospheres through a simple post-treatment process. Aggregation-free SnO2 hollow nanospheres are selected as the first target material for lithium ion storage applications. Amorphous carbon microspheres with uniformly dispersed Sn metal nanopowder are prepared in the first step of the post-treatment process under a reducing atmosphere. The post-treatment of the Sn-C composite powder at 500 °C under an air atmosphere produces carbon- and aggregation-free SnO2 hollow nanospheres through nanoscale Kirkendall diffusion. The hollow and filled SnO2 nanopowders exhibit different cycling performances, with their discharge capacities after 300 cycles being 643 and 280 mA h g−1, respectively, at a current density of 2 A g−1. The SnO2 hollow nanospheres with high structural stability exhibit superior cycling and rate performances for lithium ion storage compared to the filled ones. PMID:27033088

Applying Nanoscale Kirkendall Diffusion for Template-Free, Kilogram-Scale Production of SnO2 Hollow Nanospheres via Spray Drying System

NASA Astrophysics Data System (ADS)

Cho, Jung Sang; Ju, Hyeon Seok; Kang, Yun Chan

2016-04-01

A commercially applicable and simple process for the preparation of aggregation-free metal oxide hollow nanospheres is developed by applying nanoscale Kirkendall diffusion to a large-scale spray drying process. The precursor powders prepared by spray drying are transformed into homogeneous metal oxide hollow nanospheres through a simple post-treatment process. Aggregation-free SnO2 hollow nanospheres are selected as the first target material for lithium ion storage applications. Amorphous carbon microspheres with uniformly dispersed Sn metal nanopowder are prepared in the first step of the post-treatment process under a reducing atmosphere. The post-treatment of the Sn-C composite powder at 500 °C under an air atmosphere produces carbon- and aggregation-free SnO2 hollow nanospheres through nanoscale Kirkendall diffusion. The hollow and filled SnO2 nanopowders exhibit different cycling performances, with their discharge capacities after 300 cycles being 643 and 280 mA h g-1, respectively, at a current density of 2 A g-1. The SnO2 hollow nanospheres with high structural stability exhibit superior cycling and rate performances for lithium ion storage compared to the filled ones.

Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape.

PubMed

Yu, Hao; Dee, Derek R; Liu, Xia; Brigley, Angela M; Sosova, Iveta; Woodside, Michael T

2015-07-07

The timescale for the microscopic dynamics of proteins during conformational transitions is set by the intrachain diffusion coefficient, D. Despite the central role of protein misfolding and aggregation in many diseases, it has proven challenging to measure D for these processes because of their heterogeneity. We used single-molecule force spectroscopy to overcome these challenges and determine D for misfolding of the prion protein PrP. Observing directly the misfolding of individual dimers into minimal aggregates, we reconstructed the energy landscape governing nonnative structure formation. Remarkably, rather than displaying multiple pathways, as typically expected for aggregation, PrP dimers were funneled into a thermodynamically stable misfolded state along a single pathway containing several intermediates, one of which blocked native folding. Using Kramers' rate theory, D was found to be 1,000-fold slower for misfolding than for native folding, reflecting local roughening of the misfolding landscape, likely due to increased internal friction. The slow diffusion also led to much longer transit times for barrier crossing, allowing transition paths to be observed directly for the first time to our knowledge. These results open a new window onto the microscopic mechanisms governing protein misfolding.

Enhanced Luminescent Stability through Particle Interactions in Silicon Nanocrystal Aggregates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, Joseph B.; Dandu, Naveen; Velizhanin, Kirill A.

2015-10-27

Close-packed assemblies of ligand-passivated colloidal nanocrystals can exhibit enhanced photoluminescent stability, but the origin of this effect is unclear. Here, we use experiment, simulation, and ab initio computation to examine the influence of interparticle interactions on the photoluminescent stability of silicon nanocrystal aggregates. The time-dependent photoluminescence emitted by structures ranging in size from a single quantum dot to agglomerates of more than a thousand is compared with Monte Carlo simulations of noninteracting ensembles using measured single-particle blinking data as input. In contrast to the behavior typically exhibited by the metal chalcogenides, the measured photoluminescent stability shows an enhancement with respectmore » to the noninteracting scenario with increasing aggregate size. We model this behavior using time-dependent density functional theory calculations of energy transfer between neighboring nanocrystals as a function of nanocrystal size, separation, and the presence of charge and/or surface-passivation defects. Our results suggest that rapid exciton transfer from “bright” nanocrystals to surface trap states in nearest-neighbors can efficiently fill such traps and enhance the stability of emission by promoting the radiative recombination of slowly diffusing excited electrons.« less

An integrated platform for assessing biologics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Schein, Perry; O'Dell, Dakota; Erickson, David

2016-04-01

Protein therapeutics are a rapidly growing portion of the pharmaceuticals market and have many significant advantages over traditional small molecule drugs. As this market expands, however, critical regulatory and quality control issues remain, most notably the problem of protein aggregation. Individual target proteins often aggregate into larger masses which trigger an immune response in the body, which can reduce the efficacy of the drug for its intended purpose, or cause serious anaphylactic side-effects. Although detecting and minimizing aggregate formation is critical to ensure an effective product, aggregation dynamics are often highly complicated and there is little hope of reliable prediction and prevention from first principles. This problem is compounded for aggregates in the subvisible range of 100 nm to 10 micrometers where traditional techniques for detecting aggregates have significant limitations. Here, we present an integrated optofluidic platform for detecting nanoscale protein aggregates and characterizing interactions between these aggregates and a reference surface. By delivering light to a solution of proteins with an optical waveguide, scattered light from individual protein aggregates can be detected and analyzed to determine the force profile between each particle and the waveguide surface. Unlike existing methods which only determine size or charge, our label-free screening technique can directly measure the surface interaction forces between single aggregates and the glass substrate. This direct measurement capability may allow for better empirical predictions of the stability of protein aggregates during drug manufacturing and storage.

Theory of Stochastic Laplacian Growth

NASA Astrophysics Data System (ADS)

Alekseev, Oleg; Mineev-Weinstein, Mark

2017-07-01

We generalize the diffusion-limited aggregation by issuing many randomly-walking particles, which stick to a cluster at the discrete time unit providing its growth. Using simple combinatorial arguments we determine probabilities of different growth scenarios and prove that the most probable evolution is governed by the deterministic Laplacian growth equation. A potential-theoretical analysis of the growth probabilities reveals connections with the tau-function of the integrable dispersionless limit of the two-dimensional Toda hierarchy, normal matrix ensembles, and the two-dimensional Dyson gas confined in a non-uniform magnetic field. We introduce the time-dependent Hamiltonian, which generates transitions between different classes of equivalence of closed curves, and prove the Hamiltonian structure of the interface dynamics. Finally, we propose a relation between probabilities of growth scenarios and the semi-classical limit of certain correlation functions of "light" exponential operators in the Liouville conformal field theory on a pseudosphere.

Soot and Radiation Measurements in Microgravity Jet Diffusion Flames

NASA Technical Reports Server (NTRS)

Ku, Jerry C.

1996-01-01

The subject of soot formation and radiation heat transfer in microgravity jet diffusion flames is important not only for the understanding of fundamental transport processes involved but also for providing findings relevant to spacecraft fire safety and soot emissions and radiant heat loads of combustors used in air-breathing propulsion systems. Our objectives are to measure and model soot volume fraction, temperature, and radiative heat fluxes in microgravity jet diffusion flames. For this four-year project, we have successfully completed three tasks, which have resulted in new research methodologies and original results. First is the implementation of a thermophoretic soot sampling technique for measuring particle size and aggregate morphology in drop-tower and other reduced gravity experiments. In those laminar flames studied, we found that microgravity soot aggregates typically consist of more primary particles and primary particles are larger in size than those under normal gravity. Comparisons based on data obtained from limited samples show that the soot aggregate's fractal dimension varies within +/- 20% of its typical value of 1.75, with no clear trends between normal and reduced gravity conditions. Second is the development and implementation of a new imaging absorption technique. By properly expanding and spatially-filtering the laser beam to image the flame absorption on a CCD camera and applying numerical smoothing procedures, this technique is capable of measuring instantaneous full-field soot volume fractions. Results from this technique have shown the significant differences in local soot volume fraction, smoking point, and flame shape between normal and reduced gravity flames. We observed that some laminar flames become open-tipped and smoking under microgravity. The third task we completed is the development of a computer program which integrates and couples flame structure, soot formation, and flame radiation analyses together. We found good agreements between model predictions and experimental data for laminar and turbulent flames under both normal and reduced gravity. We have also tested in the laboratory the techniques of rapid-insertion fine-wire thermocouples and emission pyrometry for temperature measurements. These techniques as well as laser Doppler velocimetry and spectral radiative intensity measurement have been proposed to provide valuable data and improve the modeling analyses.

Short- and long-time diffusion and dynamic scaling in suspensions of charged colloidal particles.

PubMed

Banchio, Adolfo J; Heinen, Marco; Holmqvist, Peter; Nägele, Gerhard

2018-04-07

We report on a comprehensive theory-simulation-experimental study of collective and self-diffusion in concentrated suspensions of charge-stabilized colloidal spheres. In theory and simulation, the spheres are assumed to interact directly by a hard-core plus screened Coulomb effective pair potential. The intermediate scattering function, f c (q, t), is calculated by elaborate accelerated Stokesian dynamics (ASD) simulations for Brownian systems where many-particle hydrodynamic interactions (HIs) are fully accounted for, using a novel extrapolation scheme to a macroscopically large system size valid for all correlation times. The study spans the correlation time range from the colloidal short-time to the long-time regime. Additionally, Brownian Dynamics (BD) simulation and mode-coupling theory (MCT) results of f c (q, t) are generated where HIs are neglected. Using these results, the influence of HIs on collective and self-diffusion and the accuracy of the MCT method are quantified. It is shown that HIs enhance collective and self-diffusion at intermediate and long times. At short times self-diffusion, and for wavenumbers outside the structure factor peak region also collective diffusion, are slowed down by HIs. MCT significantly overestimates the slowing influence of dynamic particle caging. The dynamic scattering functions obtained in the ASD simulations are in overall good agreement with our dynamic light scattering (DLS) results for a concentration series of charged silica spheres in an organic solvent mixture, in the experimental time window and wavenumber range. From the simulation data for the time derivative of the width function associated with f c (q, t), there is indication of long-time exponential decay of f c (q, t), for wavenumbers around the location of the static structure factor principal peak. The experimental scattering functions in the probed time range are consistent with a time-wavenumber factorization scaling behavior of f c (q, t) that was first reported by Segrè and Pusey [Phys. Rev. Lett. 77, 771 (1996)] for suspensions of hard spheres. Our BD simulation and MCT results predict a significant violation of exact factorization scaling which, however, is approximately restored according to the ASD results when HIs are accounted for, consistent with the experimental findings for f c (q, t). Our study of collective diffusion is amended by simulation and theoretical results for the self-intermediate scattering function, f s (q, t), and its non-Gaussian parameter α 2 (t) and for the particle mean squared displacement W(t) and its time derivative. Since self-diffusion properties are not assessed in standard DLS measurements, a method to deduce W(t) approximately from f c (q, t) is theoretically validated.

Long-Range Interactions Restrict Water Transport in Pyrophyllite Interlayers

DOE PAGES

Zarzycki, Piotr; Gilbert, Benjamin

2016-04-27

Water diffusion within smectite clay interlayers is reduced by confinement and hence is highly determined by the interlayer spacings that are adopted during swelling. However, a molecular understanding of the short-and long-range forces governing interlayer water structure and dynamics is lacking. Using molecular dynamics simulations of water intercalated between pyrophyllite (smectite prototype) layers we provide a detailed picture of the variation of interlayered water mobility accompanying smectite expansion. Subtle changes in hydrogen bond network structure cause significant changes in water mobility that is greater for stable hydration states and reduced for intermediate separations. By studying pyrophyllite with and without externalmore » water we reveal that long-range electrostatic forces apply a restraining effect upon interlayer water mobility. Our findings are relevant for broad range of confining nanostructures with walls thin enough to permit long-range interactions that could affect the mobility of confined solvent molecules and solute species.« less

Long-Range Interactions Restrict Water Transport in Pyrophyllite Interlayers

PubMed Central

Zarzycki, Piotr; Gilbert, Benjamin

2016-01-01

Water diffusion within smectite clay interlayers is reduced by confinement and hence is highly determined by the interlayer spacings that are adopted during swelling. However, a molecular understanding of the short- and long-range forces governing interlayer water structure and dynamics is lacking. Using molecular dynamics simulations of water intercalated between pyrophyllite (smectite prototype) layers we provide a detailed picture of the variation of interlayered water mobility accompanying smectite expansion. Subtle changes in hydrogen bond network structure cause significant changes in water mobility that is greater for stable hydration states and reduced for intermediate separations. By studying pyrophyllite with and without external water we reveal that long-range electrostatic forces apply a restraining effect upon interlayer water mobility. Our findings are relevant for broad range of confining nanostructures with walls thin enough to permit long-range interactions that could affect the mobility of confined solvent molecules and solute species. PMID:27118164

Bulk and surface properties of liquid Al-Cr and Cr-Ni alloys.

PubMed

Novakovic, R

2011-06-15

The energetics of mixing and structural arrangement in liquid Al-Cr and Cr-Ni alloys has been analysed through the study of surface properties (surface tension and surface segregation), dynamic properties (chemical diffusion) and microscopic functions (concentration fluctuations in the long-wavelength limit and chemical short-range order parameter) in the framework of statistical mechanical theory in conjunction with quasi-lattice theory. The Al-Cr phase diagram exhibits the existence of different intermetallic compounds in the solid state, while that of Cr-Ni is a simple eutectic-type phase diagram at high temperatures and includes the low-temperature peritectoid reaction in the range near a CrNi(2) composition. Accordingly, the mixing behaviour in Al-Cr and Cr-Ni alloy melts was studied using the complex formation model in the weak interaction approximation and by postulating Al(8)Cr(5) and CrNi(2) chemical complexes, respectively, as energetically favoured.

Evolution and development of brain networks: from Caenorhabditis elegans to Homo sapiens.

PubMed

Kaiser, Marcus; Varier, Sreedevi

2011-01-01

Neural networks show a progressive increase in complexity during the time course of evolution. From diffuse nerve nets in Cnidaria to modular, hierarchical systems in macaque and humans, there is a gradual shift from simple processes involving a limited amount of tasks and modalities to complex functional and behavioral processing integrating different kinds of information from highly specialized tissue. However, studies in a range of species suggest that fundamental similarities, in spatial and topological features as well as in developmental mechanisms for network formation, are retained across evolution. 'Small-world' topology and highly connected regions (hubs) are prevalent across the evolutionary scale, ensuring efficient processing and resilience to internal (e.g. lesions) and external (e.g. environment) changes. Furthermore, in most species, even the establishment of hubs, long-range connections linking distant components, and a modular organization, relies on similar mechanisms. In conclusion, evolutionary divergence leads to greater complexity while following essential developmental constraints.

Development of Fast Fourier Transform (FFT) micro-mechanical simulations of concrete specimens characterized by micro-X-ray fluorescence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giorla, Alain B.

Concrete in Nuclear Power Plants (NPPs) can be exposed to a wide range of degradation phenomena. In the past years, the Light Water Reactor Sustainability (LWRS) program has investigated Radiation-Induced Volumetric Expansion (RIVE) as a potential degradation mechanism for concrete biological shields [Graves et al., 2014, Rosseel et al., 2016]. RIVE causes swelling and micro-mechanical damage in concrete due to the amorphization of mineral phases contained in the aggregates under neutron irradiation [Hilsdorf et al., 1978, Rosseel et al., 2016]. For long-term operations, it is critical to assess the durability of concrete after 60 or 80 years of exposure tomore » NPP operating conditions against this phenomenon. RIVE is dependent on the composition of the aggregates used in concrete. Quartz-bearing aggregates are more sensitive to RIVE than calcite-bearing aggregates, for example. However, the aggregate composition of a specific plant is generally not explicitly given in the concrete formulation, which makes it nearly impossible to predict the resistance of that concrete to RIVE. Additional characterization is needed to identify the radiation-sensitive mineral phases contained in the aggregates.« less

Sorbitol crystallization-induced aggregation in frozen mAb formulations.

PubMed

Piedmonte, Deirdre Murphy; Hair, Alison; Baker, Priti; Brych, Lejla; Nagapudi, Karthik; Lin, Hong; Cao, Wenjin; Hershenson, Susan; Ratnaswamy, Gayathri

2015-02-01

Sorbitol crystallization-induced aggregation of mAbs in the frozen state was evaluated. The effect of protein aggregation resulting from sorbitol crystallization was measured as a function of formulation variables such as protein concentration and pH. Long-term studies were performed on both IgG1 and IgG2 mAbs over the protein concentration range of 0.1-120 mg/mL. Protein aggregation was measured by size-exclusion HPLC (SE-HPLC) and further characterized by capillary-electrophoresis SDS. Sorbitol crystallization was monitored and characterized by subambient differential scanning calorimetry and X-ray diffraction. Aggregation due to sorbitol crystallization is inversely proportional to both protein concentration and formulation pH. At high protein concentrations, sorbitol crystallization was suppressed, and minimal aggregation by SE-HPLC resulted, presumably because of self-stabilization of the mAbs. The glass transition temperature (Tg ') and fragility index measurements were made to assess the influence of molecular mobility on the crystallization of sorbitol. Tg ' increased with increasing protein concentration for both mAbs. The fragility index decreased with increasing protein concentration, suggesting that it is increasingly difficult for sorbitol to crystallize at high protein concentrations. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

SeaWiFS long-term solar diffuser reflectance and sensor noise analyses.

PubMed

Eplee, Robert E; Patt, Frederick S; Barnes, Robert A; McClain, Charles R

2007-02-10

The NASA Ocean Biology Processing Group's Calibration and Validation (Cal/Val) team has undertaken an analysis of the mission-long Sea-Viewing Wide Field-of-View Sensor (SeaWiFS) solar calibration time series to assess the long-term degradation of the solar diffuser reflectance over 9 years on orbit. The SeaWiFS diffuser is an aluminum plate coated with YB71 paint. The bidirectional reflectance distribution function of the diffuser was not fully characterized before launch, so the Cal/Val team has implemented a regression of the solar incidence angles and the drift in the node of the satellite's orbit against the diffuser time series to correct for solar incidence angle effects. An exponential function with a time constant of 200 days yields the best fit to the diffuser time series. The decrease in diffuser reflectance over the mission is wavelength dependent, ranging from 9% in the blue (412 nm) to 5% in the red and near infrared (670-865 nm). The Cal/Val team has developed a methodology for computing the signal-to-noise ratio (SNR) for SeaWiFS on orbit from the diffuser time series corrected for both the varying solar incidence angles and the diffuser reflectance degradation. A sensor noise model is used to compare on-orbit SNRs computed for radiances reflected from the diffuser with prelaunch SNRs measured at typical radiances specified for the instrument. To within the uncertainties in the measurements, the SNRs for SeaWiFS have not changed over the mission. The on-orbit performance of the SeaWiFS solar diffuser should offer insight into the long-term on-orbit performance of solar diffusers on other instruments, such as the Moderate-Resolution Imaging Spectrometer [currently flying on the Earth Observing System (EOS) Terra and Aqua satellites], the Visible and Infrared Radiometer Suite [scheduled to fly on the NASA National Polar-orbiting Operational Environmental Satellite System (NPOESS) and NPOESS Preparatory Project (NPP) satellites] and the Advanced Baseline Imager [scheduled to fly on the National Oceanic and Atmospheric Administration Geostationary Environmental Operational Satellite Series R (GOES-R) satellites].

SeaWiFS long-term solar diffuser reflectance and sensor noise analyses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eplee, Robert E. Jr.; Patt, Frederick S.; Barnes, Robert A.

The NASA Ocean Biology Processing Group's Calibration and Validation(Cal/Val) team has undertaken an analysis of the mission-long Sea-Viewing Wide Field-of-View Sensor (SeaWiFS)solar calibration time series to assess the long-term degradation of the solar diffuser reflectance over 9 years on orbit. The SeaWiFS diffuser is an aluminum plate coated with YB71 paint. The bidirectional reflectance distribution function of the diffuser was not fully characterized before launch,so the Cal/Val team has implemented a regression of the solar incidence angles and the drift in the node of the satellite's orbit against the diffuser time series to correct for solar incidence angle effects. Anmore » exponential function with a time constant of 200 days yields the best fit to the diffuser time series.The decrease in diffuser reflectance over the mission is wavelength dependent,ranging from 9% in the blue(412 nm) to 5% in the red and near infrared(670-865 nm). The Cal/Val team has developed a methodology for computing the signal-to-noise ratio (SNR) for SeaWiFS on orbit from the diffuser time series corrected for both the varying solar incidence angles and the diffuser reflectance degradation. A sensor noise model is used to compare on-orbit SNRs computed for radiances reflected from the diffuser with prelaunch SNRs measured at typical radiances specified for the instrument. To within the uncertainties in the measurements, the SNRs for SeaWiFS have not changed over the mission. The on-orbit performance of the SeaWiFS solar diffuser should offer insight into the long-term on-orbit performance of solar diffusers on other instruments, such as the Moderate-Resolution Imaging Spectrometer [currently flying on the Earth Observing System (EOS) Terra and Aqua satellites], the Visible and Infrared Radiometer Suite [scheduled to fly on the NASA National Polar-orbiting Operational Environmental Satellite System (NPOESS) and NPOESS Preparatory Project (NPP) satellites] and the Advanced Baseline Imager [scheduled to fly on the National Oceanic and Atmospheric Administration Geostationary Environmental Operational Satellite Series R (GOES-R) satellites].« less

SeaWiFS long-term solar diffuser reflectance and sensor noise analyses

NASA Astrophysics Data System (ADS)

Eplee, Robert E., Jr.; Patt, Frederick S.; Barnes, Robert A.; McClain, Charles R.

2007-02-01

The NASA Ocean Biology Processing Group's Calibration and Validation (Cal/Val) team has undertaken an analysis of the mission-long Sea-Viewing Wide Field-of-View Sensor (SeaWiFS) solar calibration time series to assess the long-term degradation of the solar diffuser reflectance over 9 years on orbit. The SeaWiFS diffuser is an aluminum plate coated with YB71 paint. The bidirectional reflectance distribution function of the diffuser was not fully characterized before launch, so the Cal/Val team has implemented a regression of the solar incidence angles and the drift in the node of the satellite's orbit against the diffuser time series to correct for solar incidence angle effects. An exponential function with a time constant of 200 days yields the best fit to the diffuser time series. The decrease in diffuser reflectance over the mission is wavelength dependent, ranging from 9% in the blue (412 nm) to 5% in the red and near infrared (670-865 nm). The Cal/Val team has developed a methodology for computing the signal-to-noise ratio (SNR) for SeaWiFS on orbit from the diffuser time series corrected for both the varying solar incidence angles and the diffuser reflectance degradation. A sensor noise model is used to compare on-orbit SNRs computed for radiances reflected from the diffuser with prelaunch SNRs measured at typical radiances specified for the instrument. To within the uncertainties in the measurements, the SNRs for SeaWiFS have not changed over the mission. The on-orbit performance of the SeaWiFS solar diffuser should offer insight into the long-term on-orbit performance of solar diffusers on other instruments, such as the Moderate-Resolution Imaging Spectrometer [currently flying on the Earth Observing System (EOS) Terra and Aqua satellites], the Visible and Infrared Radiometer Suite [scheduled to fly on the NASA National Polar-orbiting Operational Environmental Satellite System (NPOESS) and NPOESS Preparatory Project (NPP) satellites] and the Advanced Baseline Imager [scheduled to fly on the National Oceanic and Atmospheric Administration Geostationary Environmental Operational Satellite Series R (GOES-R) satellites].

Scaling behavior in corrosion and growth of a passive film.

PubMed

Aarão Reis, F D A; Stafiej, Janusz

2007-07-01

We study a simple model for metal corrosion controlled by the reaction rate of the metal with an anionic species and the diffusion of that species in the growing passive film between the solution and the metal. A crossover from the reaction-controlled to the diffusion-controlled growth regime with different roughening properties is observed. Scaling arguments provide estimates of the crossover time and film thickness as functions of the reaction and diffusion rates and the concentration of anionic species in the film-solution interface, including a nontrivial square-root dependence on that concentration. At short times, the metal-film interface exhibits Kardar-Parisi-Zhang (KPZ) scaling, which crosses over to a diffusion-limited erosion (Laplacian growth) regime at long times. The roughness of the metal-film interface at long times is obtained as a function of the rates of reaction and diffusion and of the KPZ growth exponent. The predictions have been confirmed by simulations of a lattice version of the model in two dimensions. Relations with other erosion and corrosion models and possible applications are discussed.

Noggin4 is a long-range inhibitor of Wnt8 signalling that regulates head development in Xenopus laevis.

PubMed

Eroshkin, Fedor M; Nesterenko, Alexey M; Borodulin, Alexander V; Martynova, Natalia Yu; Ermakova, Galina V; Gyoeva, Fatima K; Orlov, Eugeny E; Belogurov, Alexey A; Lukyanov, Konstantin A; Bayramov, Andrey V; Zaraisky, Andrey G

2016-03-14

Noggin4 is a Noggin family secreted protein whose molecular and physiological functions remain unknown. In this study, we demonstrate that in contrast to other Noggins, Xenopus laevis Noggin4 cannot antagonise BMP signalling; instead, it specifically binds to Wnt8 and inhibits the Wnt/β -catenin pathway. Live imaging demonstrated that Noggin4 diffusivity in embryonic tissues significantly exceeded that of other Noggins. Using the Fluorescence Recovery After Photobleaching (FRAP) assay and mathematical modelling, we directly estimated the affinity of Noggin4 for Wnt8 in living embryos and determined that Noggin4 fine-tune the Wnt8 posterior-to-anterior gradient. Our results suggest a role for Noggin4 as a unique, freely diffusing, long-range inhibitor of canonical Wnt signalling, thus explaining its ability to promote head development.

The large area high resolution gamma ray astrophysics facility - HR-GRAF

NASA Astrophysics Data System (ADS)

Fenyves, E. J.; Chaney, R. C.; Hoffman, J. H.; Cline, D. B.; Atac, M.; Park, J.; White, S. R.; Zych, A. D.; Tumer, Q. T.; Hughes, E. B.

1990-03-01

The long-term program is described in terms of its equipment, scientific objectives, and long-range scientific studies. A prototype of a space-based large-area high-resolution gamma-ray facility (HR-GRAF) is being developed to examine pointlike and diffuse gamma-ray sources in the range 1 MeV-100 GeV. The instrument for the facility is proposed to have high angular and energy resolution and very high sensitivity to permit the study of the proposed objects. The primary research targets include the mapping of galactic gamma radiation, observing the angular variations of diffuse gamma rays, and studying the Galactic center with particular emphasis on the hypothetical black hole. Also included in the research plans are obtaining data on gamma-ray bursters, investigating the transmission of gamma rays from cold dark matter, and studying nuclear gamma-ray lines.

Mean Field Limits for Interacting Diffusions in a Two-Scale Potential

NASA Astrophysics Data System (ADS)

Gomes, S. N.; Pavliotis, G. A.

2018-06-01

In this paper, we study the combined mean field and homogenization limits for a system of weakly interacting diffusions moving in a two-scale, locally periodic confining potential, of the form considered in Duncan et al. (Brownian motion in an N-scale periodic potential, arXiv:1605.05854, 2016b). We show that, although the mean field and homogenization limits commute for finite times, they do not, in general, commute in the long time limit. In particular, the bifurcation diagrams for the stationary states can be different depending on the order with which we take the two limits. Furthermore, we construct the bifurcation diagram for the stationary McKean-Vlasov equation in a two-scale potential, before passing to the homogenization limit, and we analyze the effect of the multiple local minima in the confining potential on the number and the stability of stationary solutions.

Brain propagation of transduced α-synuclein involves non-fibrillar protein species and is enhanced in α-synuclein null mice.

PubMed

Helwig, Michael; Klinkenberg, Michael; Rusconi, Raffaella; Musgrove, Ruth E; Majbour, Nour K; El-Agnaf, Omar M A; Ulusoy, Ayse; Di Monte, Donato A

2016-03-01

Aggregation and neuron-to-neuron transmission are attributes of α-synuclein relevant to its pathogenetic role in human synucleinopathies such as Parkinson's disease. Intraparenchymal injections of fibrillar α-synuclein trigger widespread propagation of amyloidogenic protein species via mechanisms that require expression of endogenous α-synuclein and, possibly, its structural corruption by misfolded conformers acting as pathological seeds. Here we describe another paradigm of long-distance brain diffusion of α-synuclein that involves inter-neuronal transfer of monomeric and/or oligomeric species and is independent of recruitment of the endogenous protein. Targeted expression of human α-synuclein was induced in the mouse medulla oblongata through an injection of viral vectors into the vagus nerve. Enhanced levels of intra-neuronal α-synuclein were sufficient to initiate its caudo-rostral diffusion that likely involved at least one synaptic transfer and progressively reached specific brain regions such as the locus coeruleus, dorsal raphae and amygdala in the pons, midbrain and forebrain. Transfer of human α-synuclein was compared in two separate lines of α-synuclein-deficient mice versus their respective wild-type controls and, interestingly, lack of endogenous α-synuclein expression did not counteract diffusion but actually resulted in a more pronounced and advanced propagation of exogenous α-synuclein. Self-interaction of adjacent molecules of human α-synuclein was detected in both wild-type and mutant mice. In the former, interaction of human α-synuclein with mouse α-synuclein was also observed and might have contributed to differences in protein transmission. In wild-type and α-synuclein-deficient mice, accumulation of human α-synuclein within recipient axons in the pons, midbrain and forebrain caused morphological evidence of neuritic pathology. Tissue sections from the medulla oblongata and pons were stained with different antibodies recognizing oligomeric, fibrillar and/or total (monomeric and aggregated) α-synuclein. Following viral vector transduction, monomeric, oligomeric and fibrillar protein was detected within donor neurons in the medulla oblongata. In contrast, recipient axons in the pons were devoid of immunoreactivity for fibrillar α-synuclein, indicating that non-fibrillar forms of α-synuclein were primarily transferred from one neuron to the other, diffused within the brain and led to initial neuronal injury. This study elucidates a paradigm of α-synuclein propagation that may play a particularly important role under pathophysiological conditions associated with enhanced α-synuclein expression. Rapid long-distance diffusion and accumulation of monomeric and oligomeric α-synuclein does not necessarily involve pathological seeding but could still result in a significant neuronal burden during the pathogenesis of neurodegenerative diseases. © The Author (2015). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Helium diffusion parameters of hematite from a single-diffusion-domain crystal

NASA Astrophysics Data System (ADS)

Farley, K. A.

2018-06-01

This contribution reports new parameters for helium diffusion in hematite useful for interpretation of cosmogenic 3He and radiogenic 4He chronometry. Fragments of a coarse, euhedral single crystal of hematite from Minas Gerais, Brazil were subjected to bulk step-heating helium diffusion experiments after proton irradiation to make a uniform distribution of 3He. Aliquots of three different grain sizes ranging from ∼300 to ∼700 μm in equivalent-sphere radius yielded helium diffusion activation energies Ea ∼ 170 kJ/mol, very similar to previous estimates for Ea in hematite. Uniquely in this specimen, diffusivity varies with the dimensions of the analyzed fragments in precisely the fashion expected if the diffusion domain corresponds to the physical grain. This contrasts with previous studies that concluded that the analyzed hematites consist of polycrystalline aggregates in which helium migration is governed by the size distribution of the constituent crystallites. These new data permit a direct estimate of the helium diffusivity at infinite temperature for hematite of ln(Do) = -0.66 ± 0.35 in cm2/s. The major implication of the new diffusion parameters is that hematite is very retentive of helium even at very small crystal sizes. For example, a 20 nm radius hematite crystal, at the smallest end of the size range so far described in dated polycrystalline hematite specimens, will retain more than 99% of its ingrown He over 1 Myr at 30 °C, and more than 90% over 100 Myr. Under most conditions, hematite is close to quantitatively helium-retentive on the Earth's surface, simplifying radiogenic and cosmogenic helium dating of this phase. In a system cooling at 10 °C/Myr, the 20 nm hematite crystal has a He closure temperature of ∼70 °C, similar to a typical ∼100 μm apatite crystal. Helium is likely held tightly in hematite owing to its dense hexagonal closest packing structure and absence of migration-enhancing channels. The isostructural minerals corundum and ilmenite are likely to be similarly helium retentive.

The impact of physiological crowding on the diffusivity of membrane bound proteins.

PubMed

Houser, Justin R; Busch, David J; Bell, David R; Li, Brian; Ren, Pengyu; Stachowiak, Jeanne C

2016-02-21

Diffusion of transmembrane and peripheral membrane-bound proteins within the crowded cellular membrane environment is essential to diverse biological processes including cellular signaling, endocytosis, and motility. Nonetheless we presently lack a detailed understanding of the influence of physiological levels of crowding on membrane protein diffusion. Utilizing quantitative in vitro measurements, here we demonstrate that the diffusivities of membrane bound proteins follow a single linearly decreasing trend with increasing membrane coverage by proteins. This trend holds for homogenous protein populations across a range of protein sizes and for heterogeneous mixtures of proteins of different sizes, such that protein diffusivity is controlled by the total coverage of the surrounding membrane. These results demonstrate that steric exclusion within the crowded membrane environment can fundamentally limit the diffusive rate of proteins, regardless of their size. In cells this "speed limit" could be modulated by changes in local membrane coverage, providing a mechanism for tuning the rate of molecular interaction and assembly.

Algorithm refinement for stochastic partial differential equations: II. Correlated systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alexander, Francis J.; Garcia, Alejandro L.; Tartakovsky, Daniel M.

2005-08-10

We analyze a hybrid particle/continuum algorithm for a hydrodynamic system with long ranged correlations. Specifically, we consider the so-called train model for viscous transport in gases, which is based on a generalization of the random walk process for the diffusion of momentum. This discrete model is coupled with its continuous counterpart, given by a pair of stochastic partial differential equations. At the interface between the particle and continuum computations the coupling is by flux matching, giving exact mass and momentum conservation. This methodology is an extension of our stochastic Algorithm Refinement (AR) hybrid for simple diffusion [F. Alexander, A. Garcia,more » D. Tartakovsky, Algorithm refinement for stochastic partial differential equations: I. Linear diffusion, J. Comput. Phys. 182 (2002) 47-66]. Results from a variety of numerical experiments are presented for steady-state scenarios. In all cases the mean and variance of density and velocity are captured correctly by the stochastic hybrid algorithm. For a non-stochastic version (i.e., using only deterministic continuum fluxes) the long-range correlations of velocity fluctuations are qualitatively preserved but at reduced magnitude.« less

Three-Dimensional Tracking of Interfacial Hopping Diffusion

NASA Astrophysics Data System (ADS)

Wang, Dapeng; Wu, Haichao; Schwartz, Daniel K.

2017-12-01

Theoretical predictions have suggested that molecular motion at interfaces—which influences processes including heterogeneous catalysis, (bio)chemical sensing, lubrication and adhesion, and nanomaterial self-assembly—may be dominated by hypothetical "hops" through the adjacent liquid phase, where a diffusing molecule readsorbs after a given hop according to a probabilistic "sticking coefficient." Here, we use three-dimensional (3D) single-molecule tracking to explicitly visualize this process for human serum albumin at solid-liquid interfaces that exert varying electrostatic interactions on the biomacromolecule. Following desorption from the interface, a molecule experiences multiple unproductive surface encounters before readsorption. An average of approximately seven surface collisions is required for the repulsive surfaces, decreasing to approximately two and a half for surfaces that are more attractive. The hops themselves are also influenced by long-range interactions, with increased electrostatic repulsion causing hops of longer duration and distance. These findings explicitly demonstrate that interfacial diffusion is dominated by biased 3D Brownian motion involving bulk-surface coupling and that it can be controlled by influencing short- and long-range adsorbate-surface interactions.

Contact-dependent killing by Caulobacter crescentus via cell surface-associated, glycine zipper proteins.

PubMed

García-Bayona, Leonor; Guo, Monica S; Laub, Michael T

2017-03-21

Most bacteria are in fierce competition with other species for limited nutrients. Some bacteria can kill nearby cells by secreting bacteriocins, a diverse group of proteinaceous antimicrobials. However, bacteriocins are typically freely diffusible, and so of little value to planktonic cells in aqueous environments. Here, we identify an atypical two-protein bacteriocin in the α-proteobacterium Caulobacter crescentus that is retained on the surface of producer cells where it mediates cell contact-dependent killing. The bacteriocin-like proteins CdzC and CdzD harbor glycine-zipper motifs, often found in amyloids, and CdzC forms large, insoluble aggregates on the surface of producer cells. These aggregates can drive contact-dependent killing of other organisms, or Caulobacter cells not producing the CdzI immunity protein. The Cdz system uses a type I secretion system and is unrelated to previously described contact-dependent inhibition systems. However, Cdz-like systems are found in many bacteria, suggesting that this form of contact-dependent inhibition is common.

Collective diffusion and quantum chaos in holography

NASA Astrophysics Data System (ADS)

Wu, Shao-Feng; Wang, Bin; Ge, Xian-Hui; Tian, Yu

2018-05-01

We define a particular combination of charge and heat currents that is decoupled with the heat current. This "heat-decoupled" (HD) current can be transported by diffusion at long distances, when some thermoelectric conductivities and susceptibilities satisfy a simple condition. Using the diffusion condition together with the Kelvin formula, we show that the HD diffusivity can be same as the charge diffusivity and also the heat diffusivity. We illustrate that such mechanism is implemented in a strongly coupled field theory, which is dual to a Lifshitz gravity with the dynamical critical index z =2 . In particular, it is exhibited that both charge and heat diffusivities build the relationship to the quantum chaos. Moreover, we study the HD diffusivity without imposing the diffusion condition. In some homogeneous holographic lattices, it is found that the diffusivity/chaos relation holds independently of any parameters, including the strength of momentum relaxation, chemical potential, or temperature. We also show a counter example of the relation and discuss its limited universality.

Freezing Responses in DMSO-Based Cryopreservation of Human iPS Cells: Aggregates Versus Single Cells.

PubMed

Li, Rui; Yu, Guanglin; Azarin, Samira M; Hubel, Allison

2018-05-01

Inadequate preservation methods of human induced pluripotent stem cells (hiPSCs) have impeded efficient reestablishment of cell culture after the freeze-thaw process. In this study, we examined roles of the cooling rate, seeding temperature, and difference between cell aggregates (3-50 cells) and single cells in controlled rate freezing of hiPSCs. Intracellular ice formation (IIF), post-thaw membrane integrity, cell attachment, apoptosis, and cytoskeleton organization were evaluated to understand the different freezing responses between hiPSC single cells and aggregates, among cooling rates of 1, 3, and 10°C/min, and between seeding temperatures of -4°C and -8°C. Raman spectroscopy images of ice showed that a lower seeding temperature (-8°C) did not affect IIF in single cells, but significantly increased IIF in aggregates, suggesting higher sensitivity of aggregates to supercooling. In the absence of IIF, Raman images showed greater variation of dimethyl sulfoxide concentration across aggregates than single cells, suggesting cryoprotectant transport limitations in aggregates. The ability of cryopreserved aggregates to attach to culture substrates did not correlate with membrane integrity for the wide range of freezing parameters, indicating inadequacy of using only membrane integrity-based optimization metrics. Lower cooling rates (1 and 3°C/min) combined with higher seeding temperature (-4°C) were better at preventing IIF and preserving cell function than a higher cooling rate (10°C/min) or lower seeding temperature (-8°C), proving the seeding temperature range of -7°C to -12°C from literature to be suboptimal. Unique f-actin cytoskeletal organization into a honeycomb-like pattern was observed in postpassage and post-thaw colonies and correlated with successful reestablishment of cell culture.

US-23 aggregate test road long-term performance evaluation : final report.

DOT National Transportation Integrated Search

2017-03-24

The US-23 Aggregate Test Road was constructed in 1992 with the main purpose to determine the influence of coarse : aggregate of varying frost susceptibility on long-term concrete durability. The pavement structure for the entire Test Road consists : ...

Linking Intra-Aggregate Pore Size Distribution with Organic Matter Decomposition Status, Evidence from FTIR and X-Ray Tomography

NASA Astrophysics Data System (ADS)

Toosi, E. R.; Quigley, M.; Kravchenko, A. N.

2014-12-01

It has been reported that conversion of intensively cultivated lands to less disturbed systems enhances soil OM storage capacity, primarily through OM stabilization in macroaggregates. We hypothesized that the potential for OM stabilization inside macro-aggregates is influenced by presence and abundance of intra-aggregate pores. Pores determine microbial access to OM and regulate diffusion of solution/gases within aggregates which drives microbial functioning. We investigated the influence of longterm disturbance intensity on soil OM composition and its relation to pore size distribution within macroaggregates. We used quantitative FTIR to determine OM decomposition status and X-ray micro-tomography to assess pore size distribution in macroaggregates as affected by management and landuse. Macroaggregates 4-6 mm in size where selected from topsoil under long term conventional tillage (CT), cover-crop (CC), and native succession vegetation (NS) treatments at Kellogg Biological Station, Michigan. Comparison of main soil OM functional groups suggested that with increasing disturbance intensity, the proportion of aromatic and carboxylic/carbohydrates associated compounds increased and it was concomitant with a decrease in the proportion of aliphatic associated compounds and lignin derivatives. Further, FTIR-based decomposition indices revealed that overall decomposition status of macroaggregates followed the pattern of CT > CC ≈ NS. X-ray micro-tomography findings suggested that greater OM decomposition within the macroaggregates was associated with i) greater percent of pores >13 micron in size within the aggregates, as well as ii) greater proportion of small to medium pores (13-110 micron). The results develop previous findings, suggesting that shift in landuse or management indirectly affects soil OM stabilization through alteration of pore size distribution within macroaggregates that itself, is coupled with OM decomposition status.

Long-range correlations in time series generated by time-fractional diffusion: A numerical study

NASA Astrophysics Data System (ADS)

Barbieri, Davide; Vivoli, Alessandro

2005-09-01

Time series models showing power law tails in autocorrelation functions are common in econometrics. A special non-Markovian model for such kind of time series is provided by the random walk introduced by Gorenflo et al. as a discretization of time fractional diffusion. The time series so obtained are analyzed here from a numerical point of view in terms of autocorrelations and covariance matrices.

Partner aggression and problem drinking across the lifespan: how much do they decline?

PubMed

O'Leary, K Daniel; Woodin, Erica M

2005-11-01

Cross-sectional analyses from nationally-representative samples demonstrate significant age-related trends in partner aggression and problem drinking. Both behaviors are most prevalent in the early to mid-twenties and increasingly less common thereafter. Aggregate associations based on percentage of individuals displaying the behavior in each age range are dramatically stronger than those found when correlating individuals' ages and behavior. Multilevel modeling demonstrates that group-level effects do not mask associations found at the level of the individual for either problem drinking or partner aggression. An analysis of recent abstracts from psychology journals showed that issues of aggregate and individual data are rarely if ever discussed, and even well-known statistics books in psychology rarely discuss such issues. The interpretation of aggregate data will become increasing important as psychologists themselves, and in collaboration with epidemiologists and sociologists, have access to large data sets that allow for data aggregation. Both aggregate and individual analyses are valid, although they provide answers to different questions. Individual analyses are necessary for predicting individual behavior; aggregate analyses are useful in policy planning for large scale prevention and intervention. Strengths and limitations of cross-sectional community samples and aggregate data are also discussed.

Polymer diffusion in the interphase between surface and solution.

PubMed

Weger, Lukas; Weidmann, Monika; Ali, Wael; Hildebrandt, Marcus; Gutmann, Jochen Stefan; Hoffmann-Jacobsen, Kerstin

2018-05-22

Total internal reflection fluorescence correlation spectroscopy (TIR-FCS) is applied to study the self-diffusion of polyethylene glycol solutions in the presence of weakly attractive interfaces. Glass coverslips modified with aminopropyl- and propyl-terminated silanes are used to study the influence of solid surfaces on polymer diffusion. A model of three phases of polymer diffusion allows to describe the experimental fluorescence autocorrelation functions. Besides the two-dimensional diffusion of adsorbed polymer on the substrate and three-dimensional free diffusion in bulk solution, a third diffusion time scale is observed with intermediate diffusion times. This retarded three-dimensional diffusion in solution is assigned to long range effects of solid surfaces on diffusional dynamics of polymers. The respective diffusion constants show Rouse scaling (D~N -1 ) indicating a screening of hydrodynamic interactions by the presence of the surface. Hence, the presented TIR-FCS method proves to be a valuable tool to investigate the effect of surfaces on polymer diffusion beyond the first adsorbed polymer layer on the 100 nm length scale.

Colorimetric detection of biothiols based on aggregation of chitosan-stabilized silver nanoparticles

NASA Astrophysics Data System (ADS)

Mohammadi, Somayeh; Khayatian, Gholamreza

2017-10-01

We have described a simple and reliable colorimetric method for the sensing of biothiols such as cysteine, homocysteine, and glutathione in biological samples. The selective binding of chitosan capped silver nanoparticles to biothiols induced aggregation of the chitosan-Ag NPs. But the other amino acids that do not have thiol group cannot aggregate the chitosan-Ag NPs. Aggregation of chitosan-Ag NPs has been confirmed with UV-vis absorption spectra, zeta potential and transmission electron microscopy images. Under optimum conditions, good linear relationships existed between the absorption ratios (at A500/A415) and the concentrations of cysteine, homocysteine, and glutathione in the range of 0.1-10.0 μM with detection limits of 15.0, 84.6 and 40.0 nM, respectively. This probe was successfully applied to detect these biothiols in biological samples (urine and plasma).

Incorporating photon recycling into the analytical drift-diffusion model of high efficiency solar cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lumb, Matthew P.; Naval Research Laboratory, Washington, DC 20375; Steiner, Myles A.

The analytical drift-diffusion formalism is able to accurately simulate a wide range of solar cell architectures and was recently extended to include those with back surface reflectors. However, as solar cells approach the limits of material quality, photon recycling effects become increasingly important in predicting the behavior of these cells. In particular, the minority carrier diffusion length is significantly affected by the photon recycling, with consequences for the solar cell performance. In this paper, we outline an approach to account for photon recycling in the analytical Hovel model and compare analytical model predictions to GaAs-based experimental devices operating close tomore » the fundamental efficiency limit.« less

The rate of the deoxygenation reaction limits myoglobin- and hemoglobin-facilitated O₂ diffusion in cells.

PubMed

Endeward, Volker

2012-05-01

A mathematical model describing facilitation of O(2) diffusion by the diffusion of myoglobin and hemoglobin is presented. The equations are solved numerically by a finite-difference method for the conditions as they prevail in cardiac and skeletal muscle and in red cells without major simplifications. It is demonstrated that, in the range of intracellular diffusion distances, the degree of facilitation is limited by the rate of the chemical reaction between myglobin or hemoglobin and O(2). The results are presented in the form of relationships between the degree of facilitation and the length of the diffusion path on the basis of the known kinetics of the oxygenation-deoxygenation reactions. It is concluded that the limitation by reaction kinetics reduces the maximally possible facilitated oxygen diffusion in cardiomyoctes by ∼50% and in skeletal muscle fibers by ∼ 20%. For human red blood cells, a reduction of facilitated O(2) diffusion by 36% is obtained in agreement with previous reports. This indicates that, especially in cardiomyocytes and red cells, chemical equilibrium between myoglobin or hemoglobin and O(2) is far from being established, an assumption that previously has often been made. Although the "O(2) transport function" of myoglobin in cardiac muscle cells thus is severely limited by the chemical reaction kinetics, and to a lesser extent also in skeletal muscle, it is noteworthy that the speed of release of O(2) from MbO(2), the "storage function," is not limited by the reaction kinetics under physiological conditions.

DLA based compressed sensing for high resolution MR microscopy of neuronal tissue.

PubMed

Nguyen, Khieu-Van; Li, Jing-Rebecca; Radecki, Guillaume; Ciobanu, Luisa

2015-10-01

In this work we present the implementation of compressed sensing (CS) on a high field preclinical scanner (17.2 T) using an undersampling trajectory based on the diffusion limited aggregation (DLA) random growth model. When applied to a library of images this approach performs better than the traditional undersampling based on the polynomial probability density function. In addition, we show that the method is applicable to imaging live neuronal tissues, allowing significantly shorter acquisition times while maintaining the image quality necessary for identifying the majority of neurons via an automatic cell segmentation algorithm. Copyright © 2015 Elsevier Inc. All rights reserved.