Toward a more biologically accurate model of diffusion: adhesion and collisions

SIMULATION ◽  
2017 ◽  
Vol 93 (12) ◽  
pp. 1037-1044
Author(s):  
Ahmed M Fouad ◽  
John A Noel
Keyword(s):  
Large Scale ◽  
Particle Density ◽  
File Systems ◽  
Tracer Diffusion ◽  
Transport Processes ◽  
Average Particle ◽  
Diffusion Behavior ◽  
Single File ◽  
Tracer Particles ◽  
The One

In single-file dynamics, Brownian particles (referred to as tracer or tagged particles) diffuse and collide with each other in one-dimensional domains. If the average particle density is kept fixed during the diffusion, the collisions between the tracer particles result in their famous anomalous sub-diffusion behavior with time to the one half dependence. Many systems in nature are found to obey single-file dynamics, such as ion transport processes, and inter-particle adhesion plays a crucial role, either structurally or functionally, in the diffusion of such systems; however, the exact effect of adhesion on the diffusion has not been studied so far. We have examined the effect of adhesion on the collective diffusion of single-file systems. Here, we extend previous work where we perform large-scale numerical simulations that utilize Monte Carlo techniques and high-performance computing resources to examine the effect of adhesion on the diffusion of the tracer particles in systems that obey single-file dynamics. We show that if all the tracer particles experience the same adhesion coefficient, adhesion only slows down the diffusion by reducing the magnitude of the tracer diffusion coefficient; however, both the anomalous sub-diffusion behavior and time to the one half dependence of the tracer particles remain almost intact, independent of the adhesion.

scholarly journals Kinetic analysis of water transport through a single-file pore.

1992 ◽  
Vol 99 (4) ◽  
pp. 645-662 ◽  
Author(s):  
J A Hernández ◽  
J Fischbarg
Keyword(s):  
New York ◽  
Water Transport ◽  
Transport Processes ◽  
Vacancy Mechanism ◽  
Permeability Ratio ◽  
Permeability Coefficients ◽  
Single File ◽  
The One ◽  
Diagrammatic Method ◽  
Model C

We apply the diagrammatic method developed by Hill (1977. Free Energy Transduction in Biology. Academic Press, New York) to analyze single-file water transport. We use this formalism to derive explicit expressions for the osmotic and diffusive permeabilities Pf and Pd of a pore. We first consider a vacancy mechanism of transport analogous to the one-vacancy pore model previously used by Kohler and Heckmann (1979. J. Theor. Biol. 79:381-401). (a) For the general one-vacancy case, we find that the permeability ratio can be expressed by Pf/Pd = (Pf/Pd)eqf(wA,wB), where the second factor is a function of the water activities in the two adjoining compartments A and B. As a consequence, the permeability ratio in general can effectively differ from its value at equilibrium. We also find that n - 1 less than or equal to (Pf/Pd)eq less than or equal to n, a result already proposed by Kohler and Heckmann (1979. J. Theor. Biol. 79:381-401). (b) When vacancy states are transient intermediates, the model can be reduced to a diagram consisting of only fully occupied states. Such a diagram resembles the one describing a no-vacancy mechanism of transport (c), but in spite of the similarity the expressions obtained for the permeability coefficients still retain the basic relationships of the original (a) nonreduced one-vacancy model. (c) We then propose a kinetic description of a no-vacancy mechanism of single-file water transport. In this case, the expressions derived for Pf and Pd are formally equivalent to those obtained by Finkelstein and Rosenberg (1979. Membrane Transport Processes. Vol. 3. C.F. Stevens and R.W. Tsien, editors, Raven Press, New York. 73-88.) A main difference with the vacancy mechanism is that here the permeability coefficients are independent of the water activities.

scholarly journals Insights from Single-File Diffusion into Cooperativity in Higher Dimensions

2016 ◽  
Vol 11 (01) ◽  
pp. 9-38 ◽  
Author(s):  
Takeshi Ooshida ◽  
Susumu Goto ◽  
Takeshi Matsumoto ◽  
Michio Otsuki
Keyword(s):  
Large Scale ◽  
Mean Square Displacement ◽  
Colloidal Suspensions ◽  
Higher Dimensions ◽  
Colloidal Systems ◽  
One Dimensional ◽  
Single File ◽  
The Mean ◽  
The One ◽  
Single File Diffusion

Diffusion in colloidal suspensions can be very slow due to the cage effect, which confines each particle within a short radius on one hand, and involves large-scale cooperative motions on the other. In search of insight into this cooperativity, here the authors develop a formalism to calculate the displacement correlation in colloidal systems, mainly in the two-dimensional (2D) case. To clarify the idea for it, studies are reviewed on cooperativity among the particles in the one-dimensional (1D) case, i.e. the single-file diffusion (SFD). As an improvement over the celebrated formula by Alexander and Pincus on the mean-square displacement (MSD) in SFD, it is shown that the displacement correlation in SFD can be calculated from Lagrangian correlation of the particle interval in the one-dimensional case, and also that the formula can be extended to higher dimensions. The improved formula becomes exact for large systems. By combining the formula with a nonlinear theory for correlation, a correction to the asymptotic law for the MSD in SFD is obtained. In the 2D case, the linear theory gives description of vortical cooperative motion.

scholarly journals <i>tran</i>-SAS v1.0: a numerical model to compute catchment-scale hydrologic transport using StorAge Selection functions

2018 ◽  
Vol 11 (4) ◽  
pp. 1627-1639 ◽  
Author(s):  
Paolo Benettin ◽  
Enrico Bertuzzo
Keyword(s):  
Solute Transport ◽  
Large Scale ◽  
Solute Concentration ◽  
Transport Processes ◽  
Catchment Scale ◽  
Numerical Accuracy ◽  
Hydrological System ◽  
The One ◽  
Integrated Response ◽  
Programming Knowledge

Abstract. This paper presents the “tran-SAS” package, which includes a set of codes to model solute transport and water residence times through a hydrological system. The model is based on a catchment-scale approach that aims at reproducing the integrated response of the system at one of its outlets. The codes are implemented in MATLAB and are meant to be easy to edit, so that users with minimal programming knowledge can adapt them to the desired application. The problem of large-scale solute transport has both theoretical and practical implications. On the one side, the ability to represent the ensemble of water flow trajectories through a heterogeneous system helps unraveling streamflow generation processes and allows us to make inferences on plant–water interactions. On the other side, transport models are a practical tool that can be used to estimate the persistence of solutes in the environment. The core of the package is based on the implementation of an age master equation (ME), which is solved using general StorAge Selection (SAS) functions. The age ME is first converted into a set of ordinary differential equations, each addressing the transport of an individual precipitation input through the catchment, and then it is discretized using an explicit numerical scheme. Results show that the implementation is efficient and allows the model to run in short times. The numerical accuracy is critically evaluated and it is shown to be satisfactory in most cases of hydrologic interest. Additionally, a higher-order implementation is provided within the package to evaluate and, if necessary, to improve the numerical accuracy of the results. The codes can be used to model streamflow age and solute concentration, but a number of additional outputs can be obtained by editing the codes to further advance the ability to understand and model catchment transport processes.

scholarly journals Quantitative evaluation of apically extruded debris during root canal instrumentation with ProTaper Universal, ProTaper Next, WaveOne, and self-adjusting file systems

2014 ◽  
Vol 08 (04) ◽  
pp. 504-508 ◽  
Author(s):  
Damla Ozsu ◽  
Ertugrul Karatas ◽  
Hakan Arslan ◽  
Meltem C. Topcu
Keyword(s):  
Root Canal ◽  
File Systems ◽  
Universal Group ◽  
Significance Level ◽  
Root Canals ◽  
Single File ◽  
Measurable Amount ◽  
Significant Difference ◽  
The One ◽  
Root Canal Instrumentation

ABSTRACT Objectives: The aim of this study was to compare the amount of apically extruded debris during preparation with ProTaper Universal (Dentsply Maillefer, Ballaigues, Switzerland), ProTaper Next (Dentsply Maillefer), a reciprocating single-file (WaveOne; VDW GmbH, Munich, Germany), and a self-adjusting file (SAF; ReDent Nova, Ra'anna, Israel). Materials and Methods: Fifty-six intact mandibular premolar teeth were randomly assigned to four groups. The root canals were prepared according to the manufacturers’ instructions using the ProTaper Universal, ProTaper Next, WaveOne, and SAF. Apically extruded debris was collected in preweighted Eppendorf tubes during instrumentation. The net weight of the apically extruded debris was determined by subtracting the preweights and postweights of the tubes. The data were statistically analyzed using the one-way analysis of variance and the least significant difference tests at a significance level of P < 0.05. Results: A measurable amount of debris was apically extruded in all groups, and the amounts of debris extrusion in the groups were statistically significant (P < 0.001). The ProTaper Next and WaveOne groups resulted in less debris extrusion than the ProTaper Universal group (P < 0.05), and the SAF group resulted in the least debris extrusion. Conclusions: Within the limitations of the present study, it can be concluded that all systems extruded debris beyond the apical foramen.

First grammar books in the Habsburg Monarchy: individual initiative and regulatory interference by the state (1760s–1770s)

2020 ◽  
Vol 2019 (2 (11)) ◽  
pp. 137-157
Author(s):  
Olga V. Khavanova ◽  
Keyword(s):  
Eighteenth Century ◽  
State Policy ◽  
Large Scale ◽  
Language Use ◽  
Linguistic Diversity ◽  
Mother Tongue ◽  
German Language ◽  
Habsburg Monarchy ◽  
Private Initiative ◽  
The One

The second half of the eighteenth century in the lands under the sceptre of the House of Austria was a period of development of a language policy addressing the ethno-linguistic diversity of the monarchy’s subjects. On the one hand, the sphere of use of the German language was becoming wider, embracing more and more segments of administration, education, and culture. On the other hand, the authorities were perfectly aware of the fact that communication in the languages and vernaculars of the nationalities living in the Austrian Monarchy was one of the principal instruments of spreading decrees and announcements from the central and local authorities to the less-educated strata of the population. Consequently, a large-scale reform of primary education was launched, aimed at making the whole population literate, regardless of social status, nationality (mother tongue), or confession. In parallel with the centrally coordinated state policy of education and language-use, subjects-both language experts and amateur polyglots-joined the process of writing grammar books, which were intended to ease communication between the different nationalities of the Habsburg lands. This article considers some examples of such editions with primary attention given to the correlation between private initiative and governmental policies, mechanisms of verifying the textbooks to be published, their content, and their potential readers. This paper demonstrates that for grammar-book authors, it was very important to be integrated into the patronage networks at the court and in administrative bodies and stresses that the Vienna court controlled the process of selection and financing of grammar books to be published depending on their quality and ability to satisfy the aims and goals of state policy.

The Green New Deal

2019 ◽  
Author(s):  
Robert C. Hockett
Keyword(s):  
New Deal ◽  
Large Scale ◽  
Public Investment ◽  
Climate Science ◽  
Time Frame ◽  
White Paper ◽  
Good News ◽  
Carbon Neutrality ◽  
The One ◽  
In Virtue Of

This white paper lays out the guiding vision behind the Green New Deal Resolution proposed to the U.S. Congress by Representative Alexandria Ocasio-Cortez and Senator Bill Markey in February of 2019. It explains the senses in which the Green New Deal is 'green' on the one hand, and a new 'New Deal' on the other hand. It also 'makes the case' for a shamelessly ambitious, not a low-ball or slow-walked, Green New Deal agenda. At the core of the paper's argument lies the observation that only a true national mobilization on the scale of those associated with the original New Deal and the Second World War will be up to the task of comprehensively revitalizing the nation's economy, justly growing our middle class, and expeditiously achieving carbon-neutrality within the twelve-year time-frame that climate science tells us we have before reaching an environmental 'tipping point.' But this is actually good news, the paper argues. For, paradoxically, an ambitious Green New Deal also will be the most 'affordable' Green New Deal, in virtue of the enormous productivity, widespread prosperity, and attendant public revenue benefits that large-scale public investment will bring. In effect, the Green New Deal will amount to that very transformative stimulus which the nation has awaited since the crash of 2008 and its debt-deflationary sequel.

“Community Interests” and the Role of International Law in the Creation of a Global Market for Agricultural Land

2018 ◽  
Author(s):  
Jochen von Bernstorff
Keyword(s):  
International Law ◽  
Large Scale ◽  
Agricultural Land ◽  
Food Sovereignty ◽  
Global Market ◽  
Negative Consequences ◽  
Cultural Rights ◽  
Land Grab ◽  
Large Scale Land ◽  
The One

The chapter explores the notion of “community interests” with regard to the global “land-grab” phenomenon. Over the last decade, a dramatic increase of foreign investment in agricultural land could be observed. Bilateral investment treaties protect around 75 per cent of these large-scale land acquisitions, many of which came with associated social problems, such as displaced local populations and negative consequences for food security in Third World countries receiving these large-scale foreign investments. Hence, two potentially conflicting areas of international law are relevant in this context: Economic, social, and cultural rights and the principles of permanent sovereignty over natural resources and “food sovereignty” challenging large-scale investments on the one hand, and specific norms of international economic law stabilizing them on the other. The contribution discusses the usefulness of the concept of “community interests” in cases where the two colliding sets of norms are both considered to protect such interests.

scholarly journals State Management for Cloud-Native Applications

Electronics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 423
Author(s):  
Márk Szalay ◽  
Péter Mátray ◽  
László Toka
Keyword(s):  
Large Scale ◽  
Distributed Databases ◽  
Access Time ◽  
Replica Placement ◽  
State Management ◽  
Placement Decisions ◽  
Dynamic Replication ◽  
Cloud Databases ◽  
Placement Algorithm ◽  
The One

The stateless cloud-native design improves the elasticity and reliability of applications running in the cloud. The design decouples the life-cycle of application states from that of application instances; states are written to and read from cloud databases, and deployed close to the application code to ensure low latency bounds on state access. However, the scalability of applications brings the well-known limitations of distributed databases, in which the states are stored. In this paper, we propose a full-fledged state layer that supports the stateless cloud application design. In order to minimize the inter-host communication due to state externalization, we propose, on the one hand, a system design jointly with a data placement algorithm that places functions’ states across the hosts of a data center. On the other hand, we design a dynamic replication module that decides the proper number of copies for each state to ensure a sweet spot in short state-access time and low network traffic. We evaluate the proposed methods across realistic scenarios. We show that our solution yields state-access delays close to the optimal, and ensures fast replica placement decisions in large-scale settings.

scholarly journals Constructing Large-Scale Genetic Maps Using an Evolutionary Strategy Algorithm

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2269-2282
Author(s):  
D Mester ◽  
Y Ronin ◽  
D Minkov ◽  
E Nevo ◽  
A Korol
Keyword(s):  
Discrete Optimization ◽  
High Performance ◽  
Large Scale ◽  
Simulated Data ◽  
Real Data ◽  
Genetic Maps ◽  
Chromosome 1 ◽  
Evolutionary Strategy ◽  
Group A ◽  
The One

Abstract This article is devoted to the problem of ordering in linkage groups with many dozens or even hundreds of markers. The ordering problem belongs to the field of discrete optimization on a set of all possible orders, amounting to n!/2 for n loci; hence it is considered an NP-hard problem. Several authors attempted to employ the methods developed in the well-known traveling salesman problem (TSP) for multilocus ordering, using the assumption that for a set of linked loci the true order will be the one that minimizes the total length of the linkage group. A novel, fast, and reliable algorithm developed for the TSP and based on evolution-strategy discrete optimization was applied in this study for multilocus ordering on the basis of pairwise recombination frequencies. The quality of derived maps under various complications (dominant vs. codominant markers, marker misclassification, negative and positive interference, and missing data) was analyzed using simulated data with ∼50-400 markers. High performance of the employed algorithm allows systematic treatment of the problem of verification of the obtained multilocus orders on the basis of computing-intensive bootstrap and/or jackknife approaches for detecting and removing questionable marker scores, thereby stabilizing the resulting maps. Parallel calculation technology can easily be adopted for further acceleration of the proposed algorithm. Real data analysis (on maize chromosome 1 with 230 markers) is provided to illustrate the proposed methodology.

scholarly journals Evaluation of the atmospheric transport in a GCM using radon measurements: sensitivity to cumulus convection parameterization

2008 ◽  
Vol 8 (10) ◽  
pp. 2811-2832 ◽  
Author(s):  
K. Zhang ◽  
H. Wan ◽  
M. Zhang ◽  
B. Wang
Keyword(s):  
Vertical Distribution ◽  
Radon Concentration ◽  
Large Scale ◽  
Atmospheric Transport ◽  
Surface Concentration ◽  
Transport Processes ◽  
Cumulus Convection ◽  
Models Comparison ◽  
Convection Schemes ◽  
Convection Parameterization

Abstract. The radioactive species radon (222Rn) has long been used as a test tracer for the numerical simulation of large scale transport processes. In this study, radon transport experiments are carried out using an atmospheric GCM with a finite-difference dynamical core, the van Leer type FFSL advection algorithm, and two state-of-the-art cumulus convection parameterization schemes. Measurements of surface concentration and vertical distribution of radon collected from the literature are used as references in model evaluation. The simulated radon concentrations using both convection schemes turn out to be consistent with earlier studies with many other models. Comparison with measurements indicates that at the locations where significant seasonal variations are observed in reality, the model can reproduce both the monthly mean surface radon concentration and the annual cycle quite well. At those sites where the seasonal variation is not large, the model is able to give a correct magnitude of the annual mean. In East Asia, where radon simulations are rarely reported in the literature, detailed analysis shows that our results compare reasonably well with the observations. The most evident changes caused by the use of a different convection scheme are found in the vertical distribution of the tracer. The scheme associated with weaker upward transport gives higher radon concentration up to about 6 km above the surface, and lower values in higher altitudes. In the lower part of the atmosphere results from this scheme does not agree as well with the measurements as the other scheme. Differences from 6 km to the model top are even larger, although we are not yet able to tell which simulation is better due to the lack of observations at such high altitudes.

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