Spin-diffusions and diffusive molecular dynamics
Farmer, Brittan; Luskin, Mitchell; Plecháč, Petr; Simpson, Gideon
2017-12-01
Metastable configurations in condensed matter typically fluctuate about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of classical molecular dynamics (MD) methods and has spurned the development of a host of approximate algorithms. One recently proposed method is diffusive MD which aims at integrating a system of ordinary differential equations describing the likelihood of occupancy by one of two species, in the case of a binary alloy, while quasistatically evolving the locations of the atoms. While diffusive MD has shown itself to be efficient and provide agreement with observations, it is fundamentally a model, with unclear connections to classical MD. In this work, we formulate a spin-diffusion stochastic process and show how it can be connected to diffusive MD. The spin-diffusion model couples a classical overdamped Langevin equation to a kinetic Monte Carlo model for exchange amongst the species of a binary alloy. Under suitable assumptions and approximations, spin-diffusion can be shown to lead to diffusive MD type models. The key assumptions and approximations include a well-defined time scale separation, a choice of spin-exchange rates, a low temperature approximation, and a mean field type approximation. We derive several models from different assumptions and show their relationship to diffusive MD. Differences and similarities amongst the models are explored in a simple test problem.
Photoinduced diffusion molecular transport
Energy Technology Data Exchange (ETDEWEB)
Rozenbaum, Viktor M., E-mail: vik-roz@mail.ru, E-mail: litrakh@gmail.com [Chuiko Institute of Surface Chemistry, National Academy of Sciences of Ukraine, Generala Naumova St. 17, Kiev 03164 (Ukraine); Dekhtyar, Marina L. [Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanskaya St. 5, Kiev 02094 (Ukraine); Lin, Sheng Hsien [Department of Applied Chemistry, National Chiao Tung University, 1001 Ta Hsuen Road, Hsinchu 300, Taiwan (China); Trakhtenberg, Leonid I., E-mail: vik-roz@mail.ru, E-mail: litrakh@gmail.com [Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygin Street 4, Moscow 119991, Russia and Moscow Institute of Physics and Technology (State University), Institutskii Per. 9, Dolgoprudnyi, Moscow Region 141700 (Russian Federation)
2016-08-14
We consider a Brownian photomotor, namely, the directed motion of a nanoparticle in an asymmetric periodic potential under the action of periodic rectangular resonant laser pulses which cause charge redistribution in the particle. Based on the kinetics for the photoinduced electron redistribution between two or three energy levels of the particle, the time dependence of its potential energy is derived and the average directed velocity is calculated in the high-temperature approximation (when the spatial amplitude of potential energy fluctuations is small relative to the thermal energy). The thus developed theory of photoinduced molecular transport appears applicable not only to conventional dichotomous Brownian motors (with only two possible potential profiles) but also to a much wider variety of molecular nanomachines. The distinction between the realistic time dependence of the potential energy and that for a dichotomous process (a step function) is represented in terms of relaxation times (they can differ on the time intervals of the dichotomous process). As shown, a Brownian photomotor has the maximum average directed velocity at (i) large laser pulse intensities (resulting in short relaxation times on laser-on intervals) and (ii) excited state lifetimes long enough to permit efficient photoexcitation but still much shorter than laser-off intervals. A Brownian photomotor with optimized parameters is exemplified by a cylindrically shaped semiconductor nanocluster which moves directly along a polar substrate due to periodically photoinduced dipole moment (caused by the repetitive excited electron transitions to a non-resonant level of the nanocylinder surface impurity).
OH+ IN DIFFUSE MOLECULAR CLOUDS
International Nuclear Information System (INIS)
Porras, A. J.; Federman, S. R.; Welty, D. E.; Ritchey, A. M.
2014-01-01
Near ultraviolet observations of OH + and OH in diffuse molecular clouds reveal a preference for different environments. The dominant absorption feature in OH + arises from a main component seen in CH + (that with the highest CH + /CH column density ratio), while OH follows CN absorption. This distinction provides new constraints on OH chemistry in these clouds. Since CH + detections favor low-density gas with small fractions of molecular hydrogen, this must be true for OH + as well, confirming OH + and H 2 O + observations with the Herschel Space Telescope. Our observed correspondence indicates that the cosmic ray ionization rate derived from these measurements pertains to mainly atomic gas. The association of OH absorption with gas rich in CN is attributed to the need for a high enough density and molecular fraction before detectable amounts are seen. Thus, while OH + leads to OH production, chemical arguments suggest that their abundances are controlled by different sets of conditions and that they coexist with different sets of observed species. Of particular note is that non-thermal chemistry appears to play a limited role in the synthesis of OH in diffuse molecular clouds
Molecular diffusion in monolayer and submonolayer nitrogen
DEFF Research Database (Denmark)
Hansen, Flemming Yssing; Bruch, Ludwig Walter
2001-01-01
The orientational and translational motions in a monolayer fluid of physisorbed molecular nitrogen are treated using molecular dynamics simulations. Dynamical response functions and several approximations to the coefficient of translational diffusion are determined for adsorption on the basal plane...
Molecular dynamics and diffusion a compilation
Fisher, David
2013-01-01
The molecular dynamics technique was developed in the 1960s as the outgrowth of attempts to model complicated systems by using either a) direct physical simulation or (following the great success of Monte Carlo methods) by b) using computer techniques. Computer simulation soon won out over clumsy physical simulation, and the ever-increasing speed and sophistication of computers has naturally made molecular dynamics simulation into a more and more successful technique. One of its most popular applications is the study of diffusion, and some experts now even claim that molecular dynamics simulation is, in the case of situations involving well-characterised elements and structures, more accurate than experimental measurement. The present double volume includes a compilation (over 600 items) of predicted solid-state diffusion data, for all of the major materials groups, dating back nearly four decades. The double volume also includes some original papers: "Determination of the Activation Energy for Formation and ...
Molecular Diffusion through Cyanobacterial Septal Junctions.
Nieves-Morión, Mercedes; Mullineaux, Conrad W; Flores, Enrique
2017-01-03
Heterocyst-forming cyanobacteria grow as filaments in which intercellular molecular exchange takes place. During the differentiation of N 2 -fixing heterocysts, regulators are transferred between cells. In the diazotrophic filament, vegetative cells that fix CO 2 through oxygenic photosynthesis provide the heterocysts with reduced carbon and heterocysts provide the vegetative cells with fixed nitrogen. Intercellular molecular transfer has been traced with fluorescent markers, including calcein, 5-carboxyfluorescein, and the sucrose analogue esculin, which are observed to move down their concentration gradient. In this work, we used fluorescence recovery after photobleaching (FRAP) assays in the model heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 to measure the temperature dependence of intercellular transfer of fluorescent markers. We find that the transfer rate constants are directly proportional to the absolute temperature. This indicates that the "septal junctions" (formerly known as "microplasmodesmata") linking the cells in the filament allow molecular exchange by simple diffusion, without any activated intermediate state. This constitutes a novel mechanism for molecular transfer across the bacterial cytoplasmic membrane, in addition to previously characterized mechanisms for active transport and facilitated diffusion. Cyanobacterial septal junctions are functionally analogous to the gap junctions of metazoans. Although bacteria are frequently considered just as unicellular organisms, there are bacteria that behave as true multicellular organisms. The heterocyst-forming cyanobacteria grow as filaments in which cells communicate. Intercellular molecular exchange is thought to be mediated by septal junctions. Here, we show that intercellular transfer of fluorescent markers in the cyanobacterial filament has the physical properties of simple diffusion. Thus, cyanobacterial septal junctions are functionally analogous to metazoan gap junctions
High efficiency diffusion molecular retention tumor targeting.
Directory of Open Access Journals (Sweden)
Yanyan Guo
Full Text Available Here we introduce diffusion molecular retention (DMR tumor targeting, a technique that employs PEG-fluorochrome shielded probes that, after a peritumoral (PT injection, undergo slow vascular uptake and extensive interstitial diffusion, with tumor retention only through integrin molecular recognition. To demonstrate DMR, RGD (integrin binding and RAD (control probes were synthesized bearing DOTA (for (111 In(3+, a NIR fluorochrome, and 5 kDa PEG that endows probes with a protein-like volume of 25 kDa and decreases non-specific interactions. With a GFP-BT-20 breast carcinoma model, tumor targeting by the DMR or i.v. methods was assessed by surface fluorescence, biodistribution of [(111In] RGD and [(111In] RAD probes, and whole animal SPECT. After a PT injection, both probes rapidly diffused through the normal and tumor interstitium, with retention of the RGD probe due to integrin interactions. With PT injection and the [(111In] RGD probe, SPECT indicated a highly tumor specific uptake at 24 h post injection, with 352%ID/g tumor obtained by DMR (vs 4.14%ID/g by i.v.. The high efficiency molecular targeting of DMR employed low probe doses (e.g. 25 ng as RGD peptide, which minimizes toxicity risks and facilitates clinical translation. DMR applications include the delivery of fluorochromes for intraoperative tumor margin delineation, the delivery of radioisotopes (e.g. toxic, short range alpha emitters for radiotherapy, or the delivery of photosensitizers to tumors accessible to light.
Molecular Diffusion through Cyanobacterial Septal Junctions
Directory of Open Access Journals (Sweden)
Mercedes Nieves-Morión
2017-01-01
Full Text Available Heterocyst-forming cyanobacteria grow as filaments in which intercellular molecular exchange takes place. During the differentiation of N2-fixing heterocysts, regulators are transferred between cells. In the diazotrophic filament, vegetative cells that fix CO2 through oxygenic photosynthesis provide the heterocysts with reduced carbon and heterocysts provide the vegetative cells with fixed nitrogen. Intercellular molecular transfer has been traced with fluorescent markers, including calcein, 5-carboxyfluorescein, and the sucrose analogue esculin, which are observed to move down their concentration gradient. In this work, we used fluorescence recovery after photobleaching (FRAP assays in the model heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 to measure the temperature dependence of intercellular transfer of fluorescent markers. We find that the transfer rate constants are directly proportional to the absolute temperature. This indicates that the “septal junctions” (formerly known as “microplasmodesmata” linking the cells in the filament allow molecular exchange by simple diffusion, without any activated intermediate state. This constitutes a novel mechanism for molecular transfer across the bacterial cytoplasmic membrane, in addition to previously characterized mechanisms for active transport and facilitated diffusion. Cyanobacterial septal junctions are functionally analogous to the gap junctions of metazoans.
Calculating effective diffusivities in the limit of vanishing molecular diffusion
International Nuclear Information System (INIS)
Pavliotis, G.A.; Stuart, A.M.; Zygalakis, K.C.
2009-01-01
In this paper we study the problem of the numerical calculation (by Monte Carlo methods) of the effective diffusivity for a particle moving in a periodic divergent-free velocity field, in the limit of vanishing molecular diffusion. In this limit traditional numerical methods typically fail, since they do not represent accurately the geometry of the underlying deterministic dynamics. We propose a stochastic splitting method that takes into account the volume-preserving property of the equations of motion in the absence of noise, and when inertial effects can be neglected. An extension of the method is then proposed for the cases where the noise has a non-trivial time-correlation structure and when inertial effects cannot be neglected. The method of modified equations is used to explain failings of Euler-based methods. The new stochastic geometric integrators are shown to outperform standard Euler-based integrators. Various asymptotic limits of physical interest are investigated by means of numerical experiments, using the new integrators
Observational Constraints for Modeling Diffuse Molecular Clouds
Federman, S. R.
2014-02-01
Ground-based and space-borne observations of diffuse molecular clouds suggest a number of areas where further improvements to modeling efforts is warranted. I will highlight those that have the widest applicability. The range in CO fractionation caused by selective isotope photodissociation, in particular the large 12C16O/13C16O ratios observed toward stars in Ophiuchus, is not reproduced well by current models. Our ongoing laboratory measurements of oscillator strengths and predissociation rates for Rydberg transitions in CO isotopologues may help clarify the situtation. The CH+ abundance continues to draw attention. Small scale structure seen toward ζ Per may provide additional constraints on the possible synthesis routes. The connection between results from optical transitions and those from radio and sub-millimeter wave transitions requires further effort. A study of OH+ and OH toward background stars reveals that these species favor different environments. This brings to focus the need to model each cloud along the line of sight separately, and to allow the physical conditions to vary within an individual cloud, in order to gain further insight into the chemistry. Now that an extensive set of data on molecular excitation is available, the models should seek to reproduce these data to place further constraints on the modeling results.
Diffusion in Liquids : Equilibrium Molecular Simulations and Predictive Engineering Models
Liu, X.
2013-01-01
The aim of this thesis is to study multicomponent diffusion in liquids using Molecular Dynamics (MD) simulations. Diffusion plays an important role in mass transport processes. In binary systems, mass transfer processes have been studied extensively using both experiments and molecular simulations.
A consistent transported PDF model for treating differential molecular diffusion
Wang, Haifeng; Zhang, Pei
2016-11-01
Differential molecular diffusion is a fundamentally significant phenomenon in all multi-component turbulent reacting or non-reacting flows caused by the different rates of molecular diffusion of energy and species concentrations. In the transported probability density function (PDF) method, the differential molecular diffusion can be treated by using a mean drift model developed by McDermott and Pope. This model correctly accounts for the differential molecular diffusion in the scalar mean transport and yields a correct DNS limit of the scalar variance production. The model, however, misses the molecular diffusion term in the scalar variance transport equation, which yields an inconsistent prediction of the scalar variance in the transported PDF method. In this work, a new model is introduced to remedy this problem that can yield a consistent scalar variance prediction. The model formulation along with its numerical implementation is discussed, and the model validation is conducted in a turbulent mixing layer problem.
Rotational diffusion of a molecular cat
Katz-Saporta, Ori; Efrati, Efi
We show that a simple isolated system can perform rotational random walk on account of internal excitations alone. We consider the classical dynamics of a ''molecular cat'': a triatomic molecule connected by three harmonic springs with non-zero rest lengths, suspended in free space. In this system, much like for falling cats, the angular momentum constraint is non-holonomic allowing for rotations with zero overall angular momentum. The geometric nonlinearities arising from the non-zero rest lengths of the springs suffice to break integrability and lead to chaotic dynamics. The coupling of the non-integrability of the system and its non-holonomic nature results in an angular random walk of the molecule. We study the properties and dynamics of this angular motion analytically and numerically. For low energy excitations the system displays normal-mode-like motion, while for high enough excitation energy we observe regular random-walk. In between, at intermediate energies we observe an angular Lévy-walk type motion associated with a fractional diffusion coefficient interpolating between the two regimes.
Molecular Diffusion Coefficients: Experimental Determination and Demonstration.
Fate, Gwendolyn; Lynn, David G.
1990-01-01
Presented are laboratory methods which allow the demonstration and determination of the diffusion coefficients of compounds ranging in size from water to small proteins. Included are the procedures involving the use of a spectrometer, UV cell, triterated agar, and oxygen diffusion. Results including quantification are described. (CW)
Extracting the diffusion tensor from molecular dynamics simulation with Milestoning
International Nuclear Information System (INIS)
Mugnai, Mauro L.; Elber, Ron
2015-01-01
We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide
Molecular Dynamics Simulation of Salt Diffusion in Polyelectrolyte Assemblies.
Zhang, Ran; Duan, Xiaozheng; Ding, Mingming; Shi, Tongfei
2018-06-05
The diffusion of salt ions and charged probe molecules in polyelectrolyte assemblies is often assumed to follow a theoretical hopping model, in which the diffusing ion is hopping between charged sites of chains based on electroneutrality. However, experimental verification of diffusing pathway at such microscales is difficult, and the corresponding molecular mechanisms remain elusive. In this study, we perform all-atom molecular dynamics (MD) simulations of salt diffusion in polyelectrolyte (PE) assembly of poly (sodium 4-styrenesulfonate) (PSS) and poly (diallyldimethylammonium chloride) (PDAC). Besides the ion hopping mode, the diffusing trajectories are found presenting common features of a jump process, i.e., subjecting to PE relaxation, water pockets in the structure open and close, thus the ion can move from one pocket to another. Anomalous subdiffusion of ions and water is observed due to the trapping scenarios in these water pockets. The jump events are much rarer compared with ion hopping but significantly increases salt diffusion with increasing temperature. Our result strongly indicates that salt diffusion in hydrated PDAC/PSS is a combined process of ion hopping and jump motion. This provides new molecular explanation for the coupling of salt motion with chain motion and the nonlinear increase of salt diffusion at glass transition temperature.
Oxygen and nitrogen diffusion in coal-molecular sieve
International Nuclear Information System (INIS)
Stefanescu, Doina Maria
1996-01-01
Recently, the air separation process based on selective adsorption of carbon-molecular sieves has been developed strongly. The separation is based on the system kinematics and depends on the oxygen diffusion in adsorber micropores. The oxygen is preferentially adsorbed and in given conditions it is possible to obtain nitrogen of high purity. Recent theoretical and experimental studies concerning the production of nitrogen by PSA process have shown that the obtained performances can not be described by a constant diffusion model. The paper present the 'dual' model assumed for O 2 and N 2 diffusion through molecular sieve as well as the experimental data obtained in the adsorption study on carbon material produced at ICIS to determine the diffusivity values in micropores
Time scale of diffusion in molecular and cellular biology
International Nuclear Information System (INIS)
Holcman, D; Schuss, Z
2014-01-01
Diffusion is the driver of critical biological processes in cellular and molecular biology. The diverse temporal scales of cellular function are determined by vastly diverse spatial scales in most biophysical processes. The latter are due, among others, to small binding sites inside or on the cell membrane or to narrow passages between large cellular compartments. The great disparity in scales is at the root of the difficulty in quantifying cell function from molecular dynamics and from simulations. The coarse-grained time scale of cellular function is determined from molecular diffusion by the mean first passage time of molecular Brownian motion to a small targets or through narrow passages. The narrow escape theory (NET) concerns this issue. The NET is ubiquitous in molecular and cellular biology and is manifested, among others, in chemical reactions, in the calculation of the effective diffusion coefficient of receptors diffusing on a neuronal cell membrane strewn with obstacles, in the quantification of the early steps of viral trafficking, in the regulation of diffusion between the mother and daughter cells during cell division, and many other cases. Brownian trajectories can represent the motion of a molecule, a protein, an ion in solution, a receptor in a cell or on its membrane, and many other biochemical processes. The small target can represent a binding site or an ionic channel, a hidden active site embedded in a complex protein structure, a receptor for a neurotransmitter on the membrane of a neuron, and so on. The mean time to attach to a receptor or activator determines diffusion fluxes that are key regulators of cell function. This review describes physical models of various subcellular microdomains, in which the NET coarse-grains the molecular scale to a higher cellular-level, thus clarifying the role of cell geometry in determining subcellular function. (topical review)
Time scale of diffusion in molecular and cellular biology
Holcman, D.; Schuss, Z.
2014-05-01
Diffusion is the driver of critical biological processes in cellular and molecular biology. The diverse temporal scales of cellular function are determined by vastly diverse spatial scales in most biophysical processes. The latter are due, among others, to small binding sites inside or on the cell membrane or to narrow passages between large cellular compartments. The great disparity in scales is at the root of the difficulty in quantifying cell function from molecular dynamics and from simulations. The coarse-grained time scale of cellular function is determined from molecular diffusion by the mean first passage time of molecular Brownian motion to a small targets or through narrow passages. The narrow escape theory (NET) concerns this issue. The NET is ubiquitous in molecular and cellular biology and is manifested, among others, in chemical reactions, in the calculation of the effective diffusion coefficient of receptors diffusing on a neuronal cell membrane strewn with obstacles, in the quantification of the early steps of viral trafficking, in the regulation of diffusion between the mother and daughter cells during cell division, and many other cases. Brownian trajectories can represent the motion of a molecule, a protein, an ion in solution, a receptor in a cell or on its membrane, and many other biochemical processes. The small target can represent a binding site or an ionic channel, a hidden active site embedded in a complex protein structure, a receptor for a neurotransmitter on the membrane of a neuron, and so on. The mean time to attach to a receptor or activator determines diffusion fluxes that are key regulators of cell function. This review describes physical models of various subcellular microdomains, in which the NET coarse-grains the molecular scale to a higher cellular-level, thus clarifying the role of cell geometry in determining subcellular function.
Molecular weight dependence of exciton diffusion in poly(3-hexylthiophene)
DEFF Research Database (Denmark)
Masri, Zarifi; Ruseckas, Arvydas; Emelianova, Evguenia V.
2013-01-01
A joint experimental and theoretical study of singlet exciton diffusion in spin-coated poly(3-hexylthiophene) (P3HT) films and its dependence on molecular weight is presented. The results show that exciton diffusion is fast along the co-facial π–π aggregates of polymer chromophores and about 100...... times slower in the lateral direction between aggregates. Exciton hopping between aggregates is found to show a subtle dependence on interchain coupling, aggregate size, and Boltzmann statistics. Additionally, a clear correlation is observed between the effective exciton diffusion coefficient...
On the coupling between molecular diffusion and solvation shell exchange
DEFF Research Database (Denmark)
Møller, Klaus Braagaard; Rey, Rossend; Masia, Marco
2005-01-01
The connection between diffusion and solvent exchanges between first and second solvation shells is studied by means of molecular dynamics simulations and analytic calculations, with detailed illustrations for water exchange for the Li+ and Na+ ions, and for liquid argon. First, two methods...
Anatomic mapping of molecular subtypes in diffuse glioma.
Tang, Qisheng; Lian, Yuxi; Yu, Jinhua; Wang, Yuanyuan; Shi, Zhifeng; Chen, Liang
2017-09-15
Tumor location served as an important prognostic factor in glioma patients was considered to postulate molecular features according to cell origin theory. However, anatomic distribution of unique molecular subtypes was not widely investigated. The relationship between molecular phenotype and histological subgroup were also vague based on tumor location. Our group focuses on the study of glioma anatomic location of distinctive molecular subgroups and histology subtypes, and explores the possibility of their consistency based on clinical background. We retrospectively reviewed 143 cases with both molecular information (IDH1/TERT/1p19q) and MRI images diagnosed as cerebral diffuse gliomas. The anatomic distribution was analyzed between distinctive molecular subgroups and its relationship with histological subtypes. The influence of tumor location, molecular stratification and histology diagnosis on survival outcome was investigated as well. Anatomic locations of cerebral diffuse glioma indicate varied clinical outcome. Based on that, it can be stratified into five principal molecular subgroups according to IDH1/TERT/1p19q status. Triple-positive (IDH1 and TERT mutation with 1p19q codeletion) glioma tended to be oligodendroglioma present with much better clinical outcome compared to TERT mutation only group who is glioblastoma inclined (median overall survival 39 months VS 18 months). Five molecular subgroups were demonstrated with distinctive locational distribution. This kind of anatomic feature is consistent with its corresponding histological subtypes. Each molecular subgroup in glioma has unique anatomic location which indicates distinctive clinical outcome. Molecular diagnosis can be served as perfect complementary tool for the precise diagnosis. Integration of histomolecular diagnosis will be much more helpful in routine clinical practice in the future.
Neutron diffuse scattering in magnetite due to molecular polarons
International Nuclear Information System (INIS)
Yamada, Y.; Wakabayashi, N.; Nicklow, R.M.
1980-01-01
A detailed neutron diffuse scattering study has been carried out in order to verify a model which describes the property of valence fluctuations in magnetite above T/sub V/. This model assumes the existence of a complex which is composed of two excess electrons and a local displacement mode of oxygens within the fcc primitive cell. The complex is called a molecular polaron. It is assumed that at sufficiently high temperatures there is a random distribution of molecular polarons, which are fluctuating independently by making hopping motions through the crystal or by dissociating into smaller polarons. The lifetime of each molecular polaron is assumed to be long enough to induce an instantaneous strain field around it. Based on this model, the neutron diffuse scattering cross section due to randomly distributed dressed molecular polarons has been calculated. A precise measurement of the quasielastic scattering of neutrons has been carried out at 150 K. The observed results definitely show the characteristics which are predicted by the model calculation and, thus, give evidence for the existence of the proposed molecular polarons. From this standpoint, the Verwey transition of magnetite may be viewed as the cooperative ordering process of dressed molecular polarons. Possible extensions of the model to describe the ordering and the dynamical behavior of the molecular polarons are discussed
Post-processing interstitialcy diffusion from molecular dynamics simulations
International Nuclear Information System (INIS)
Bhardwaj, U.; Bukkuru, S.; Warrier, M.
2016-01-01
An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms. -- Graphical abstract:
Post-processing interstitialcy diffusion from molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Bhardwaj, U., E-mail: haptork@gmail.com [Computational Analysis Division, BARC, Visakhapatnam, Andhra Pradesh, 530012 (India); Bukkuru, S. [Nuclear Physics Dept., Andhra University, Visakhapatnam, 530003 (India); Warrier, M. [Computational Analysis Division, BARC, Visakhapatnam, Andhra Pradesh, 530012 (India)
2016-01-15
An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms. -- Graphical abstract:.
In Vivo Diffuse Optical Tomography and Fluorescence Molecular Tomography
Directory of Open Access Journals (Sweden)
Mingze Li
2010-01-01
Full Text Available Diffuse optical tomography (DOT and fluorescence molecular tomography (FMT are two attractive imaging techniques for in vivo physiological and psychological research. They have distinct advantages such as non-invasiveness, non-ionizing radiation, high sensitivity and longitudinal monitoring. This paper reviews the key components of DOT and FMT. Light propagation model, mathematical reconstruction algorithm, imaging instrumentation and medical applications are included. Future challenges and perspective on optical tomography are discussed.
CO2 diffusion in champagne wines: a molecular dynamics study.
Perret, Alexandre; Bonhommeau, David A; Liger-Belair, Gérard; Cours, Thibaud; Alijah, Alexander
2014-02-20
Although diffusion is considered as the main physical process responsible for the nucleation and growth of carbon dioxide bubbles in sparkling beverages, the role of each type of molecule in the diffusion process remains unclear. In the present study, we have used the TIP5P and SPC/E water models to perform force field molecular dynamics simulations of CO2 molecules in water and in a water/ethanol mixture respecting Champagne wine proportions. CO2 diffusion coefficients were computed by applying the generalized Fick's law for the determination of multicomponent diffusion coefficients, a law that simplifies to the standard Fick's law in the case of champagnes. The CO2 diffusion coefficients obtained in pure water and water/ethanol mixtures composed of TIP5P water molecules were always found to exceed the coefficients obtained in mixtures composed of SPC/E water molecules, a trend that was attributed to a larger propensity of SPC/E water molecules to form hydrogen bonds. Despite the fact that the SPC/E model is more accurate than the TIP5P model to compute water self-diffusion and CO2 diffusion in pure water, the diffusion coefficients of CO2 molecules in the water/ethanol mixture are in much better agreement with the experimental values of 1.4 - 1.5 × 10(-9) m(2)/s obtained for Champagne wines when the TIP5P model is employed. This difference was deemed to rely on the larger propensity of SPC/E water molecules to maintain the hydrogen-bonded network between water molecules and form new hydrogen bonds with ethanol, although statistical issues cannot be completely excluded. The remarkable agreement between the theoretical CO2 diffusion coefficients obtained within the TIP5P water/ethanol mixture and the experimental data specific to Champagne wines makes us infer that the diffusion coefficient in these emblematic hydroalcoholic sparkling beverages is expected to remain roughly constant whathever their proportions in sugars, glycerol, or peptides.
The CO Transition from Diffuse Molecular Gas to Dense Clouds
Rice, Johnathan S.; Federman, Steven
2017-06-01
The atomic to molecular transitions occurring in diffuse interstellar gas surrounding molecular clouds are affected by the local physical conditions (density and temperature) and the radiation field penetrating the material. Our optical observations of CH, CH^{+}, and CN absorption from McDonald Observatory and the European Southern Observatory are useful tracers of this gas and provide the velocity structure needed for analyzing lower resolution ultraviolet observations of CO and H_{2} absorption from Far Ultraviolet Spectroscopic Explorer. We explore the changing environment between diffuse and dense gas by using the column densities and excitation temperatures from CO and H_{2} to determine the gas density. The resulting gas densities from this method are compared to densities inferred from other methods such as C_{2} and CN chemistry. The densities allow us to interpret the trends from the combined set of tracers. Groupings of sight lines, such as those toward h and χ Persei or Chameleon provide a chance for further characterization of the environment. The Chameleon region in particular helps illuminate CO-dark gas, which is not associated with emission from H I at 21 cm or from CO at 2.6 mm. Expanding this analysis to include emission data from the GOT C+ survey allows the further characterization of neutral diffuse gas, including CO-dark gas.
Diffuse Gliomas for Nonneuropathologists: The New Integrated Molecular Diagnostics.
Lee, Sunhee C
2018-05-18
Diffuse gliomas comprise the bulk of "brain cancer" in adults. The recent update to the 4th edition of the World Health Organization's classification of tumors of the central nervous system reflects an unprecedented change in the landscape of the diagnosis and management of diffuse gliomas that will affect all those involved in the management and care of patients. Of the recently discovered gene alterations, mutations in the Krebs cycle enzymes isocitrate dehydrogenases (IDHs) 1 and 2 have fundamentally changed the way the gliomas are understood and classified. Incorporating information on a few genetic parameters (IDH, ATRX and/or p53, and chromosome 1p19q codeletion), a relatively straightforward diagnostic algorithm has been generated with robust and reproducible results that correlate with patients' survival far better than relying on conventional histology alone. Evidence also supports the conclusion that the vast majority of diffuse gliomas without IDH mutations (IDH-wild-type astrocytomas) behave like IDH-wild-type glioblastomas ("molecular GBM"). Together, these changes reflect a big shift in the practice of diagnostic neuropathology in which tumor risk stratification aligns better with molecular information than histology/grading. The purpose of this review is to provide the readers with a brief synopsis of the changes in the 2016 World Health Organization update with an emphasis on diffuse gliomas and to summarize key gene abnormalities on which these classifications are based. Practical points involved in day-to-day diagnostic workup are also discussed, along with a comparison of the various diagnostic tests, including immunohistochemistry, with an emphasis on targeted next-generation sequencing panel technology as a future universal approach.
Directory of Open Access Journals (Sweden)
Zhenfeng Zheng
Full Text Available BACKGROUND: To explore the characteristics of diffusion tensor imaging (DTI and magnetic resonance (MR imaging in healthy native kidneys. METHODS: Seventy-three patients without chronic kidney disease underwent DTI-MRI with spin echo-echo planar (SE-EPI sequences accompanied by an array spatial sensitivity encoding technique (ASSET. Cortical and medullary mean, axial and radial diffusivity (MD, AD and RD, fractional anisotropy (FA and primary, secondary and tertiary eigenvalues (λ1, λ2, λ3 were analysed in both kidneys and in different genders. RESULTS: Cortical MD, λ2, λ3, and RD values were higher than corresponding medullary values. The cortical FA value was lower than the medullary FA value. Medullary λ1 and RD values in the left kidney were lower than in the right kidney. Medullary λ2, and λ3 values in women were higher than those in men. Medullary FA values in women were lower than those in men. Medullary FA (r = 0.351, P = 0.002 and λ1 (r = 0.277, P = 0.018 positively correlated with eGFR. Medullary FA (r = -0.25, P = 0.033 negatively correlated with age. CONCLUSIONS: Renal water molecular diffusion differences exist in human kidneys and genders. Age and eGFR correlate with medullary FA and primary eigenvalue.
Translationally invariant and non-translationally invariant empirical effective interactions
International Nuclear Information System (INIS)
Golin, M.; Zamick, L.
1975-01-01
In this work empirical deficiencies of the core-renormalized realistic effective interactions are examined and simple corrective potentials are sought. The inability of the current realistic interactions to account for the energies of isobaric analog states is noted, likewise they are unable to reproduce the changes in the single-particle energies, as one goes from one closed shell to another. It is noted that the Schiffer interaction gives better results for these gross properties and this is attributed to a combination of several facts. First, to the inclusion of long range terms in the Schiffer potential, then to the presence of relative p-state terms (l=1), in addition to the usual relative s-state terms (l=0). The strange shape of the above interaction is further attributed to the fact that it is translationally invariant whereas the theory of core-polarization yields non-translationally invariant potentials. Consequently, as a correction to the monopole deficiencies of the realistic interactions the term Vsub(mon)=ar 2 (1)r 2 (2)+r 2 (1)+β[r 4 (1)r 2 (2)r 4 (2) ] is proposed. (Auth.)
Molecular dynamics investigation of tracer diffusion in a simple liquid
International Nuclear Information System (INIS)
Ould-Kaddour, F.; Barrat, J.L.
1991-05-01
Extensive Molecular-Dynamics (MD) simulations have been carried out for a model trace-solvent system made up of 100 solvent molecules and 8 tracer molecules interacting through truncated Lennard-Jones potentials. The influence of the size ratio between solute and solvent, of their mass ratio and of the solvent viscosity on the diffusivity of a small tracer were investigated. Positive deviations from a Stokes-Einstein behaviour are observed, in qualitative agreement with experimental observations. It was also observed that as tracer and solvent become increasingly dissimilar, their respective dynamics becomes decoupled. We suggest that such decouplings can be interpreted by writing their mobility of the tracer as the sum of two terms, the first one arising from a coupling between tracer dynamics and hydrodynamics modes of the solvent, and the second one describing jump motion in a locally nearly frozen environment. (author). 17 refs, 4 figs, 6 tabs
Empirical molecular-dynamics study of diffusion in liquid semiconductors
Yu, W.; Wang, Z. Q.; Stroud, D.
1996-11-01
We report the results of an extensive molecular-dynamics study of diffusion in liquid Si and Ge (l-Si and l-Ge) and of impurities in l-Ge, using empirical Stillinger-Weber (SW) potentials with several choices of parameters. We use a numerical algorithm in which the three-body part of the SW potential is decomposed into products of two-body potentials, thereby permitting the study of large systems. One choice of SW parameters agrees very well with the observed l-Ge structure factors. The diffusion coefficients D(T) at melting are found to be approximately 6.4×10-5 cm2/s for l-Si, in good agreement with previous calculations, and about 4.2×10-5 and 4.6×10-5 cm2/s for two models of l-Ge. In all cases, D(T) can be fitted to an activated temperature dependence, with activation energies Ed of about 0.42 eV for l-Si, and 0.32 or 0.26 eV for two models of l-Ge, as calculated from either the Einstein relation or from a Green-Kubo-type integration of the velocity autocorrelation function. D(T) for Si impurities in l-Ge is found to be very similar to the self-diffusion coefficient of l-Ge. We briefly discuss possible reasons why the SW potentials give D(T)'s substantially lower than ab initio predictions.
DEFF Research Database (Denmark)
Martinez-Lopez, Brais; Huguet, P.; Gontard, N.
2016-01-01
Raman microspectroscopy was used to determine the Fickian diffusivity of two families of low molecular weight molecules through amorphous polystyrene in the rubbery state. Different effects of the temperature on diffusivity for each of the families suggested that molecular mobility is controlled...... by both the volume and flexibility of the diffusing substance when the movement of polymer chains can generate stress induced deformation of molecules. The diffusing molecules were represented as Newtonian spring–bead systems, which allowed us to quantify their flexibility, in function of the vibration...... frequency of their bonds by reconstructing their theoretical spectra. Results showed that the use of molecular descriptors that take into account flexibility rather than the most stable conformation of the diffusing molecules may improve the description of the diffusion behavior caused by variations...
Can molecular diffusion explain Space Shuttle plume spreading?
Meier, R. R.; Plane, John M. C.; Stevens, Michael H.; Paxton, L. J.; Christensen, A. B.; Crowley, G.
2010-04-01
The satellite-borne Global Ultraviolet Imager (GUVI) has produced more than 20 images of NASA Space Shuttle main engine plumes in the lower thermosphere. These reveal atomic hydrogen and, by inference, water vapor transport over hemispherical-scale distances with speeds much faster than expected from models of thermospheric wind motions. Furthermore, the hydrogen plumes expand rapidly. We find rates that exceed the horizontal diffusion speed at nominal plume altitudes of 104-112 km. Kelley et al. (2009) have proposed a 2-D turbulence mechanism to explain the observed spreading rates (and rapid advection) of the plumes. But upon further investigation, we conclude that H atom diffusion can indeed account for the observed expansion rates by recognizing that vertical diffusion quickly conveys atoms to higher altitudes where horizontal diffusion is much more rapid. We also find evidence for H atom production directly during the Shuttle's main engine burn.
Energy Technology Data Exchange (ETDEWEB)
Neudert, Oliver; Stapf, Siegfried; Mattea, Carlos, E-mail: carlos.mattea@tu-ilmenau.de [Fachgebiet Technische Physik II/Polymerphysik, Institute of Physics, Technische Universitaet Ilmenau, PO Box 100 565, 98684 Ilmenau (Germany)
2011-03-15
Molecular exchange properties and diffusion of n-hexane embedded in a bimodal pore structure with characteristic length scales in the order of nano and micrometres, respectively, formed by packing of zeolite particles, are studied. Two-dimensional (2D) nuclear magnetic resonance (NMR) diffusion correlation experiments together with relaxation-diffusion correlation experiments are performed at low magnetic field using a single-sided NMR scanner. The exchange time covers a range from 10{sup -3} to 10{sup -1} s. The molecular exchange properties are modulated by transport inside the zeolite particles. Different exchange regimes are observed for molecules starting from different positions inside the porous sample. The influence of the spin-lattice relaxation properties of the fluid molecules inside the zeolite particles on the signal intensity is also studied. A Monte Carlo simulation of the exchange process is performed and is used to support the analysis of the experimental data.
A dirty window diffuse and translucent molecular gas in the interstellar medium
Magnani, Loris
2017-01-01
This book provides an introduction to the physics of interstellar gas in the Galaxy. It deals with the diffuse interstellar medium which supplies a complex environment for exploring the neutral gas content of a galaxy like the Milky Way and the techniques necessary for studying this non-stellar component. After an initial exposition of the phases of the interstellar medium and the role of gas in a spiral galaxy, the authors discuss the transition from atomic to molecular gas. They then consider basic radiative transfer and molecular spectroscopy with particular emphasis on the molecules useful for studying low-density molecular gas. Observational techniques for investigating the gas and the dust component of the diffuse interstellar medium throughout the electromagnetic spectrum are explored emphasizing results from the recent Herschel and Planck missions. A brief exposition on dust in the diffuse interstellar medium is followed by a discussion of molecular clouds in general and high-latitude molecular clouds...
Molecular dynamics simulation of diffusion bonding of Al–Cu interface
International Nuclear Information System (INIS)
Li, Chang; Li, Dongxu; Tao, Xiaoma; Chen, Hongmei; Ouyang, Yifang
2014-01-01
The effects of temperature on diffusion bonding of Al–Cu interface have been investigated by using molecular dynamics (MD) technique with the embedded atomic method (EAM) potentials. The simulated results indicate that the Cu atoms predominantly diffuse into the Al side in the process of diffusion bonding, and the thickness of the interfacial region depends on temperature, with higher temperatures resulting in larger thickness. In the course of diffusion bonding, the interfacial region became disordered. In addition, the Cu atoms diffuse at low ratios but can deeply diffuse into the interior of Al, and the Al atoms diffuse at high ratios but hardly diffuse into the interior of Cu. The results show that the appropriate temperature range for diffusion bonding of Al–Cu interface is 750–800 K, and the diffusion activation energies of Al and Cu are 0.77 eV and 0.50 eV, respectively. Finally, in this work, three diffusion mechanisms of Cu atoms in Al lattice have been found and the main diffusion mechanism is the nearest neighbor hopping mechanism. (paper)
Reaction-diffusion systems in intracellular molecular transport and control.
Soh, Siowling; Byrska, Marta; Kandere-Grzybowska, Kristiana; Grzybowski, Bartosz A
2010-06-07
Chemical reactions make cells work only if the participating chemicals are delivered to desired locations in a timely and precise fashion. Most research to date has focused on active-transport mechanisms, although passive diffusion is often equally rapid and energetically less costly. Capitalizing on these advantages, cells have developed sophisticated reaction-diffusion (RD) systems that control a wide range of cellular functions-from chemotaxis and cell division, through signaling cascades and oscillations, to cell motility. These apparently diverse systems share many common features and are "wired" according to "generic" motifs such as nonlinear kinetics, autocatalysis, and feedback loops. Understanding the operation of these complex (bio)chemical systems requires the analysis of pertinent transport-kinetic equations or, at least on a qualitative level, of the characteristic times of the constituent subprocesses. Therefore, in reviewing the manifestations of cellular RD, we also describe basic theory of reaction-diffusion phenomena.
Chen, Tai-Yen; Jung, Won; Santiago, Ace George; Yang, Feng; Krzemiński, Łukasz; Chen, Peng
2015-11-12
Single-molecule tracking (SMT) of fluorescently tagged cytoplasmic proteins can provide valuable information on the underlying biological processes in living cells via subsequent analysis of the displacement distributions; however, the confinement effect originated from the small size of a bacterial cell skews the protein's displacement distribution and complicates the quantification of the intrinsic diffusive behaviors. Using the inverse transformation method, we convert the skewed displacement distribution (for both 2D and 3D imaging conditions) back to that in free space for systems containing one or multiple (non)interconverting Brownian diffusion states, from which we can reliably extract the number of diffusion states as well as their intrinsic diffusion coefficients and respective fractional populations. We further demonstrate a successful application to experimental SMT data of a transcription factor in living E. coli cells. This work allows a direct quantitative connection between cytoplasmic SMT data with diffusion theory for analyzing molecular diffusive behavior in live bacteria.
A model for self-diffusion of guanidinium-based ionic liquids: a molecular simulation study.
Klähn, Marco; Seduraman, Abirami; Wu, Ping
2008-11-06
We propose a novel self-diffusion model for ionic liquids on an atomic level of detail. The model is derived from molecular dynamics simulations of guanidinium-based ionic liquids (GILs) as a model case. The simulations are based on an empirical molecular mechanical force field, which has been developed in our preceding work, and it relies on the charge distribution in the actual liquid. The simulated GILs consist of acyclic and cyclic cations that were paired with nitrate and perchlorate anions. Self-diffusion coefficients are calculated at different temperatures from which diffusive activation energies between 32-40 kJ/mol are derived. Vaporization enthalpies between 174-212 kJ/mol are calculated, and their strong connection with diffusive activation energies is demonstrated. An observed formation of cavities in GILs of up to 6.5% of the total volume does not facilitate self-diffusion. Instead, the diffusion of ions is found to be determined primarily by interactions with their immediate environment via electrostatic attraction between cation hydrogen and anion oxygen atoms. The calculated average time between single diffusive transitions varies between 58-107 ps and determines the speed of diffusion, in contrast to diffusive displacement distances, which were found to be similar in all simulated GILs. All simulations indicate that ions diffuse by using a brachiation type of movement: a diffusive transition is initiated by cleaving close contacts to a coordinated counterion, after which the ion diffuses only about 2 A until new close contacts are formed with another counterion in its vicinity. The proposed diffusion model links all calculated energetic and dynamic properties of GILs consistently and explains their molecular origin. The validity of the model is confirmed by providing an explanation for the variation of measured ratios of self-diffusion coefficients of cations and paired anions over a wide range of values, encompassing various ionic liquid classes
Lattice dynamics and thermal diffuse scattering for molecular crystals
International Nuclear Information System (INIS)
Kroon, P.A.
1977-01-01
Thermal diffuse scattering (TDS) corrections on the observed reflection intensities in the accurate determination of crystal structures by X-ray diffraction are emphasized. A lattice-dynamical model and procedure for lattice-dynamical calculations are set up. Expression for first- and second-order TDS intensity distributions are derived. A comparison with other models is made. First-order TDS corrections for naphtalene at 100 K are presented
Negligible fractionation of Kr and Xe isotopes by molecular diffusion in water
Tyroller, Lina; Brennwald, Matthias S.; Busemann, Henner; Maden, Colin; Baur, Heinrich; Kipfer, Rolf
2018-06-01
Molecular diffusion is a key transport process for noble gases in water. Such diffusive transport is often thought to cause a mass-dependent fractionation of noble gas isotopes that is inversely proportional to the square root of the ratio of their atomic mass, referred to as the square root relation. Previous studies, challenged the commonly held assumption that the square root relation adequately describes the behaviour of noble gas isotopes diffusing through water. However, the effect of diffusion on noble gas isotopes has only been determined experimentally for He, Ne and Ar to date, whereas the extent of fractionation of Kr and Xe has not been measured. In the present study the fractionation of Kr and Xe isotopes diffusing through water immobilised by adding agar was quantified through measuring the respective isotope ratio after diffusing through the immobilised water. No fractionation of Kr and Xe isotopes was observed, even using high-precision noble gas analytics. These results complement our current understanding on isotopic fractionation of noble gases diffusing through water. Therefore this complete data set builds a robust basis to describe molecular diffusion of noble gases in water in a physical sound manner which is fundamental to assess the physical aspects of gas dynamics in aquatic systems.
International Nuclear Information System (INIS)
Kubaschewski, O.
1983-01-01
The diffusion rate values of titanium, its compounds and alloys are summarized and tabulated. The individual chemical diffusion coefficients and self-diffusion coefficients of certain isotopes are given. Experimental methods are listed which were used for the determination of diffusion coefficients. Some values have been taken over from other studies. Also given are graphs showing the temperature dependences of diffusion and changes in the diffusion coefficient with concentration changes
Glitters of warm H2 in cold diffuse molecular gas
Falgarone, Edith; Beichman, Chaz; Boulanger, Francois; Combes, Francoise; Gry, Cecile; Helou, Georges; Laureijs, Rene; Pineau Des Forets, Guillaume; Valentijn, Edwin; Verstraete, Laurent
2004-01-01
Cold molecular hydrogen, a possibly dominant gas fraction in galaxies, does not radiate due to the symmetry and small moment of inertia of the molecule. The only tracers of cold H2, the rotational lines of CO and dust thermal emission operate only in metal-rich environments. By detecting the lowest
Dense fluid self-diffusion coefficient calculations using perturbation theory and molecular dynamics
Directory of Open Access Journals (Sweden)
COELHO L. A. F.
1999-01-01
Full Text Available A procedure to correlate self-diffusion coefficients in dense fluids by using the perturbation theory (WCA coupled with the smooth-hard-sphere theory is presented and tested against molecular simulations and experimental data. This simple algebraic expression correlates well the self-diffusion coefficients of carbon dioxide, ethane, propane, ethylene, and sulfur hexafluoride. We have also performed canonical ensemble molecular dynamics simulations by using the Hoover-Nosé thermostat and the mean-square displacement formula to compute self-diffusion coefficients for the reference WCA intermolecular potential. The good agreement obtained from both methods, when compared with experimental data, suggests that the smooth-effective-sphere theory is a useful procedure to correlate diffusivity of pure substances.
Krishna, R.; van Baten, J.M.
2011-01-01
Molecular Dynamics (MD) simulations were carried out to determine the self-diffusivitiy, Di,self, the Maxwell-Stefan diffusivity, Ði, and the Fick diffusivity, Di, for methane (C1), ethane (C2), propane (C3), n-butane (nC4), n-pentane (nC5), n-hexane (nC6), n-heptane (nC7), and cyclohexane (cC6) in
Molecular Dynamics Simulations of Grain Boundary and Bulk Diffusion in Metals.
Plimpton, Steven James
Diffusion is a microscopic mass transport mechanism that underlies many important macroscopic phenomena affecting the structural, electrical, and mechanical properties of metals. This thesis presents results from atomistic simulation studies of diffusion both in bulk and in the fast diffusion paths known as grain boundaries. Using the principles of molecular dynamics single boundaries are studied and their structure and dynamic properties characterized. In particular, tilt boundary bicrystal and bulk models of fcc Al and bcc alpha-Fe are simulated. Diffusion coefficients and activation energies for atomic motion are calculated for both models and compared to experimental data. The influence of the interatomic pair potential on the diffusion is studied in detail. A universal relation between the melting temperature that a pair potential induces in a simulated bulk model and the potential energy barrier height for atomic hopping is derived and used to correlate results for a wide variety of pair potentials. Using these techniques grain boundary and bulk diffusion coefficients for any fcc material can be estimated from simple static calculations without the need to perform more time-consuming dynamic simulations. The influences of two other factors on grain boundary diffusion are also studied because of the interest of the microelectronics industry in the diffusion related reliability problem known as electromigration. The first factor, known to affect the self diffusion rate of Al, is the presence of Cu impurity atoms in Al tilt boundaries. The bicrystal model for Al is seeded randomly with Cu atoms and a simple hybrid Morse potential used to model the Al-Cu interaction. While some effect due to the Cu is noted, it is concluded that pair potentials are likely an inadequate approximation for the alloy system. The second factor studied is the effect of the boundary orientation angle on the diffusion rate. Symmetric bcc Fe boundaries are relaxed to find optimal
Molecular diffusion of stable water isotopes in polar firn as a proxy for past temperatures
Holme, Christian; Gkinis, Vasileios; Vinther, Bo M.
2018-03-01
Polar precipitation archived in ice caps contains information on past temperature conditions. Such information can be retrieved by measuring the water isotopic signals of δ18O and δD in ice cores. These signals have been attenuated during densification due to molecular diffusion in the firn column, where the magnitude of the diffusion is isotopologue specific and temperature dependent. By utilizing the differential diffusion signal, dual isotope measurements of δ18O and δD enable multiple temperature reconstruction techniques. This study assesses how well six different methods can be used to reconstruct past surface temperatures from the diffusion-based temperature proxies. Two of the methods are based on the single diffusion lengths of δ18O and δD , three of the methods employ the differential diffusion signal, while the last uses the ratio between the single diffusion lengths. All techniques are tested on synthetic data in order to evaluate their accuracy and precision. We perform a benchmark test to thirteen high resolution Holocene data sets from Greenland and Antarctica, which represent a broad range of mean annual surface temperatures and accumulation rates. Based on the benchmark test, we comment on the accuracy and precision of the methods. Both the benchmark test and the synthetic data test demonstrate that the most precise reconstructions are obtained when using the single isotope diffusion lengths, with precisions of approximately 1.0 °C . In the benchmark test, the single isotope diffusion lengths are also found to reconstruct consistent temperatures with a root-mean-square-deviation of 0.7 °C . The techniques employing the differential diffusion signals are more uncertain, where the most precise method has a precision of 1.9 °C . The diffusion length ratio method is the least precise with a precision of 13.7 °C . The absolute temperature estimates from this method are also shown to be highly sensitive to the choice of fractionation factor
Measurement of molecular diffusion coefficients of carbon dioxide and methane in heavy oil
Energy Technology Data Exchange (ETDEWEB)
Gu, Y.; Tharanivasan, A.K.; Yang, C. [Regina Univ., SK (Canada)
2004-07-01
Vapour extraction (VAPEX) is a solvent-based thermal recovery process which is considered to be a viable process for recovering heavy oil. In order to develop a solvent-based enhanced oil recovery (EOR) operation, it is necessary to know the rate and extent of oil mobilization by the solvent. The molecular diffusion coefficient of solvent gas in heavy oil must be known. In this study, the pressure decay method was used to measure the molecular diffusivity of a gas solvent in heavy oil by monitoring the decaying pressure. The pressure decay method is a non-intrusive method in which physical contact is made between the gas solvent and the heavy oil. The pressure versus time data are measured until the heavy oil reaches complete saturation. The diffusion coefficient can be determined from the measured data and a mathematical model. In this study, the molecular diffusion coefficients of carbon dioxide-heavy oil and methane-heavy oil systems were measured and compared. The experiments were performed in closed high-pressure cells at constant reservoir temperature. An analytical solution was also obtained to predict the pressure in the gas phase and for the boundary conditions at the solvent-heavy oil interface for each solvent. Solvent diffusivity was determined by finding the best match of the numerically predicted and experimentally measured pressures.
RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials
Dubbeldam, D.; Calero, S.; Ellis, D.E.; Snurr, R.Q.
2016-01-01
A new software package, RASPA, for simulating adsorption and diffusion of molecules in flexible nanoporous materials is presented. The code implements the latest state-of-the-art algorithms for molecular dynamics and Monte Carlo (MC) in various ensembles including symplectic/measure-preserving
Energy Technology Data Exchange (ETDEWEB)
Barbante, Paolo [Dipartimento di Matematica, Politecnico di Milano - Piazza Leonardo da Vinci 32 - 20133 Milano (Italy); Frezzotti, Aldo; Gibelli, Livio [Dipartimento di Scienze e Tecnologie Aerospaziali, Politecnico di Milano - Via La Masa 34 - 20156 Milano (Italy)
2014-12-09
The unsteady evaporation of a thin planar liquid film is studied by molecular dynamics simulations of Lennard-Jones fluid. The obtained results are compared with the predictions of a diffuse interface model in which capillary Korteweg contributions are added to hydrodynamic equations, in order to obtain a unified description of the liquid bulk, liquid-vapor interface and vapor region. Particular care has been taken in constructing a diffuse interface model matching the thermodynamic and transport properties of the Lennard-Jones fluid. The comparison of diffuse interface model and molecular dynamics results shows that, although good agreement is obtained in equilibrium conditions, remarkable deviations of diffuse interface model predictions from the reference molecular dynamics results are observed in the simulation of liquid film evaporation. It is also observed that molecular dynamics results are in good agreement with preliminary results obtained from a composite model which describes the liquid film by a standard hydrodynamic model and the vapor by the Boltzmann equation. The two mathematical model models are connected by kinetic boundary conditions assuming unit evaporation coefficient.
Molecular dynamics simulations of adsorption and diffusion of Xe on bare and Xe covered Pt(111)
Jong, de F.; Jansen, A.P.J.
1994-01-01
Molecular dynamics simulations are used to calculate adsorption probabilities and diffusion coefficients of Xe on Pt(111) and Xe/Pt(111). Experimental trends are reproduced. The adsorption mechanism is found to be the modified Kisliuk model, with the addition of direct and indirect insertion in the
Self-diffusion in monodisperse three-dimensional magnetic fluids by molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Dobroserdova, A.B. [Ural Federal University, Lenin Av. 51, Ekaterinburg (Russian Federation); Kantorovich, S.S., E-mail: alla.dobroserdova@urfu.ru [Ural Federal University, Lenin Av. 51, Ekaterinburg (Russian Federation); University of Vienna, Sensengasse 8, Vienna (Austria)
2017-06-01
In the present work we study the self-diffusion behaviour in the three-dimensional monodisperse magnetic fluids using the Molecular Dynamics Simulation and Density Functional Theory. The peculiarity of computer simulation is to study two different systems: dipolar and soft sphere ones. In the theoretical method, it is important to choose the approximation for the main structures, which are chains. We compare the theoretical results and the computer simulation data for the self-diffusion coefficient as a function of the particle volume fraction and magnetic dipole-dipole interaction parameter and find the qualitative and quantitative agreement to be good. - Highlights: • The paper deals with the study of the self-diffusion in monodisperse three-dimensional magnetic fluids. • The theoretical approach contains the free energy density functional minimization. • Computer simulations are performed by the molecular dynamics method. • We have a good qualitative and quantitative agreement between the theoretical results and computer simulation data.
Calculation of the mutual diffusion coefficient by equilibrium and nonequilibrium molecular dynamics
International Nuclear Information System (INIS)
Erpenbeck, J.J.; Kincaid, J.M.
1985-01-01
A nonequilibrium molecular dynamics method for the calculation of the mutual diffusion coefficient for a mixture of hard spheres is described. The method is applied to a 50-50 mixture of equidiameter particles having a mass ratio of 0.1 for the two species, at a volume of three times close-packing. By extrapolating the results to the limit of vanishing concentration gradient and infinite system size, we obtain a value in statistical agreement with the result obtained using a Green-Kubo molecular dynamics procedure which is also described. The nonequilibrium calculation yields a mutual diffusion coefficient which decreases slightly with increasing concentration gradient. The Green-Kubo time correlation function for mutual diffusion displays a slow decay with time, qualitatively similar to the long-time tail which has been predicted by the hydrodynamic theory of Pomeau
Calculation of the mutual diffusion coefficient by equilibrium and nonequilibrium molecular dynamics
International Nuclear Information System (INIS)
Erpenbeck, J.J.; Kincaid, J.M.
1986-01-01
A nonequilibrium molecular dynamics method for the calculation of the mutual diffusion coefficient for a mixture of hard spheres is described. The method is applied to a 50-50 mixture of equidiameter particles having a mass ratio of 0.1 for the two species, at a volume of three times close-packing. By extrapolating the results to the limit of vanishing concentration gradient and infinite system size, we obtain a value in statistical agreement with the result obtained using a Green-Kubo molecular dynamics procedure, which is also described. The nonequilibrium calculation yields a mutual diffusion coefficient which decreases slightly with increasing concentration gradient. The Green-Kubo timecorrelation function for mutual diffusion displays a slow decay with time, qualitatively similar to the long-time tail which has been predicted by the hydrodynamic theory of Pomeau
Carbon diffusion in molten uranium: an ab initio molecular dynamics study
Garrett, Kerry E.; Abrecht, David G.; Kessler, Sean H.; Henson, Neil J.; Devanathan, Ram; Schwantes, Jon M.; Reilly, Dallas D.
2018-04-01
In this work we used ab initio molecular dynamics within the framework of density functional theory and the projector-augmented wave method to study carbon diffusion in liquid uranium at temperatures above 1600 K. The electronic interactions of carbon and uranium were described using the local density approximation (LDA). The self-diffusion of uranium based on this approach is compared with literature computational and experimental results for liquid uranium. The temperature dependence of carbon and uranium diffusion in the melt was evaluated by fitting the resulting diffusion coefficients to an Arrhenius relationship. We found that the LDA calculated activation energy for carbon was nearly twice that of uranium: 0.55 ± 0.03 eV for carbon compared to 0.32 ± 0.04 eV for uranium. Structural analysis of the liquid uranium-carbon system is also discussed.
Self-consistent molecular dynamics calculation of diffusion in higher n-alkanes.
Kondratyuk, Nikolay D; Norman, Genri E; Stegailov, Vladimir V
2016-11-28
Diffusion is one of the key subjects of molecular modeling and simulation studies. However, there is an unresolved lack of consistency between Einstein-Smoluchowski (E-S) and Green-Kubo (G-K) methods for diffusion coefficient calculations in systems of complex molecules. In this paper, we analyze this problem for the case of liquid n-triacontane. The non-conventional long-time tails of the velocity autocorrelation function (VACF) are found for this system. Temperature dependence of the VACF tail decay exponent is defined. The proper inclusion of the long-time tail contributions to the diffusion coefficient calculation results in the consistency between G-K and E-S methods. Having considered the major factors influencing the precision of the diffusion rate calculations in comparison with experimental data (system size effects and force field parameters), we point to hydrogen nuclear quantum effects as, presumably, the last obstacle to fully consistent n-alkane description.
Diffusion of hydrogen, hydrogen sulfide and large molecular weight anions in bentonite
International Nuclear Information System (INIS)
Eriksen, T.E.; Jacobsson, A.
1982-01-01
The diffusivities of HS - and H 2 have been determined from profile analysis and steady state transport experiments. The diffusivity of HS - was found to be 9x10 - 12 and 4x10xsec 1 in MX-80 and Erbsloeh bentonite respectively. The results are in fair agreement with the results earlier obtained for Cl - and I - . The H 2 diffusivity calculated from steady state transport was found to be surprisingly low (3.6x10 - 12 m 2 xsec - 1 ). Various heavy anions with molecular weights 290-30x10 3 were found to migrate through MX-80 bentonite with diffusivities in the range (2,1-0,75)x10 - 15 m 2 xsec - 1 . (Author)
Nikonov, Eduard G.; Pavluš, Miron; Popovičová, Mária
2018-02-01
One of the varieties of pores, often found in natural or artificial building materials, are the so-called blind pores of dead-end or saccate type. Three-dimensional model of such kind of pore has been developed in this work. This model has been used for simulation of water vapor interaction with individual pore by molecular dynamics in combination with the diffusion equation method. Special investigations have been done to find dependencies between thermostats implementations and conservation of thermodynamic and statistical values of water vapor - pore system. The two types of evolution of water - pore system have been investigated: drying and wetting of the pore. Full research of diffusion coefficient, diffusion velocity and other diffusion parameters has been made.
Diffusion constant in hot and dense hadronic matter. A hadro-molecular-dynamic calculation
International Nuclear Information System (INIS)
Sasaki, N.; Miyamura, O.; Muroya, S.; Nonaka, C.
2002-01-01
We evaluate baryon/charge diffusion constant of dense and hot hadronic matter based on the molecular dynamical method by using a hadronic collision generator which describes nuclear collisions at energies 10 1-2 GeV/A and satisfies detailed balance at low temperatures (T ≤ 200 MeV). For the hot and dense hadronic matter of the temperature range, T = 100 - 200 MeV and baryon number density, n B =0.16 fm -3 - 0.32 fm -3 , charge diffusion constant D gradually increases from 0.5 fmc to 2 fmc with temperature and is almost independent of baryon number density. Based on the obtained diffusion constant we make simple discussions on the diffusion of charge fluctuation in ultrarelativistic nuclear collisions. (author)
Molecular dynamics simulation of helium and oxygen diffusion in UO{sub 2+}-{sub x}
Energy Technology Data Exchange (ETDEWEB)
Govers, K., E-mail: kgovers@sckcen.b [Service de Metrologie Nucleaire (CP 165/84), Universite Libre de Bruxelles, 50 av. F.D. Roosevelt, B-1050 Bruxelles (Belgium); Institute for Nuclear Materials Sciences, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Lemehov, S. [Institute for Nuclear Materials Sciences, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Hou, M. [Physique des Solides Irradies et des Nanostructures (CP 234), Universite Libre de Bruxelles, Bd du Triomphe, B-1050 Bruxelles (Belgium); Verwerft, M. [Institute for Nuclear Materials Sciences, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium)
2009-12-15
Atomic scale simulation techniques based on empirical potentials have been considered in the present work to get insight on helium diffusion in uranium dioxide. By varying the stoichiometry, together with the system temperature, the performed molecular dynamics simulations indicate two diffusion regimes for He. The first one presents a low activation energy (0.5 eV) and suggests oxygen vacancies assisted migration. This regime seems to provide the major contribution to diffusion when structural defects are present (extrinsic defects, imposed, e.g. by the stoichiometry). The second regime presents a higher activation energy, around 2 eV, and dominates in the higher temperature range or at perfect stoichiometry, suggesting an intrinsic migration process. Considering the dependence of He behaviour with oxygen defects, oxygen diffusion has been considered as well in the different stoichiometry domains. Finally, further investigations were made with nudged elastic bands calculations for a better interpretation of the operating migration mechanisms, both for He and O.
Molecular dynamics simulation of helium and oxygen diffusion in UO2±x
International Nuclear Information System (INIS)
Govers, K.; Lemehov, S.; Hou, M.; Verwerft, M.
2009-01-01
Atomic scale simulation techniques based on empirical potentials have been considered in the present work to get insight on helium diffusion in uranium dioxide. By varying the stoichiometry, together with the system temperature, the performed molecular dynamics simulations indicate two diffusion regimes for He. The first one presents a low activation energy (0.5 eV) and suggests oxygen vacancies assisted migration. This regime seems to provide the major contribution to diffusion when structural defects are present (extrinsic defects, imposed, e.g. by the stoichiometry). The second regime presents a higher activation energy, around 2 eV, and dominates in the higher temperature range or at perfect stoichiometry, suggesting an intrinsic migration process. Considering the dependence of He behaviour with oxygen defects, oxygen diffusion has been considered as well in the different stoichiometry domains. Finally, further investigations were made with nudged elastic bands calculations for a better interpretation of the operating migration mechanisms, both for He and O.
Symbol Synchronization for Diffusion-Based Molecular Communications.
Jamali, Vahid; Ahmadzadeh, Arman; Schober, Robert
2017-12-01
Symbol synchronization refers to the estimation of the start of a symbol interval and is needed for reliable detection. In this paper, we develop several symbol synchronization schemes for molecular communication (MC) systems where we consider some practical challenges, which have not been addressed in the literature yet. In particular, we take into account that in MC systems, the transmitter may not be equipped with an internal clock and may not be able to emit molecules with a fixed release frequency. Such restrictions hold for practical nanotransmitters, e.g., modified cells, where the lengths of the symbol intervals may vary due to the inherent randomness in the availability of food and energy for molecule generation, the process for molecule production, and the release process. To address this issue, we develop two synchronization-detection frameworks which both employ two types of molecule. In the first framework, one type of molecule is used for symbol synchronization and the other one is used for data detection, whereas in the second framework, both types of molecule are used for joint symbol synchronization and data detection. For both frameworks, we first derive the optimal maximum likelihood (ML) symbol synchronization schemes as performance upper bounds. Since ML synchronization entails high complexity, for each framework, we also propose three low-complexity suboptimal schemes, namely a linear filter-based scheme, a peak observation-based scheme, and a threshold-trigger scheme, which are suitable for MC systems with limited computational capabilities. Furthermore, we study the relative complexity and the constraints associated with the proposed schemes and the impact of the insertion and deletion errors that arise due to imperfect synchronization. Our simulation results reveal the effectiveness of the proposed synchronization schemes and suggest that the end-to-end performance of MC systems significantly depends on the accuracy of the symbol
Molecular dynamics simulation of three plastic additives' diffusion in polyethylene terephthalate.
Li, Bo; Wang, Zhi-Wei; Lin, Qin-Bao; Hu, Chang-Ying
2017-06-01
Accurate diffusion coefficient data of additives in a polymer are of paramount importance for estimating the migration of the additives over time. This paper shows how this diffusion coefficient can be estimated for three plastic additives [2-(2'-hydroxy-5'-methylphenyl) (UV-P), 2,6-di-tert-butyl-4-methylphenol (BHT) and di-(2-ethylhexyl) phthalate (DEHP)] in polyethylene terephthalate (PET) using the molecular dynamics (MD) simulation method. MD simulations were performed at temperatures of 293-433 K. The diffusion coefficient was calculated through the Einstein relationship connecting the data of mean-square displacement at different times. Comparison of the diffusion coefficients simulated by the MD simulation technique, predicted by the Piringer model and experiments, showed that, except for a few samples, the MD-simulated values were in agreement with the experimental values within one order of magnitude. Furthermore, the diffusion process for additives is discussed in detail, and four factors - the interaction energy between additive molecules and PET, fractional free volume, molecular shape and size, and self-diffusion of the polymer - are proposed to illustrate the microscopic diffusion mechanism. The movement trajectories of additives in PET cell models suggested that the additive molecules oscillate slowly rather than hopping for a long time. Occasionally, when a sufficiently large hole was created adjacently, the molecule could undergo spatial motion by jumping into the free-volume hole and consequently start a continuous oscillation and hop. The results indicate that MD simulation is a useful approach for predicting the microstructure and diffusion coefficient of plastic additives, and help to estimate the migration level of additives from PET packaging.
Molecular dynamics simulation of metallic impurity diffusion in liquid lead-bismuth eutectic (LBE)
Gao, Yun; Takahashi, Minoru; Cavallotti, Carlo; Raos, Guido
2018-04-01
Corrosion of stainless steels by lead-bismuth eutectic (LBE) is an important problem which depends, amongst other things, on the diffusion of the steel components inside this liquid alloy. Here we present the results of classical molecular dynamics simulations of the diffusion of Fe and Ni within LBE. The simulations complement experimental studies of impurity diffusion by our group and provide an atomic-level understanding of the relevant diffusion phenomena. They are based on the embedded atom method (EAM) to represent many-body interactions among atoms. The EAM potentials employed in our simulations have been validated against ab initio density functional calculations. We show that the experimental and simulation results for the temperature-dependent viscosity of LBE and the impurity diffusion coefficients can be reconciled by assuming that the Ni and Fe diffuse mainly as nanoscopic clusters below 1300 K. The average Fe and Ni cluster sizes decrease with increasing the temperature and there is essentially single-atom diffusion at higher temperatures.
Molecular dynamics simulation of self-diffusion coefficients for liquid metals
International Nuclear Information System (INIS)
Ju Yuan-Yuan; Zhang Qing-Ming; Gong Zi-Zheng; Ji Guang-Fu
2013-01-01
The temperature-dependent coefficients of self-diffusion for liquid metals are simulated by molecular dynamics methods based on the embedded-atom-method (EAM) potential function. The simulated results show that a good inverse linear relation exists between the natural logarithm of self-diffusion coefficients and temperature, though the results in the literature vary somewhat, due to the employment of different potential functions. The estimated activation energy of liquid metals obtained by fitting the Arrhenius formula is close to the experimental data. The temperature-dependent shear-viscosities obtained from the Stokes—Einstein relation in conjunction with the results of molecular dynamics simulation are generally consistent with other values in the literature. (atomic and molecular physics)
Penetration of Cosmic Rays into Dense Molecular Clouds: Role of Diffuse Envelopes
Ivlev, A. V.; Dogiel, V. A.; Chernyshov, D. O.; Caselli, P.; Ko, C.-M.; Cheng, K. S.
2018-03-01
A flux of cosmic rays (CRs) propagating through a diffuse ionized gas can excite MHD waves, thus generating magnetic disturbances. We propose a generic model of CR penetration into molecular clouds through their diffuse envelopes, and identify the leading physical processes controlling their transport on the way from a highly ionized interstellar medium to the dense interior of the cloud. The model allows us to describe a transition between a free streaming of CRs and their diffusive propagation, determined by the scattering on the self-generated disturbances. A self-consistent set of equations, governing the diffusive transport regime in an envelope and the MHD turbulence generated by the modulated CR flux, is characterized by two dimensionless numbers. We demonstrate a remarkable mutual complementarity of different mechanisms leading to the onset of the diffusive regime, which results in a universal energy spectrum of the modulated CRs. In conclusion, we briefly discuss implications of our results for several fundamental astrophysical problems, such as the spatial distribution of CRs in the Galaxy as well as the ionization, heating, and chemistry in dense molecular clouds. This paper is dedicated to the memory of Prof. Vadim Tsytovich.
International Nuclear Information System (INIS)
Lu, Jing; Liu, Dongmei; Yang, Xiaonan; Zhao, Ying; Liu, Haixing; Tang, Huan; Cui, Fuyi
2015-01-01
Graphical abstract: - Highlights: • Diffusion-limited aggregation is analyzed using molecular dynamic simulations. • The aggregation processand aggregate structure vary with particle size. • Particle-particle interaction and surface diffusion result in direct bonding. • Water-mediated interaction is responsible for the separation betweennanoparticles. - Abstract: Due to the limitations of experimental methods at the atomic level, research on the aggregation of small nanoparticles (D < 5 nm) in aqueous solutions is quite rare. The aggregation of small nanoparticles in aqueous solutions is very different than that of normal sized nanoparticles. The interfacial interactions play a dominant role in the aggregation of small nanoparticles. In this paper, molecular dynamics simulations, which can explore the microscopic behavior of nanoparticles during the diffusion-limited aggregation at an atomic level, were employed to reveal the aggregation mechanism of small nanoparticles in aqueous solutions. First, the aggregation processes and aggregate structure were depicted. Second, the particle–particle interaction and surface diffusion of nanoparticles during aggregation were investigated. Third, the water-mediated interactions during aggregation were ascertained. The results indicate that the aggregation of nanoparticle in aqueous solutions is affected by particle size. The strong particle–particle interaction and high surface diffusion result in the formation of particle–particle bonds of 2 nm TiO 2 nanoparticles, and the water-mediated interaction plays an important role in the aggregation process of 3 and 4 nm TiO 2 nanoparticles.
HIGH-ENERGY COSMIC-RAY DIFFUSION IN MOLECULAR CLOUDS: A NUMERICAL APPROACH
International Nuclear Information System (INIS)
Fatuzzo, M.; Melia, F.; Todd, E.; Adams, F. C.
2010-01-01
The propagation of high-energy cosmic rays (CRs) through giant molecular clouds constitutes a fundamental process in astronomy and astrophysics. The diffusion of CRs through these magnetically turbulent environments is often studied through the use of energy-dependent diffusion coefficients, although these are not always well motivated theoretically. Now, however, it is feasible to perform detailed numerical simulations of the diffusion process computationally. While the general problem depends upon both the field structure and particle energy, the analysis may be greatly simplified by dimensionless analysis. That is, for a specified purely turbulent field, the analysis depends almost exclusively on a single parameter-the ratio of the maximum wavelength of the turbulent field cells to the particle gyration radius. For turbulent magnetic fluctuations superimposed over an underlying uniform magnetic field, particle diffusion depends on a second dimensionless parameter that characterizes the ratio of the turbulent to uniform magnetic field energy densities. We consider both of these possibilities and parametrize our results to provide simple quantitative expressions that suitably characterize the diffusion process within molecular cloud environments. Doing so, we find that the simple scaling laws often invoked by the high-energy astrophysics community to model CR diffusion through such regions appear to be fairly robust for the case of a uniform magnetic field with a strong turbulent component, but are only valid up to ∼50 TeV particle energies for a purely turbulent field. These results have important consequences for the analysis of CR processes based on TeV emission spectra associated with dense molecular clouds.
Hydroxyl and molecular H2O diffusivity in a haploandesitic melt
Ni, Huaiwei; Xu, Zhengjiu; Zhang, Youxue
2013-02-01
H2O diffusion in a haploandesitic melt (a high-silica and Fe-free andesitic melt, NBO/T = 0.173) has been investigated at 1 GPa in a piston-cylinder apparatus. We adopted a double diffusion couple technique, in which one couple was composed of a nominally anhydrous glass with 0.01 wt.% H2O and a hydrous glass with 5.7 wt.% H2O, and the other contained the same nominally anhydrous glass and a hydrous glass with 3.3 wt.% H2O. Both couples were annealed in a single experimental run and hence experienced exactly the same P-T history, which is crucial for constraining the dependence of H2O diffusivity on water content. H2O concentration profiles were measured by both Fourier transform infrared (FTIR) microspectroscopy and confocal Raman microspectroscopy. Nearly identical profiles were obtained from Raman and FTIR methods for profile length >1 mm (produced at 1619-1842 K). By contrast, for profile lengths <100 μm (produced at 668-768 K), FTIR profiles show marked convolution effects compared to Raman profiles. A comparison between the short FTIR and Raman profiles indicates that the real spatial resolution (FWHM) of FTIR analyses is about 28 μm for a 7 μm wide aperture on ˜200 μm thick glasses. While the short profiles are not reliable for quantitative modeling, the long diffusion profiles at superliquidus temperatures can be fit reasonably well by a diffusivity model previously developed for felsic melts, in which molecular H2O (H2Om) is the only diffusive species and its diffusivity (D) increases exponentially with the content of total water (H2Ot). However, there is noticeable misfit of the data at low H2Ot concentrations, suggesting that OH diffusivity (DOH) cannot be neglected in this andesitic melt at high temperatures and low water contents. We hence develop a new fitting procedure that simultaneously fits both diffusion profiles from a single experimental run and accounts for the roles of both OH and H2Om diffusion. With this procedure, DOH/D is constrained
Ionic Diffusion in a Ternary Superionic Conductor: An {ital Ab Initio} Molecular Dynamics Study
Energy Technology Data Exchange (ETDEWEB)
Wengert, S.; Nesper, R.; Andreoni, W.; Parrinello, M. [Laboratorium fuer Anorganische Chemie, ETH Zuerich, 8092 Zuerich (Switzerland)]|[IBM Research Division, Zurich Research Laboratory, 8803 Rueschlikon (Switzerland)]|[Max-Planck-Institut fuer Festkoerperforschung, 70569 Stuttgart (Germany)
1996-12-01
We present Car-Parrinello molecular dynamics simulations of a novel superionic conductor, Li{sub 2{minus}2{ital x}}Mg{sub 1+{ital x}}Si ({ital x}{approximately}0.06), at different temperatures. The calculations clarify the nature of the ionic conduction and lead to the prediction of the first inorganic magnesium superionic conductor. In fact, both lithium and magnesium are found to act as charge carriers. The diffusion is fast and can be described as vacancy migration through directed jumps. The calculated diffusion constants for lithium are consistent with recent electrochemical measurements. {copyright} {ital 1996 The American Physical Society.}
Chude-Okonkwo, Uche A. K.; Malekian, Reza; Maharaj, B. T.
2015-12-01
Inspired by biological systems, molecular communication has been proposed as a new communication paradigm that uses biochemical signals to transfer information from one nano device to another over a short distance. The biochemical nature of the information transfer process implies that for molecular communication purposes, the development of molecular channel models should take into consideration diffusion phenomenon as well as the physical/biochemical kinetic possibilities of the process. The physical and biochemical kinetics arise at the interfaces between the diffusion channel and the transmitter/receiver units. These interfaces are herein termed molecular antennas. In this paper, we present the deterministic propagation model of the molecular communication between an immobilized nanotransmitter and nanoreceiver, where the emission and reception kinetics are taken into consideration. Specifically, we derived closed-form system-theoretic models and expressions for configurations that represent different communication systems based on the type of molecular antennas used. The antennas considered are the nanopores at the transmitter and the surface receptor proteins/enzymes at the receiver. The developed models are simulated to show the influence of parameters such as the receiver radius, surface receptor protein/enzyme concentration, and various reaction rate constants. Results show that the effective receiver surface area and the rate constants are important to the system's output performance. Assuming high rate of catalysis, the analysis of the frequency behavior of the developed propagation channels in the form of transfer functions shows significant difference introduce by the inclusion of the molecular antennas into the diffusion-only model. It is also shown that for t > > 0 and with the information molecules' concentration greater than the Michaelis-Menten kinetic constant of the systems, the inclusion of surface receptors proteins and enzymes in the models
Energy Technology Data Exchange (ETDEWEB)
Tringe, J.W., E-mail: tringe2@llnl.gov [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Ileri, N. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Levie, H.W. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Stroeve, P.; Ustach, V.; Faller, R. [Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Renaud, P. [Swiss Federal Institute of Technology, Lausanne, (EPFL) (Switzerland)
2015-08-18
Highlights: • WGA proteins in nanochannels modeled by Molecular Dynamics and Monte Carlo. • Protein surface coverage characterized by atomic force microscopy. • Models indicate transport characteristics depend strongly on surface coverage. • Results resolve of a four orders of magnitude difference in diffusion coefficient values. - Abstract: We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage. Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.
Directory of Open Access Journals (Sweden)
Le Novère Nicolas
2010-03-01
Full Text Available Abstract Background Most cellular signal transduction mechanisms depend on a few molecular partners whose roles depend on their position and movement in relation to the input signal. This movement can follow various rules and take place in different compartments. Additionally, the molecules can form transient complexes. Complexation and signal transduction depend on the specific states partners and complexes adopt. Several spatial simulator have been developed to date, but none are able to model reaction-diffusion of realistic multi-state transient complexes. Results Meredys allows for the simulation of multi-component, multi-feature state molecular species in two and three dimensions. Several compartments can be defined with different diffusion and boundary properties. The software employs a Brownian dynamics engine to simulate reaction-diffusion systems at the reactive particle level, based on compartment properties, complex structure, and hydro-dynamic radii. Zeroth-, first-, and second order reactions are supported. The molecular complexes have realistic geometries. Reactive species can contain user-defined feature states which can modify reaction rates and outcome. Models are defined in a versatile NeuroML input file. The simulation volume can be split in subvolumes to speed up run-time. Conclusions Meredys provides a powerful and versatile way to run accurate simulations of molecular and sub-cellular systems, that complement existing multi-agent simulation systems. Meredys is a Free Software and the source code is available at http://meredys.sourceforge.net/.
Ceccarelli, Michele; Barthel, Floris P.; Malta, Tathiane M.; Sabedot, Thais S.; Salama, Sofie R.; Murray, Bradley A.; Morozova, Olena; Newton, Yulia; Radenbaugh, Amie; Pagnotta, Stefano M.; Anjum, Samreen; Wang, Jiguang; Manyam, Ganiraju; Zoppoli, Pietro; Ling, Shiyung; Rao, Arjun A.; Grifford, Mia; Cherniack, Andrew D.; Zhang, Hailei; Poisson, Laila; Carlotti, Carlos Gilberto; Pretti da Cunha Tirapelli, Daniela; Rao, Arvind; Mikkelsen, Tom; Lau, Ching C.; Yung, W.K. Alfred; Rabadan, Raul; Huse, Jason; Brat, Daniel J.; Lehman, Norman L.; Barnholtz-Sloan, Jill S.; Zheng, Siyuan; Hess, Kenneth; Rao, Ganesh; Meyerson, Matthew; Beroukhim, Rameen; Cooper, Lee; Akbani, Rehan; Wrensch, Margaret; Haussler, David; Aldape, Kenneth D.; Laird, Peter W.; Gutmann, David H.; Noushmehr, Houtan; Iavarone, Antonio; Verhaak, Roel G.W.
2015-01-01
SUMMARY Therapy development for adult diffuse glioma is hindered by incomplete knowledge of somatic glioma driving alterations and suboptimal disease classification. We defined the complete set of genes associated with 1,122 diffuse grade II-III-IV gliomas from The Cancer Genome Atlas and used molecular profiles to improve disease classification, identify molecular correlations, and provide insights into the progression from low- to high-grade disease. Whole genome sequencing data analysis determined that ATRX but not TERT promoter mutations are associated with increased telomere length. Recent advances in glioma classification based on IDH mutation and 1p/19q co-deletion status were recapitulated through analysis of DNA methylation profiles, which identified clinically relevant molecular subsets. A subtype of IDH-mutant glioma was associated with DNA demethylation and poor outcome; a group of IDH-wildtype diffuse glioma showed molecular similarity to pilocytic astrocytoma and relatively favorable survival. Understanding of cohesive disease groups may aid improved clinical outcomes. PMID:26824661
Speciation of copper diffused in a bi-porous molecular sieve
International Nuclear Information System (INIS)
Huang, C.-H.; Paul Wang, H.; Wei, Y.-L.; Chang, J.-E.
2010-01-01
To better understand diffusion of copper in the micro- and mesopores, speciation of copper in a bi-porous molecular sieve (BPMS) possessing inter-connecting 3-D micropores (0.50-0.55 nm) and 2-D mesopores (4.1 nm) has been studied by X-ray absorption near edge structure (XANES) spectroscopy. It is found that about 77% (16% of CuO nanoparticles and 61% of CuO clusters) and 23% (CuO ads ) of copper can be diffused into the meso- and micropores, respectively, in the BPMS. At least two diffusion steps in the BPMS may be involved: (i) free diffusion of copper in the mesopores and (ii) diffusion-controlled copper migrating into the micropores of the BPMS. The XANES data also indicate that diffusion rate of copper in the BPMS (4.68x10 -5 g/s) is greater than that in the ZSM-5 (1.11x10 -6 g/s) or MCM-41 (1.17x10 -5 g/s).
Molecular dynamics simulation of nanoscale surface diffusion of heterogeneous adatoms clusters
International Nuclear Information System (INIS)
Imran, Muhammad; Hussain, Fayyaz; Ullah, Hafeez; Ahmad, Ejaz; Rashid, Muhammad; Ismail, Muhammad; Cai, Yongqing; Javid, M Arshad; Ahmad, S A
2016-01-01
Molecular dynamics simulation employing the embedded atom method potential is utilized to investigate nanoscale surface diffusion mechanisms of binary heterogeneous adatoms clusters at 300 K, 500 K, and 700 K. Surface diffusion of heterogeneous adatoms clusters can be vital for the binary island growth on the surface and can be useful for the formation of alloy-based thin film surface through atomic exchange process. The results of the diffusion process show that at 300 K, the diffusion of small adatoms clusters shows hopping, sliding, and shear motion; whereas for large adatoms clusters (hexamer and above), the diffusion is negligible. At 500 K, small adatoms clusters, i.e., dimer, show almost all possible diffusion mechanisms including the atomic exchange process; however no such exchange is observed for adatoms clusters greater than dimer. At 700 K, the exchange mechanism dominates for all types of clusters, where Zr adatoms show maximum tendency and Ag adatoms show minimum or no tendency toward the exchange process. Separation and recombination of one or more adatoms are also observed at 500 K and 700 K. The Ag adatoms also occupy pop-up positions over the adatoms clusters for short intervals. At 700 K, the vacancies are also generated in the vicinity of the adatoms cluster, vacancy formation, filling, and shifting can be observed from the results. (paper)
Speciation of copper diffused in a bi-porous molecular sieve
Huang, C.-H.; Paul Wang, H.; Wei, Y.-L.; Chang, J.-E.
2010-07-01
To better understand diffusion of copper in the micro- and mesopores, speciation of copper in a bi-porous molecular sieve (BPMS) possessing inter-connecting 3-D micropores (0.50-0.55 nm) and 2-D mesopores (4.1 nm) has been studied by X-ray absorption near edge structure (XANES) spectroscopy. It is found that about 77% (16% of CuO nanoparticles and 61% of CuO clusters) and 23% (CuO ads) of copper can be diffused into the meso- and micropores, respectively, in the BPMS. At least two diffusion steps in the BPMS may be involved: (i) free diffusion of copper in the mesopores and (ii) diffusion-controlled copper migrating into the micropores of the BPMS. The XANES data also indicate that diffusion rate of copper in the BPMS (4.68×10 -5 g/s) is greater than that in the ZSM-5 (1.11×10 -6 g/s) or MCM-41 (1.17×10 -5 g/s).
Diffusion of inorganic ion aqueous solution into hydrophilic polymer fiber and molecular orientation
International Nuclear Information System (INIS)
Kawaguchi, Akio
2001-01-01
The adsorption process of iodine to nylon 6 (polyamide-6), as well as deiodination process, has been an issue of controversy in the past half century from the view points related to the conversion of hydrogen bonding (α phase vs. γ phase). In the researches since late '80s, it has been revealed that the adsorption or inclusion of iodine to polyamides causes formations of various kind of structures to be called complexes whether they are crystalline or amorphous, and the formation of complex is reflected on the physical properties (especially on adsorption and ion mobility). Among them, it has been reported about both the doubly-oriented samples and the non-oriented samples that the ion diffusion causes molecular chain orientation during the complex formation. In the present experiment the change of molecular orientation in the early stage of the complex formation is studied by the time-resolved measurement with synchrotron radiation facility at SPring-8. Through-view and edge-view diffraction patterns of doubly oriented nylon 6 and non-oriented one were measured at 0.1 nm wavelength introducing I2-KI aqueous solution. It is observed that the formation of complex (i.e. diffusion of polyiodine) is attained in about 0.3 to 0.4 sec. even in non-oriented sample. From the analysis of the diffraction behavior, it is summarized that the inclusion of iodine into the crystalline phase of nylon 6 is possible from either sides of the molecular directions, namely normal diffusion and parallel diffusion. It is concluded that the diffusion and adsorption of inorganic ions including polyiodine to polyamide causes not only the formation of complexes in the crystalline phase but also give motive force to change structure in the surrounding non-crystalline region. (S. Funahashi)
Multiscale diffusion of a molecular probe in a crowded environment: a concept
Currie, Megan; Thao, Chang; Timerman, Randi; Welty, Robb; Berry, Brenden; Sheets, Erin D.; Heikal, Ahmed A.
2015-08-01
Living cells are crowded with macromolecules and organelles. Yet, it is not fully understood how macromolecular crowding affects the myriad of biochemical reactions, transport and the structural stability of biomolecules that are essential to cellular function and survival. These molecular processes, with or without electrostatic interactions, in living cells are therefore expected to be distinct from those carried out in test tube in dilute solutions where excluded volumes are absent. Thus there is an urgent need to understand the macromolecular crowding effects on cellular and molecular biophysics towards quantitative cell biology. In this report, we investigated how biomimetic crowding affects both the rotational and translation diffusion of a small probe (rhodamine green, RhG). For biomimetic crowding agents, we used Ficoll-70 (synthetic polymer), bovine serum albumin and ovalbumin (proteins) at various concentrations in a buffer at room temperature. As a control, we carried out similar measurements on glycerolenriched buffer as an environment with homogeneous viscosity as a function of glycerol concentration. The corresponding bulk viscosity was measured independently to test the validity of the Stokes-Einstein model of a diffusing species undergoing a random walk. For rotational diffusion (ps-ns time scale), we used time-resolved anisotropy measurements to examine potential binding of RhG as a function of the crowding agents (surface structure and size). For translational diffusion (μs-s time scale), we used fluorescence correlation spectroscopy for single-molecule fluctuation analysis. Our results allow us to examine the diffusion model of a molecular probe in crowded environments as a function of concentration, length scale, homogeneous versus heterogeneous viscosity, size and surface structures. These biomimetic crowding studies, using non-invasive fluorescence spectroscopy methods, represent an important step towards understanding cellular biophysics and
De Mezquia, D Alonso; Bou-Ali, M Mounir; Larrañaga, M; Madariaga, J A; Santamaría, C
2012-03-08
In this work we have measured the molecular diffusion coefficient of the n-alkane binary series nC(i)-nC(6), nC(i)-nC(10), and nC(i)-nC(12) at 298 K and 1 atm and a mass fraction of 0.5 by using the so-called sliding symmetric tubes technique. The results show that the diffusion coefficient at this concentration is proportional to the inverse viscosity of the mixture. In addition, we have also measured the diffusion coefficient of the systems nC(12)-nC(6), nC(12)-nC(7), and nC(12)-nC(8) as a function of concentration. From the data obtained, it is shown that the diffusion coefficient of the n-alkane binary mixtures at any concentration can be calculated from the molecular weight of the components and the dynamic viscosity of the corresponding mixture at 50% mass fraction.
On Medium Chemical Reaction in Diffusion-Based Molecular Communication: a Two-Way Relaying Example
Farahnak-Ghazani, Maryam; Aminian, Gholamali; Mirmohseni, Mahtab; Gohari, Amin; Nasiri-Kenari, Masoumeh
2016-01-01
Chemical reactions are a prominent feature of molecular communication (MC) systems, with no direct parallels in wireless communications. While chemical reactions may be used inside the transmitter nodes, receiver nodes or the communication medium, we focus on its utility in the medium in this paper. Such chemical reactions can be used to perform computation over the medium as molecules diffuse and react with each other (physical-layer computation). We propose the use of chemical reactions for...
Molecular dynamics on diffusive time scales from the phase-field-crystal equation.
Chan, Pak Yuen; Goldenfeld, Nigel; Dantzig, Jon
2009-03-01
We extend the phase-field-crystal model to accommodate exact atomic configurations and vacancies by requiring the order parameter to be non-negative. The resulting theory dictates the number of atoms and describes the motion of each of them. By solving the dynamical equation of the model, which is a partial differential equation, we are essentially performing molecular dynamics simulations on diffusive time scales. To illustrate this approach, we calculate the two-point correlation function of a fluid.
Energy Technology Data Exchange (ETDEWEB)
Kekenes-Huskey, P. M., E-mail: pkekeneshuskey@ucsd.edu [Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0636 (United States); Gillette, A. K. [Department of Mathematics, University of Arizona, Tucson, Arizona 85721-0089 (United States); McCammon, J. A. [Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0636 (United States); Department of Chemistry, Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0636 (United States)
2014-05-07
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
Fuson, Michael M.
2017-01-01
Laboratories studying the anisotropic rotational diffusion of bromobenzene using nuclear spin relaxation and molecular dynamics simulations are described. For many undergraduates, visualizing molecular motion is challenging. Undergraduates rarely encounter laboratories that directly assess molecular motion, and so the concept remains an…
Molecular dynamics study of water molecule diffusion in oil-paper insulation materials
International Nuclear Information System (INIS)
Liao Ruijin; Zhu Mengzhao; Yang Lijun; Zhou Xin; Gong Chunyan
2011-01-01
Moisture is an important factor that influences the safe operation of transformers. In this study, molecular dynamics was employed to investigate the diffusion behavior of water molecules in the oil-paper insulation materials of transformers. Two oil-cellulose models were built. In the first model, water molecules were initially distributed in oil, and in the second model, water molecules were distributed in cellulose. The non-bonding energies of interaction between water molecules and oil, and between water molecules and cellulose, were calculated by the Dreiding force field. The interaction energy was found to play a dominant role in influencing the equilibrium distribution of water molecules. The radial direction functions of water molecules toward oil and cellulose indicate that the hydrogen bonds between water molecules and cellulose are sufficiently strong to withstand the operating temperature of the transformer. Mean-square displacement analysis of water molecules diffusion suggests that water molecules initially distributed in oil showed anisotropic diffusion; they tended to diffuse toward cellulose. Water molecules initially distributed in cellulose diffused isotropically. This study provides a theoretical contribution for improvements in online monitoring of water in transformers, and for subsequent research on new insulation materials.
Molecular dynamics study of water molecule diffusion in oil-paper insulation materials
Energy Technology Data Exchange (ETDEWEB)
Liao Ruijin [State Key Laboratory of Power Transmission Equipment and System Security and New Technology, Chongqing University, Chongqing 400044 (China); Zhu Mengzhao, E-mail: xiaozhupost@163.co [State Key Laboratory of Power Transmission Equipment and System Security and New Technology, Chongqing University, Chongqing 400044 (China); Yang Lijun; Zhou Xin; Gong Chunyan [State Key Laboratory of Power Transmission Equipment and System Security and New Technology, Chongqing University, Chongqing 400044 (China)
2011-03-01
Moisture is an important factor that influences the safe operation of transformers. In this study, molecular dynamics was employed to investigate the diffusion behavior of water molecules in the oil-paper insulation materials of transformers. Two oil-cellulose models were built. In the first model, water molecules were initially distributed in oil, and in the second model, water molecules were distributed in cellulose. The non-bonding energies of interaction between water molecules and oil, and between water molecules and cellulose, were calculated by the Dreiding force field. The interaction energy was found to play a dominant role in influencing the equilibrium distribution of water molecules. The radial direction functions of water molecules toward oil and cellulose indicate that the hydrogen bonds between water molecules and cellulose are sufficiently strong to withstand the operating temperature of the transformer. Mean-square displacement analysis of water molecules diffusion suggests that water molecules initially distributed in oil showed anisotropic diffusion; they tended to diffuse toward cellulose. Water molecules initially distributed in cellulose diffused isotropically. This study provides a theoretical contribution for improvements in online monitoring of water in transformers, and for subsequent research on new insulation materials.
International Nuclear Information System (INIS)
Liao, Liqiong; Fu, Yizheng; Liang, Ziaoyan; Mei, Linyu; Liu, Yaqing
2013-01-01
Molecular dynamics (MD) simulations have been used to study the diffusion behavior of small gas molecules (CO 2 ) in polyethylene terephthalate (PET)/polylactide (PLA) blends. The Flory-Huggins interaction parameters (χ) determined from the cohesive energy densities are smaller than the critical value of Flory-Huggins interaction parameters (χ critical ), and that indicates the good compatibility of PET/PLA blends. The diffusion coefficients of CO 2 are determined via MD simulations at 298 K. That the order of diffusion coefficients is correlated with the availably fractional free volume (FFV) of CO 2 in the PET/PLA blends means that the FFV plays a vital role in the diffusion behavior of CO 2 molecules in PET/PLA blends. The slopes of the log (MSD) as a function of log (t) are close to unity over the entire composition range of PET/PLA blends, which confirms the feasibility of MD approach reaches the normal diffusion regime of CO 2 in PET/PLA blends
Energy Technology Data Exchange (ETDEWEB)
Goemans, M.G.E.; Gloyna, E.F. [Univ. of Texas, Austin, TX (United States). Dept. of Civil Engineering; Buelow, S.J. [Los Alamos National Lab., NM (United States)
1996-04-01
Molecular diffusion coefficients of lithium-, sodium-, potassium-, cesium-, calcium-, and strontium nitrate in subcritical water were determined by analysis of Taylor dispersion profiles. Pressures ranged from 300 to 500 bar at temperatures ranging from 25{degrees}C to 300{degrees}C. The reported diffusion values were determined at infinite dilution. Molecular diffusion coefficients were 10 to 20 times faster in near-critical subcritical water than in water at ambient temperature and pressure (ATP). These findings implied that the diffusion rates were more liquid like than they were gas like, hence experimental results were correlated with diffusion models for liquids. The subcritical diffusion data presented in this work, and supercritical diffusion results published elsewhere were correlated with hydrodynamic diffusion equations. Both the Wilke-Chang correlation and the Stokes-Einstein equation yielded predictions within 10% of the experimental results if the structure of the diffusing species could be estimated. The effect of the increased diffusion rates on mass transfer rates in supercritical water oxidation applications was quantified, with emphasis on heterogeneous oxidation processes. This study and results published elsewhere showed that diffusion limited conditions are much more likely to be encountered in SCWO processes than commonly acknowledged.
Computing the blood brain barrier (BBB) diffusion coefficient: A molecular dynamics approach
Energy Technology Data Exchange (ETDEWEB)
Shamloo, Amir, E-mail: shamloo@sharif.edu; Pedram, Maysam Z.; Heidari, Hossein; Alasty, Aria, E-mail: aalasti@sharif.edu
2016-07-15
Various physical and biological aspects of the Blood Brain Barrier (BBB) structure still remain unfolded. Therefore, among the several mechanisms of drug delivery, only a few have succeeded in breaching this barrier, one of which is the use of Magnetic Nanoparticles (MNPs). However, a quantitative characterization of the BBB permeability is desirable to find an optimal magnetic force-field. In the present study, a molecular model of the BBB is introduced that precisely represents the interactions between MNPs and the membranes of Endothelial Cells (ECs) that form the BBB. Steered Molecular Dynamics (SMD) simulations of the BBB crossing phenomenon have been carried out. Mathematical modeling of the BBB as an input-output system has been considered from a system dynamics modeling viewpoint, enabling us to analyze the BBB behavior based on a robust model. From this model, the force profile required to overcome the barrier has been extracted for a single NP from the SMD simulations at a range of velocities. Using this data a transfer function model has been obtained and the diffusion coefficient is evaluated. This study is a novel approach to bridge the gap between nanoscale models and microscale models of the BBB. The characteristic diffusion coefficient has the nano-scale molecular effects inherent, furthermore reducing the computational costs of a nano-scale simulation model and enabling much more complex studies to be conducted. - Highlights: • Molecular dynamics simulation of crossing nano-particles through the BBB membrane at different velocities. • Recording the position of nano-particle and the membrane-NP interaction force profile. • Identification of a frequency domain model for the membrane. • Calculating the diffusion coefficient based on MD simulation and identified model. • Obtaining a relation between continuum medium and discrete medium.
A new scaling for the rotational diffusion of molecular probes in polymer solutions.
Qing, Jing; Chen, Anpu; Zhao, Nanrong
2017-12-13
In the present work, we propose a new scaling form for the rotational diffusion coefficient of molecular probes in semi-dilute polymer solutions, based on a theoretical study. The mean-field theory for depletion effect and semi-empirical scaling equation for the macroscopic viscosity of polymer solutions are properly incorporated to specify the space-dependent concentration and viscosity profiles in the vicinity of the probe surface. Following the scheme of classical fluid mechanics, we numerically evaluate the shear torque exerted on the probes, which then allows us to further calculate the rotational diffusion coefficient D r . Particular attention is given to the scaling behavior of the retardation factor R rot ≡ D/D r with D being the diffusion coefficient in pure solvent. We find that R rot has little relevance to the macroscopic viscosity of the polymer solution, while it can be well featured by the characteristic length scale r h /δ, i.e. the ratio between the hydrodynamic radius of the probe r h and the depletion thickness δ. Correspondingly, we obtain a novel scaling form for the rotational retardation factor, following R rot = exp[a(r h /δ) b ] with rather robust parameters of a ≃ 0.51 and b ≃ 0.56. We apply the theory to an extensive calculation for various probes in specific polymer solutions of poly(ethylene glycol) (PEG) and dextran. Our theoretical results show good agreements with the experimental data, and clearly demonstrate the validity of the new scaling form. In addition, the difference of the scaling behavior between translational and rotational diffusions is clarified, from which we conclude that the depletion effect plays a more significant role on the local rotational diffusion rather than the long-range translation diffusion.
Energy Technology Data Exchange (ETDEWEB)
Lei, Huaping; Wang, Caizhuang; Yao, Yongxin; Hupalo, Myron [Ames Laboratory, USDOE, Ames, Iowa 50011 (United States); Wang, Yangang [Ames Laboratory, USDOE, Ames, Iowa 50011 (United States); Supercomputing Center of Computer Network Information Center, CAS, Beijing 100190 (China); McDougall, Dan; Tringides, Michael; Ho, Kaiming [Ames Laboratory, USDOE, Ames, Iowa 50011 (United States); Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011 (United States)
2013-12-14
The adsorption, diffusion, and molecular dissociation of hydrogen on the biaxially strained Mg (0001) surface have been systematically investigated by the first principle calculations based on density functional theory. When the strain changes from the compressive to tensile state, the adsorption energy of H atom linearly increases while its diffusion barrier linearly decreases oppositely. The dissociation barrier of H{sub 2} molecule linearly reduces in the tensile strain region. Through the chemical bonding analysis including the charge density difference, the projected density of states and the Mulliken population, the mechanism of the strain effect on the adsorption of H atom and the dissociation of H{sub 2} molecule has been elucidated by an s-p charge transfer model. With the reduction of the orbital overlap between the surface Mg atoms upon the lattice expansion, the charge transfers from p to s states of Mg atoms, which enhances the hybridization of H s and Mg s orbitals. Therefore, the bonding interaction of H with Mg surface is strengthened and then the atomic diffusion and molecular dissociation barriers of hydrogen decrease accordingly. Our works will be helpful to understand and to estimate the influence of the lattice deformation on the performance of Mg-containing hydrogen storage materials.
International Nuclear Information System (INIS)
Rhee, C.K.; Ferry, J.D.; Fetters, L.J.
1977-01-01
The diffusion of radioactively tagged n-hexadecane, n-dotriacontane, and a polybutadiene oligomer with molecular weight 1600 has been studied in 12 rubbery polymers. Diffusion coefficients were obtained from the theory for the thin smear method: for n-hexadecane and for n-dotriacontane (with one exception), in the form appropriate for a completely miscible polymer-penetrant pair, and for the oligomer in the form appropriate for slow entry of the pentrant across the penetrant-polymer interface. For the four flexible linear penetrants, n-dodecane, n-hexadecane, n-dotriacontane, and oligomer, the ratios of diffusion coefficients (or translational friction coefficients) are nearly the same in every polymer. It is concluded that these penetrants travel with similar segmentwise motions, although that is not the case with bulkier, more rigid penetrants. For the three normal paraffins, the friction coefficient is approximately proportional to molecular weight, but that for the oligomer is smaller than would be predicted on this basis
Zhang, Wei; Ye, Chao; Hong, Linbi; Yang, Zaixing; Zhou, Ruhong
2016-12-06
Phosphorene, a newly fabricated two-dimensional (2D) nanomaterial, has emerged as a promising material for biomedical applications with great potential. Nonetheless, understanding the wetting and diffusive properties of bio-fluids on phosphorene which are of fundamental importance to these applications remains elusive. In this work, using molecular dynamics (MD) simulations, we investigated the structural and dynamic properties of water on both pristine and strained phosphorene. Our simulations indicate that the diffusion of water molecules on the phosphorene surface is anisotropic, with strain-enhanced diffusion clearly present, which arises from strain-induced smoothing of the energy landscape. The contact angle of water droplet on phosphorene exhibits a non-monotonic variation with the transverse strain. The structure of water on transverse stretched phosphorene is demonstrated to be different from that on longitudinal stretched phosphorene. Moreover, the contact angle of water on strained phosphorene is proportional to the quotient of the longitudinal and transverse diffusion coefficients of the interfacial water. These findings thereby offer helpful insights into the mechanism of the wetting and transport of water at nanoscale, and provide a better foundation for future biomedical applications of phosphorene.
A molecular dynamics study of nuclear quantum effect on the diffusion of hydrogen in condensed phase
International Nuclear Information System (INIS)
Nagashima, Hiroki; Tokumasu, Takashi; Tsuda, Shin-ichi; Tsuboi, Nobuyuki; Koshi, Mitsuo; Hayashie, A. Koichi
2014-01-01
In this paper, the quantum effect of hydrogen molecule on its diffusivity is analyzed using Molecular Dynamics (MD) method. The path integral centroid MD (CMD) method is applied for the reproduction method of time evolution of the molecules. The diffusion coefficient of liquid hydrogen is calculated using the Green-Kubo method. The simulation is performed at wide temperature region and the temperature dependence of the quantum effect of hydrogen molecule is addressed. The calculation results are compared with those of classical MD results. As a result, it is confirmed that the diffusivity of hydrogen molecule is changed depending on temperature by the quantum effect. It is clarified that this result can be explained that the dominant factor by quantum effect on the diffusivity of hydrogen changes from the swollening the potential to the shallowing the potential well around 30 K. Moreover, it is found that this tendency is related to the temperature dependency of the ratio of the quantum kinetic energy and classical kinetic energy
Derivatization and diffusive motion of molecular fullerenes: Ab initio and atomistic simulations
Energy Technology Data Exchange (ETDEWEB)
Berdiyorov, G., E-mail: gberdiyorov@qf.org.qa; Tabet, N. [Qatar Environment and Energy Research Institute (QEERI), Hamad Ben Khalifa University (HBKU), Qatar Foundation, P.O. Box 5825, Doha (Qatar); Harrabi, K. [Department of Physics, King Fahd University of Petroleum and Minerals, 31261 Dhahran (Saudi Arabia); Mehmood, U.; Hussein, I. A. [Department of Chemical Engineering, King Fahd University of Petroleum and Minerals, 31261 Dharan (Saudi Arabia); Peeters, F. M. [Departement Fysica, Universiteit Antwerpen, Groenenborgerlaan 171, B-2020 Antwerpen (Belgium); Zhang, J. [Department of Materials and London Centre for Nanotechnology, Imperial College London, SW7 2AZ London (United Kingdom); McLachlan, M. A. [Department of Materials and Centre for Plastic Electronics, Imperial College London, SW7 2AZ London (United Kingdom)
2015-07-14
Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C{sub 60} fullerene. As a typical example, we consider [6,6]-phenyl-C{sub 61}-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect on the electronic transport properties of the fullerene molecular junctions. Both C{sub 60} and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside poly(3-hexylthiophene) lamella using reactive molecular dynamics simulations. We found that the mobility of the fullerene reduces considerably due to derivatization; the diffusion coefficient of C{sub 60} is an order of magnitude larger than the one for PCBM.
International Nuclear Information System (INIS)
Vree, C; Mayr, S G
2010-01-01
The impact of free surfaces on the mobility and conformational fluctuations of model polymer chains is investigated with the help of classical molecular dynamics simulations over a broad temperature range. Below a critical temperature, T*, similar to the critical temperature of the mode coupling theory, the center-of-mass displacements and temporal fluctuations of the radius of gyration of individual chains-as a fingerprint of structural reconfigurations-reveal a strong enhancement close to surfaces, while this effect diminishes with increasing temperature and observation time. Interpreting conformational fluctuations as a random walk in conformational space, identical activation enthalpies for structural reconfigurations and diffusion are obtained within the error bars in the bulk and at the surfaces, thus indicating a coupling of diffusive and conformational dynamics.
Energy Technology Data Exchange (ETDEWEB)
Hepburn, I.; De Schutter, E., E-mail: erik@oist.jp [Computational Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495 (Japan); Theoretical Neurobiology & Neuroengineering, University of Antwerp, Antwerp 2610 (Belgium); Chen, W. [Computational Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495 (Japan)
2016-08-07
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification.
Directory of Open Access Journals (Sweden)
Itsuo Hanasaki, Akihiro Nakatani and Hiroshi Kitagawa
2004-01-01
Full Text Available A carbon nanotube junction consists of two connected nanotubes with different diameters. It has been extensively investigated as a molecular electronic device since carbon nanotubes can be metallic and semiconductive, depending on their structure. However, a carbon nanotube junction can also be viewed as a nanoscale nozzle andv diffuser. Here, we focus on the nanotube junction from the perspective of an intersection between machine, material and device. We have conducted a molecular dynamics simulation of the molecular flow inside a modeled (12,12–(8,8 nanotube junction. A strong gravitational field and a periodic boundary condition are applied in the flow direction. We investigated dense-Ar flows and dense-He flows while controlling the temperature of the nanotube junction. The results show that Ar atoms tend to be near to the wall and the density of the Ar is higher in the wide (12,12 nanotube than in the narrow (8,8 nanotube, while it is lower in the wide tube when no flow occurs. The streaming velocities of both the Ar and the He are higher in the narrow nanotube than in the wide nanotube, but the velocity of the Ar is higher than the velocity of the He and the temperature of the flowing Ar is higher than the temperature of the He when the same magnitude of gravitational field is applied.
International Nuclear Information System (INIS)
Yan Shi-Chao; Xie Nan; Gong Hui-Qi; Guo Yang; Shan Xin-Yan; Lu Xing-Hua; Sun Qian
2012-01-01
The adsorption and diffusion behaviors of benzene molecules on an Au(111) surface are investigated by low-temperature scanning tunneling microscopy. A herringbone surface reconstruction of the Au(111) surface is imaged with atomic resolution, and significantly different behaviors are observed for benzene molecules adsorbed on step edges and terraces. The electric field induced modification in the molecular diffusion potential is revealed with a 2D molecular gas model, and a new method is developed to map the diffusion potential over the reconstructed Au(111) surface at the nanometer scale. (condensed matter: structure, mechanical and thermal properties)
Molecular dynamics simulations of the diffusion and coalescence of helium in tungsten
Energy Technology Data Exchange (ETDEWEB)
Zhou, Y.L. [Key Lab for Radiation Physics and Technology, Institute of Nuclear Science and Technology, Sichuan University, Chengdu 610064 (China); Department of Physics, Guangxi University, Nanning 530004 (China); Wang, J. [Key Lab for Radiation Physics and Technology, Institute of Nuclear Science and Technology, Sichuan University, Chengdu 610064 (China); Hou, Q., E-mail: qhou@scu.edu.cn [Key Lab for Radiation Physics and Technology, Institute of Nuclear Science and Technology, Sichuan University, Chengdu 610064 (China); Deng, A.H. [Department of Physics, Sichuan University, Chengdu 610064 (China)
2014-03-15
Molecular dynamics (MD) simulations are performed on the diffusion and coalescence of helium in tungsten. A new method for determining the effective capture radii (ECRs) and the dissociation energies of helium-related defects is proposed in this work. It is observed that the ECR of an interstitial helium atom trapping helium interstitials (denoted as He–He{sub n}, n = 1–3) decreases with increasing temperature, except for He–He{sub 2} at T < 400 K. The traditional view that the ECR is approximately equal to the lattice constant, which has been widely used in kinetic Monte Carlo (KMC) and rate theory (RT) models, is only valid in some cases. However, the ECR between an interstitial helium atom and a substitutional helium atom (denoted as He–HeV) always approximates the third nearest-neighbor tetrahedral positions of the HeV. The diffusion coefficients D{sub n} for helium clusters are also investigated. He{sub 2} migrates more quickly than a single He atom does at T < 400 K, whereas the diffusion path of He{sub 2} changes at higher temperatures. Another counterintuitive observation is that D{sub 5} > D{sub 3} > D{sub 4} at T < 500 K, which can be attributed to the disordered structure of He{sub 5}. The Arrhenius relation describes the diffusion of He{sub n} well in the temperature range from 300 K to 550 K, whereas the diffusion is not a standard thermally activated process at higher temperatures. Taken together, these results help elucidate the initial stage of helium bubble formation in tungsten as well as the requirements of long-term evolution methods such as KMC or RT models.
Sorbate Transport in Carbon Molecular Sieve Membranes and FAU/EMT Intergrowth by Diffusion NMR
Directory of Open Access Journals (Sweden)
John J. Low
2012-02-01
Full Text Available In this paper we present and discuss selected results of our recent studies of sorbate self-diffusion in microporous materials. The main focus is given to transport properties of carbon molecular sieve (CMS membranes as well as of the intergrowth of FAU-type and EMT-type zeolites. CMS membranes show promise for applications in separations of mixtures of small gas molecules, while FAU/EMT intergrowth can be used as an active and selective cracking catalyst. For both types of applications diffusion of guest molecules in the micropore networks of these materials is expected to play an important role. Diffusion studies were performed by a pulsed field gradient (PFG NMR technique that combines advantages of high field (17.6 T NMR and high magnetic field gradients (up to 30 T/m. This technique has been recently introduced at the University of Florida in collaboration with the National Magnet Lab. In addition to a more conventional proton PFG NMR, also carbon-13 PFG NMR was used.
Heyes, D. M.; Nuevo, M. J.; Morales, J. J.
Following on from our previous study (Heyes, D. M., Nuevo, M. J, and Morales, J. J., 1996, Molec. Phys., 88, 1503), molecular dynamics simulations have been carried out of translational and rotational diffusion of atomistically rough near-spherical solid Lennard-Jones (LJ) clusters immersed in a Weeks-Chandler-Andersen liquid solvent. A single cluster consisting of up to about 100LJ particles as part of an 8000 atom fluid system was considered in each case. The translational and rotational diffusion coefficients decrease with increasing cluster size and solvent density (roughly in proportion to the molar volume of the solvent). The simulations reveal that for clusters in excess of about 30LJ atoms there is a clear separation of timescales between angular velocity and orientation relaxation which adhere well to the small-step diffusion model encapsulated in Hubbard's relationship. For 100 atom clusters both the StokesEinstein (translation) and Stokes-Einstein-Debye (rotation) equations apply approximately. The small departures from these reference solutions indicate that the translational relaxation experiences a local viscosity in excess of the bulk value (typically by ~ 30%), whereas rotational relaxation experiences a smaller viscosity than the bulk (typically by ~ 30%) reasonably in accord with the Gierer-Wirtz model. Both of these observations are consistent with an observed layering of the liquid molecules next to the cluster observed in our previous study.
Molecular dynamics simulations of the diffusion and coalescence of helium in tungsten
International Nuclear Information System (INIS)
Zhou, Y.L.; Wang, J.; Hou, Q.; Deng, A.H.
2014-01-01
Molecular dynamics (MD) simulations are performed on the diffusion and coalescence of helium in tungsten. A new method for determining the effective capture radii (ECRs) and the dissociation energies of helium-related defects is proposed in this work. It is observed that the ECR of an interstitial helium atom trapping helium interstitials (denoted as He–He n , n = 1–3) decreases with increasing temperature, except for He–He 2 at T n for helium clusters are also investigated. He 2 migrates more quickly than a single He atom does at T 2 changes at higher temperatures. Another counterintuitive observation is that D 5 > D 3 > D 4 at T 5 . The Arrhenius relation describes the diffusion of He n well in the temperature range from 300 K to 550 K, whereas the diffusion is not a standard thermally activated process at higher temperatures. Taken together, these results help elucidate the initial stage of helium bubble formation in tungsten as well as the requirements of long-term evolution methods such as KMC or RT models
Bicen, A Ozan; Lehtomaki, Janne J; Akyildiz, Ian F
2018-03-01
Molecular communication (MC) over a microfluidic channel with flow is investigated based on Shannon's channel capacity theorem and Fick's laws of diffusion. Specifically, the sum capacity for MC between a single transmitter and multiple receivers (broadcast MC) is studied. The transmitter communicates by using different types of signaling molecules with each receiver over the microfluidic channel. The transmitted molecules propagate through microfluidic channel until reaching the corresponding receiver. Although the use of different types of molecules provides orthogonal signaling, the sum broadcast capacity may not scale with the number of the receivers due to physics of the propagation (interplay between convection and diffusion based on distance). In this paper, the performance of broadcast MC on a microfluidic chip is characterized by studying the physical geometry of the microfluidic channel and leveraging the information theory. The convergence of the sum capacity for microfluidic broadcast channel is analytically investigated based on the physical system parameters with respect to the increasing number of molecular receivers. The analysis presented here can be useful to predict the achievable information rate in microfluidic interconnects for the biochemical computation and microfluidic multi-sample assays.
Diffusion-driven growth of nanowires by low-temperature molecular beam epitaxy
Energy Technology Data Exchange (ETDEWEB)
Rueda-Fonseca, P.; Orrù, M. [Univ. Grenoble Alpes, F-38000 Grenoble (France); CNRS, Institut NEEL, F-38000 Grenoble (France); CEA, INAC, F-38000 Grenoble (France); Bellet-Amalric, E.; Robin, E. [Univ. Grenoble Alpes, F-38000 Grenoble (France); CEA, INAC, F-38000 Grenoble (France); Den Hertog, M.; Genuist, Y.; André, R.; Tatarenko, S.; Cibert, J., E-mail: joel.cibert@neel.cnrs.fr [Univ. Grenoble Alpes, F-38000 Grenoble (France); CNRS, Institut NEEL, F-38000 Grenoble (France)
2016-04-28
With ZnTe as an example, we use two different methods to unravel the characteristics of the growth of nanowires (NWs) by gold-catalyzed molecular beam epitaxy at low temperature. In the first approach, CdTe insertions have been used as markers, and the nanowires have been characterized by scanning transmission electron microscopy, including geometrical phase analysis and energy dispersive electron spectrometry; the second approach uses scanning electron microscopy and the statistics of the relationship between the length of the tapered nanowires and their base diameter. Axial and radial growth are quantified using a diffusion-limited model adapted to the growth conditions; analytical expressions describe well the relationship between the NW length and the total molecular flux (taking into account the orientation of the effusion cells), and the catalyst-nanowire contact area. A long incubation time is observed. This analysis allows us to assess the evolution of the diffusion lengths on the substrate and along the nanowire sidewalls, as a function of temperature and deviation from stoichiometric flux.
Oulebsir, Fouad; Vermorel, Romain; Galliero, Guillaume
2018-01-16
With the advent of graphene material, membranes based on single-layer nanoporous solids appear as promising devices for fluid separation, be it liquid or gaseous mixtures. The design of such architectured porous materials would greatly benefit from accurate models that can predict their transport and separation properties. More specifically, there is no universal understanding of how parameters such as temperature, fluid loading conditions, or the ratio of the pore size to the fluid molecular diameter influence the permeation process. In this study, we address the problem of pure supercritical fluids diffusing through simplified models of single-layer porous materials. Basically, we investigate a toy model that consists of a single-layer lattice of Lennard-Jones interaction sites with a slit gap of controllable width. We performed extensive equilibrium and biased molecular dynamics simulations to document the physical mechanisms involved at the molecular scale. We propose a general constitutive equation for the diffusional transport coefficient derived from classical statistical mechanics and kinetic theory, which can be further simplified in the ideal gas limit. This transport coefficient relates the molecular flux to the fluid density jump across the single-layer membrane. It is found to be proportional to the accessible surface porosity of the single-layer porous solid and to a thermodynamic factor accounting for the inhomogeneity of the fluid close to the pore entrance. Both quantities directly depend on the potential of mean force that results from molecular interactions between solid and fluid atoms. Comparisons with the simulations data show that the kinetic model captures how narrowing the pore size below the fluid molecular diameter lowers dramatically the value of the transport coefficient. Furthermore, we demonstrate that our general constitutive equation allows for a consistent interpretation of the intricate effects of temperature and fluid loading
International Nuclear Information System (INIS)
Devkota, J.; Shrestha, S.P.
2007-12-01
We have performed Kinetic Monte Carlo simulation work to study the effect of diffusion anisotropy, bonding anisotropy and edge diffusion on island formation at different temperatures during the sub-monolayer film growth in Molecular Beam Epitaxy. We use simple cubic solid on solid model and event based Bortz, Kalos and Labowitch (BKL) algorithm on the Kinetic Monte Carlo method to simulate the physical phenomena. We have found that the island morphology and growth exponent are found to be influenced by substrate anisotropy as well as edge diffusion, however they do not play a significant role in island elongation. The growth exponent and island size distribution are observed to be influenced by substrate anisotropy but are negligibly influenced by edge diffusion. We have found fractal islands when edge diffusion is excluded and compact islands when edge diffusion is included. (author)
INFLUENCE VARIOUS REAGENTS ON THE MOLECULAR DIFFUSION INDEX OF SUCROSE FROM BEET
Directory of Open Access Journals (Sweden)
N. G. Kulneva
2015-01-01
Full Text Available Food products from vegetable raw materials play a special role in the food industry. Sugar is one of the strategically important products. The significance of its is great due to its wide use in confectionery, bakery, liquor, canning, biochemical, pharmaceutical and other branches of human activity. Effective development of the domestic sugar industry depends on the terms of competition with European partners. Production of granulated sugar includes a significant amount of energy-intensive and technologically complex operations, one of which is the extraction of sucrose from beet chips by means of hot countercurrent extraction. The most important criterion for the extraction process efficiency evaluation is the coefficient of molecular diffusion. The efficiency of using of beet chips thermo chemical processing before extraction depending on the quality of processed beet was investigated. It was found out that when using a low quality beet the diffusion coefficient decreases compared to healthy beet. The use of solutio ns of some salts for beet chips heat treatment has an overall positive effect on the diffusion coefficient. A method for recovering sucrose from beet with the use of compounds of Al2(SO4, Ca(SO4, and (NH42SO4 as the extractants was proposed. It was found out that beet samples treatment with solutions of proposed salts provides a sucrose smooth transition from the pores of sugar beet tissue into the extractant due to intense convective washout. It is caused by the high degree of tissue cells plasmolysis achieved in its processing with solutions of proposed reagents. The results obtained indicate a significant increase of the sucrose diffusion coefficient in the ammonium sulfate solution used as the extractant.
A Study of diffusion and grain boundaries in ionic compounds by the molecular dynamic method
International Nuclear Information System (INIS)
Karakasidis, Theodoros
1995-01-01
In the first part, we present a model of variable cationic charges based on a rigid ion potential. In order to implement the model we performed static and dynamic simulations in calcium fluoride. The structural properties do not depend on the way the model is adjusted but the anion diffusion and the high frequency dielectric constant do. These results allowed to specify the criteria to adjust the variable charge model. As indicated by the behaviour of optical phonons this model introduced a supplementary polarisation mechanism to the rigid ion model. In the second part of this work, we studied the structural and diffusional behaviour of a high angle tilt grain boundary in NiO by molecular dynamics, using a usual rigid ion model. We examined structures with and without point defects between 0 K and 2500 K. The structure without defects presents always the lowest potential energy. In the others structures the defects can cluster and sometimes cause local changes in the boundary. Computer simulated images of high resolution electron microscopy, produced using these structures, present a similarity with the experimental ones. We calculated in the same boundary the diffusion coefficient of a doubly charged nickel vacancy between 2250 K and 2650 K. The atomic trajectories reveal the existence of preferential migration paths for the vacancy. The grain boundary diffusion is slightly anisotropic which is in agreement with an extrapolation of experimental results. A similar study in the volume reveals a migration energy higher than in the grain boundary. The calculated quantities allow for an estimation of the nickel diffusion acceleration due to the boundary. This acceleration is significant, but lower than the one measured by certain authors in polycrystalline, NiO; other authors studying bicrystals have not observed any acceleration. (author) [fr
Energy Technology Data Exchange (ETDEWEB)
Barnard, L., E-mail: lmbarnard@wisc.edu; Morgan, D., E-mail: ddmorgan@wisc.edu
2014-06-01
In this study, ab initio molecular dynamics, implemented via density functional theory, is used to simulate self-interstitial diffusion in pure Ni and in the Ni-18 at.% Cr model alloy. Interstitial tracer diffusivities are measured from simulation results for pure Ni and for both Ni and Cr in the Ni–18Cr alloy. An Arrhenius function fit to these tracer diffusivities is then used in a rate theory model for radiation induced segregation, along with the experimentally measured vacancy diffusivities. It is predicted that interstitial diffusion has a tendency to cause Cr enrichment near grain boundaries, partially counterbalancing the tendency for vacancy diffusion to cause Cr depletion. This results in more mild Cr depletion than would result if only the vacancy diffusion were accounted for, in better agreement with experiment. This physical description of RIS in Ni–Cr alloys, which invokes the effects of both vacancy and interstitial diffusion, is distinct from the conventional description which accounts only for the effect of vacancy diffusion.
International Nuclear Information System (INIS)
Barnard, L.; Morgan, D.
2014-01-01
In this study, ab initio molecular dynamics, implemented via density functional theory, is used to simulate self-interstitial diffusion in pure Ni and in the Ni-18 at.% Cr model alloy. Interstitial tracer diffusivities are measured from simulation results for pure Ni and for both Ni and Cr in the Ni–18Cr alloy. An Arrhenius function fit to these tracer diffusivities is then used in a rate theory model for radiation induced segregation, along with the experimentally measured vacancy diffusivities. It is predicted that interstitial diffusion has a tendency to cause Cr enrichment near grain boundaries, partially counterbalancing the tendency for vacancy diffusion to cause Cr depletion. This results in more mild Cr depletion than would result if only the vacancy diffusion were accounted for, in better agreement with experiment. This physical description of RIS in Ni–Cr alloys, which invokes the effects of both vacancy and interstitial diffusion, is distinct from the conventional description which accounts only for the effect of vacancy diffusion
Bourg, Ian C; Sposito, Garrison
2010-03-15
In this paper, we address the manner in which the continuum-scale diffusive properties of smectite-rich porous media arise from their molecular- and pore-scale features. Our starting point is a successful model of the continuum-scale apparent diffusion coefficient for water tracers and cations, which decomposes it as a sum of pore-scale terms describing diffusion in macropore and interlayer "compartments." We then apply molecular dynamics (MD) simulations to determine molecular-scale diffusion coefficients D(interlayer) of water tracers and representative cations (Na(+), Cs(+), Sr(2+)) in Na-smectite interlayers. We find that a remarkably simple expression relates D(interlayer) to the pore-scale parameter δ(nanopore) ≤ 1, a constrictivity factor that accounts for the lower mobility in interlayers as compared to macropores: δ(nanopore) = D(interlayer)/D(0), where D(0) is the diffusion coefficient in bulk liquid water. Using this scaling expression, we can accurately predict the apparent diffusion coefficients of tracers H(2)0, Na(+), Sr(2+), and Cs(+) in compacted Na-smectite-rich materials.
Sushko, Gennady B; Verkhovtsev, Alexey V; Yakubovich, Alexander V; Schramm, Stefan; Solov'yov, Andrey V
2014-08-21
The process of self-diffusion of titanium atoms in a bulk material, on grain junctions and on surface is explored numerically in a broad temperature range by means of classical molecular dynamics simulation. The analysis is carried out for a nanoscale cylindrical sample consisting of three adjacent sectors and various junctions between nanocrystals. The calculated diffusion coefficient varies by several orders of magnitude for different regions of the sample. The calculated values of the bulk diffusion coefficient correspond reasonably well to the experimental data obtained for solid and molten states of titanium. Investigation of diffusion in the nanocrystalline titanium is of a significant importance because of its numerous technological applications. This paper aims to reduce the lack of data on diffusion in titanium and describe the processes occurring in bulk, at different interfaces and on surface of the crystalline titanium.
Molecular rotations and diffusion in solids, in particular hydrogen in metals
International Nuclear Information System (INIS)
Springer, T.
1977-01-01
The chapter deals mainly with problems related to physical chemistry. The author treats diffusion in solids, in particular of hydrogen in metals, and studies of molecular rotations, in particular studies of tunneling transitions which is a relatively new and rapidly developing field of high resolution neutron spectroscopy. Typical neutron spectra to be discussed appear in energy ranges of a few 10 -6 to a few 10 -3 eV, or 10 -5 to 10 -2 cm -1 . The discussion is restricted to scattering from the protons which is predominantly incoherent. This means that only the motions, or excitations, of individual protons or protonic groups are discussed, ignoring collective excitations and interference. (HPOE) [de
Balik, Vladimir; Trojanec, Radek; Holzerova, Milena; Tuckova, Lucie; Sulla, Igor; Megova, Magdalena; Vaverka, Miroslav; Hrabalek, Lumir; Ehrmann, Jiri
2015-01-01
Medulloblastoma (MB), the most common malignant tumor typically affecting children, occurs only exceptionally in adults. Multifocal presentation of this malignancy in adulthood is even much rarer—only four cases with favorable postoperative course have been reported, so far. The study illustrates a very rare rapid postoperative clinical deterioration due to diffuse cerebellar swelling (DCS) in an adult multifocal MB (MMB). To the best of their knowledge, authors for the first time performed genetic analysis of MMB and demonstrated expression patterns of selected markers that put the patient within the sonic hedgehog (SHH) molecular subgroup and at least partially explain her unsatisfactory clinical course. Herein, authors summarized the relevant literature concerning this issue with the aim to determine features that would facilitate diagnosis and therapy of such a scarce clinical entity.
Molecular dynamics simulations of self-diffusion near a symmetrical tilt grain boundary in UO{sub 2}
Energy Technology Data Exchange (ETDEWEB)
Vincent-Aublant, E.; Delaye, J.M. [CEA-Marcoule, DEN/DTCD/SECM, B.P. 17171, 30207 Bagnols sur Ceze cedex (France); Van Brutzel, L. [CEA-Saclay, DEN-DANS/DPC/SCP/LM2T, 91191 Gif-sur-Yvette (France)
2008-07-01
Molecular dynamics (MD) simulations have been used to study the influence of symmetrical tilt grain boundaries (GBs) in stoichiometric UO{sub 2} on uranium and oxygen self-diffusions. The study was performed on a large range of temperature varying from 300 K to 2100 K. First, the effect of the temperature on the structure and the formation energies of 6 relaxed tilt GBs was investigated. The {sigma}5 and {sigma}41 GBs geometries were chosen to study the diffusion. O and U diffusion coefficients have been calculated and compared to those obtained in a perfect stoichiometric UO{sub 2} as well as in over and under-stoichiometric matrices. (authors)
International Nuclear Information System (INIS)
Huang, Jin
1989-01-01
The variation of the core structure of an easy glide dislocation with temperature and its influence on the stacking fault energy (γ) have been investigated for the first time by molecular-dynamics simulation in copper. The calculations have been performed at various temperatures, using an ab-initio pseudo-potential. Our results show that the core of the Shockley partials, into which the perfect edge dislocation dissociates, becomes increasingly extended as temperature increases. However their separation remains constant. The calculated energy values of the infinite extension stacking fault and the ribbon fault between the partials are quite different, but the evolution of the core structure does not affect the temperature dependence of the latter. We have found that a high disorder appears in the core region when temperature increases due to important anharmonicity effects of the atomic vibrations. The core structure remains solid-like for T m (T m : melting point of bulk) in spite of the high disorder. Above T m , the liquid nucleus germinates in the core region, and then propagates into the bulk. In addition we studied the mobility of vacancies and interstitials trapped on the partials. Although fast diffusion is thought to occur exclusively in a pipe surrounding the dislocation core, in the present study a quasi two-dimensional diffusion is observed for both defects not only in the cores but also in the stacking fault ribbon. On the opposite of current assumptions, the activation energy for diffusion is found to be identical for both defects, which may therefore comparably contribute to mass transport along the dislocations. (author) [fr
Molecular structure effects on the post irradiation diffusion in polymer gel dosimeters
Energy Technology Data Exchange (ETDEWEB)
Mattea, F.; Romero, M.; Strumia, M. [Instituto Multidisciplinario de Biologia Vegetal / CONICET, Universidad Nacional de Cordoba, Departamento de Quimica Organica, Ciudad Universitaria, 5000 Cordoba (Argentina); Vedelago, J. [Laboratorio de Investigaciones e Instrumentacion en Fisica Aplicada a la Medicina e Imagenes por Rayos X, Laboratorio 448 FaMAF - UNC, Ciudad Universitaria, 5000 Cordoba (Argentina); Quiroga, A. [Centro de Investigacion y Estudios de Matematica / CONICET, Oficina 318 FaMAF - UNC, Ciudad Universitaria, 5000 Cordoba (Argentina); Valente, M., E-mail: fmattea@gmail.com [Instituto de Fisica E. Gaviola / CONICET, LIIFAMIRx, Oficina 102 FaMAF - UNC, 5000 Cordoba (Argentina)
2014-08-15
Polymer gel dosimeters have specific advantages for recording 3D radiation dose distribution representing a key factor for most of the therapeutic and diagnostic radiation techniques. Radiation-induced polymerization and crosslinking reactions that take place in the dosimeter have been studied for different monomers like acrylamide and N,N-methylene-bis acrylamide (Bis) and most recently for less toxic monomers like N-isopropylacrylamide and Bis. In this work a novel system based on itaconic acid and Bis is proposed, the radical polymerization or gel formation of these monomers has been already studied for the formation of an hydrogel for non dosimetric applications and their reactivity are comparable with the already mentioned systems. Although the 3D structure is maintained after the dosimeter has been irradiated, it is not possible to eliminate the diffusion of the reacted and monomer species in regions of dose gradients within the gel after irradiation. As a consequence the dose information of the dosimeters loose quality over time. The mobility within the gelatin structure of the already mentioned species is related to their chemical structure, and nature. In this work the effect of changes in the chemical structure of the monomers over the dosimetric sensitivity and over the post-irradiation diffusion of species is studied. One of the acrylic acid groups of the itaconic acid molecule is modified to obtain molecules with similar reactivity but different molecular sizes. Dosimetric systems with these modified species, Bis, an antioxidant to avoid oxygen polymerization inhibition, water and gelatin are irradiated in an X-ray tomography at different doses, and the resulting dosimeters are characterized by Raman spectroscopy and optical absorbance to study their feasibility and capabilities as dosimetric systems, and by optical-CT to analyze the diffusion degree after being irradiated. (Author)
Magnetic diffusion and ionization fractions in dense molecular clouds: The role of charged grains
International Nuclear Information System (INIS)
Elmegreen, B.G.
1979-01-01
The ionization fraction is determined for dense molecular clouds by considering charge exchange, dissociative recombination, radiative recombination, and collisions between grains and charged species. The inclusion of grains tends to lower the ionization fraction for a given cosmic-ray ionization rate zeta and metal depletion delta. The observed values of the ionization fractions in dense cloud cores (i.e., -8 ) are obtained for reasonable values of zeta=10 -17 s -1 and delta=0.1.For temperatures less than 30 K, each grain alternates in charge between -e and 0. The resulting motion of the grains in a self-graviting cloud that contains a magnetic field will be periodic; their response to electromagnetic forces will depend on their instantaneous charge. This complex motion is calculated in order to determine the average viscous force between the grains and the neutral molecules in the cloud. The grain-neutral viscous force combines with the ion-neutral viscous force to regulate the motion of the neutral molecules relative to the magnetic field. The resultant The result neutral drift leads to a diffusion of the magnetic field out of the cloud. The time scale for this diffusion is calculated. Grain-related viscous forces dominate ion-related forces for ionization fractions less than 5 x 10 -8 . The magnetic diffusion time in a self-gravitating cloud that is supported by an internal magnetic field is shown to be at least 10 times larger thanthe free-fall time even when the ionization fraction is much less than 10 -8
Molecular structure effects on the post irradiation diffusion in polymer gel dosimeters
International Nuclear Information System (INIS)
Mattea, F.; Romero, M.; Strumia, M.; Vedelago, J.; Quiroga, A.; Valente, M.
2014-08-01
Polymer gel dosimeters have specific advantages for recording 3D radiation dose distribution representing a key factor for most of the therapeutic and diagnostic radiation techniques. Radiation-induced polymerization and crosslinking reactions that take place in the dosimeter have been studied for different monomers like acrylamide and N,N-methylene-bis acrylamide (Bis) and most recently for less toxic monomers like N-isopropylacrylamide and Bis. In this work a novel system based on itaconic acid and Bis is proposed, the radical polymerization or gel formation of these monomers has been already studied for the formation of an hydrogel for non dosimetric applications and their reactivity are comparable with the already mentioned systems. Although the 3D structure is maintained after the dosimeter has been irradiated, it is not possible to eliminate the diffusion of the reacted and monomer species in regions of dose gradients within the gel after irradiation. As a consequence the dose information of the dosimeters loose quality over time. The mobility within the gelatin structure of the already mentioned species is related to their chemical structure, and nature. In this work the effect of changes in the chemical structure of the monomers over the dosimetric sensitivity and over the post-irradiation diffusion of species is studied. One of the acrylic acid groups of the itaconic acid molecule is modified to obtain molecules with similar reactivity but different molecular sizes. Dosimetric systems with these modified species, Bis, an antioxidant to avoid oxygen polymerization inhibition, water and gelatin are irradiated in an X-ray tomography at different doses, and the resulting dosimeters are characterized by Raman spectroscopy and optical absorbance to study their feasibility and capabilities as dosimetric systems, and by optical-CT to analyze the diffusion degree after being irradiated. (Author)
Lü, Yongjun; Cheng, Hao; Chen, Min
2012-06-01
The self-diffusion coefficients D and the viscosities η of elemental Ni, Cu, and Ni-Si alloys have been calculated over a wide temperature range by molecular dynamics simulations. For elemental Ni and Cu, Arrhenius-law variations of D and η with temperature dominate. The temperature dependence of Dη can be approximated by a linear relation, whereas the Stokes-Einstein relation is violated. The calculations of D and η are extended to the regions close to the crystallization of Ni95Si5, Ni90Si10, and the glass transitions of Ni80Si20 and Ni75Si25. The results show that both D and η strongly deviate from the Arrhenius law in the vicinity of phase transitions, exhibiting a power-law divergence. We find a decoupling of diffusion and viscous flow just above the crystallization of Ni95Si5 and Ni90Si10. For the two glass-forming alloys, Ni80Si20 and Ni75Si25, the relation Dη = const is obeyed as the glass transition is approached, indicating a dynamic coupling as predicted by the mode-coupling theory. This coupling is enhanced with increasing Si composition and at 25%, Si spans a wide temperature range through the melting point. The decoupling is found to be related to the distribution of local ordered structure in the melts. The power-law governing the growth of solid-like clusters prior to crystallization creates a dynamic heterogeneity responsible for decoupling.
Energy Technology Data Exchange (ETDEWEB)
Bhatia, Harsh [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gyulassy, Attila [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ong, Mitchell [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Lordi, Vincenzo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Draeger, Erik [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pask, John [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pascucci, Valerio [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bremer, Peer -Timo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2016-09-27
The performance of lithium-ion batteries is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact, both, the solvation and diffusivity of Li ions. In this work, we present our application of the topological techniques to extract and predict such behavior in the data generated by the first-principles molecular dynamics simulation of Li ions in an important organic solvent -ethylene carbonate. More specifically, we use the scalar topology of the electron charge density field to analyze the evolution of the solvation structures. This allows us to derive a parameter-free bond definition for lithium-oxygen bonds, to provide a quantitative measure for bond strength, and to understand the regions of influence of each atom in the simulation. This has provided new insights into how and under what conditions certain bonds may form and break. As a result, we can identify and, more importantly, predict, unstable configurations in solvation structures. This can be very useful in understanding when small changes to the atoms' movements can cause significantly different bond structures to evolve. Ultimately, this promises to allow scientists to explore lithium ion solvation and diffusion more systematically, with the aim of new insights and potentially accelerating the calculations themselves.
Energy Technology Data Exchange (ETDEWEB)
Hsu, Po Jen; Lai, S. K., E-mail: sklai@coll.phy.ncu.edu.tw [Complex Liquids Laboratory, Department of Physics, National Central University, Chungli 320, Taiwan and Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan (China); Rapallo, Arnaldo [Istituto per lo Studio delle Macromolecole (ISMAC) Consiglio Nazionale delle Ricerche (CNR), via E. Bassini 15, C.A.P 20133 Milano (Italy)
2014-03-14
Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit
International Nuclear Information System (INIS)
Hsu, Po Jen; Lai, S. K.; Rapallo, Arnaldo
2014-01-01
Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit
Management of diffuse low-grade gliomas in adults - use of molecular diagnostics.
Buckner, Jan; Giannini, Caterina; Eckel-Passow, Jeanette; Lachance, Daniel; Parney, Ian; Laack, Nadia; Jenkins, Robert
2017-06-01
Diffuse WHO grade II gliomas are histologically and genetically heterogeneous. The 2016 WHO classification redefines grade II gliomas with respect to morphological and molecular tumour alterations: grade II oligodendrogliomas are defined by the presence of whole-arm codeletion in chromosomal arms 1p/19q, whereas isocitrate dehydrogenase (IDH) mutations define subclasses of astrocytoma. Although histological grade remains useful, the prognoses of patients with glioma are more tightly associated with molecular alterations than with grade, and chromosomal and gene array technologies are becoming increasingly beneficial in understanding tumour genetic heterogeneity. The indolent nature of the disease often creates subtle neurological symptoms that can be overlooked or misunderstood, resulting in delayed diagnosis. Seizures often herald the diagnosis, especially in patients who have IDH mutations, which are associated with an increased production of 2-hydroxyglutarate. Treatment paradigms have shifted, owing to new diagnostic criteria and new clinical trial evidence. Patients benefit more from chemoradiation than radiation alone, especially those with tumour IDH1 Arg132His mutations; gross total resection of the tumour, including tumours with IDH mutations, is associated with prolonged survival. Initial observation remains appropriate in patients whose rate of disease growth is not yet completely defined; such patients could include those with completely resected disease and those with 1p/19q codeleted tumours.
Wyrick, Jonathan; Einstein, T. L.; Bartels, Ludwig
2015-03-01
We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species' diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.
Vermorel, Romain; Oulebsir, Fouad; Galliero, Guillaume
2017-09-14
The computation of diffusion coefficients in molecular systems ranks among the most useful applications of equilibrium molecular dynamics simulations. However, when dealing with the problem of fluid diffusion through vanishingly thin interfaces, classical techniques are not applicable. This is because the volume of space in which molecules diffuse is ill-defined. In such conditions, non-equilibrium techniques allow for the computation of transport coefficients per unit interface width, but their weak point lies in their inability to isolate the contribution of the different physical mechanisms prone to impact the flux of permeating molecules. In this work, we propose a simple and accurate method to compute the diffusional transport coefficient of a pure fluid through a planar interface from equilibrium molecular dynamics simulations, in the form of a diffusion coefficient per unit interface width. In order to demonstrate its validity and accuracy, we apply our method to the case study of a dilute gas diffusing through a smoothly repulsive single-layer porous solid. We believe this complementary technique can benefit to the interpretation of the results obtained on single-layer membranes by means of complex non-equilibrium methods.
Pinto de Magalhães, Halua; Brennwald, Matthias S; Kipfer, Rolf
2017-03-22
Atmospheric noble gases are routinely used as natural tracers to analyze gas transfer processes in aquatic systems. Their isotopic ratios can be employed to discriminate between different physical transport mechanisms by comparison to the unfractionated atmospheric isotope composition. In many applications of aquatic systems molecular diffusion was thought to cause a mass dependent fractionation of noble gases and their isotopes according to the square root ratio of their masses. However, recent experiments focusing on isotopic fractionation within a single element challenged this broadly accepted assumption. The determined fractionation factors of Ne, Ar, Kr and Xe isotopes revealed that only Ar follows the prediction of the so-called square root relation, whereas within the Ne, Kr and Xe elements no mass-dependence was found. The reason for this unexpected divergence of Ar is not yet understood. The aim of our computational exercise is to establish the molecular-resolved mechanisms behind molecular diffusion of noble gases in water. We make the hypothesis that weak intermolecular interactions are relevant for the dynamical properties of noble gases dissolved in water. Therefore, we used ab initio molecular dynamics to explicitly account for the electronic degrees of freedom. Depending on the size and polarizability of the hydrophobic particles such as noble gases, their motion in dense and polar liquids like water is subject to different diffusive regimes: the inter-cavity hopping mechanism of small particles (He, Ne) breaks down if a critical particle size achieved. For the case of large particles (Kr, Xe), the motion through the water solvent is governed by mass-independent viscous friction leading to hydrodynamical diffusion. Finally, Ar falls in between the two diffusive regimes, where particle dispersion is propagated at the molecular collision time scale of the surrounding water molecules.
Krishna, R.; van Baten, J.M.
2012-01-01
The primary objective of this article is to investigate the relative influences of molecular dimensions and adsorption binding energies on unary diffusivities of guest species inside nanoporous crystalline materials such as zeolites and metal-organic frameworks (MOFs). The investigations are based
International Nuclear Information System (INIS)
Cai Congbo; Chen Zhong; Cai Shuhui; Zhong Jianhui
2005-01-01
In this paper, behaviors of single-quantum coherences and inter-molecular multiple-quantum coherences under restricted diffusion in nuclear magnetic resonance experiments were investigated. The propagator formalism based on the loss of spin phase memory during random motion was applied to describe the diffusion-induced signal attenuation. The exact expression of the signal attenuation under the short gradient pulse approximation for restricted diffusion between two parallel plates was obtained using this propagator method. For long gradient pulses, a modified formalism was proposed. The simulated signal attenuation under the effects of gradient pulses of different width based on the Monte Carlo method agrees with the theoretical predictions. The propagator formalism and computer simulation can provide convenient, intuitive and precise methods for the study of the diffusion behaviors
Maxwell–Stefan diffusion and dynamical correlation in molten LiF-KF: A molecular dynamics study
Energy Technology Data Exchange (ETDEWEB)
Jain, Richa Naja, E-mail: ltprichanaja@gmail.com; Chakraborty, Brahmananda; Ramaniah, Lavanya M. [High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-85 (India)
2016-05-23
In this work our main objective is to compute Dynamical correlations, Onsager coefficients and Maxwell-Stefan (MS) diffusivities for molten salt LiF-KF mixture at various thermodynamic states through Green–Kubo formalism for the first time. The equilibrium molecular dynamics (MD) simulations were performed using BHM potential for LiF–KF mixture. The velocity autocorrelations functions involving Li ions reflect the endurance of cage dynamics or backscattering with temperature. The magnitude of Onsager coefficients for all pairs increases with increase in temperature. Interestingly most of the Onsager coefficients has almost maximum magnitude at the eutectic composition indicating the most dynamic character of the eutectic mixture. MS diffusivity hence diffusion for all ion pairs increases in the system with increasing temperature. Smooth variation of the diffusivity values denies any network formation in the mixture. Also, the striking feature is the noticeable concentration dependence of MS diffusivity between cation-cation pair, Đ{sub Li-K} which remains negative for most of the concentration range but changes sign to become positive for higher LiF concentration. The negative MS diffusivity is acceptable as it satisfies the non-negative entropy constraint governed by 2{sup nd} law of thermodynamics. This high diffusivity also vouches the candidature of molten salt as a coolant.
The au-scale structure in diffuse molecular gas towards ζ Persei
Boissé, P.; Federman, S. R.; Pineau des Forêts, G.; Ritchey, A. M.
2013-11-01
Context. Spatial structure in molecular material has a strong impact on its physical and chemical evolution and is still poorly known, especially on very small scales. Aims: To better characterize the small-scale structure in diffuse molecular gas and in particular to investigate the CH+ production mechanism, we study the spatial distribution of CH+, CH, and CN towards the bright star ζ Per on scales in the range 1-20 AU. Methods: We use ζ Per's proper motion and the implied drift of the line of sight through the foreground gas at a rate of about 2 AU yr-1 to probe absorption line variations between adjacent lines of sight. The good S/N, high or intermediate resolution spectra of ζ Per, obtained in the interval 2003-2011, allow us to search for low column-density and line width variations for CH+, CH, and CN. Results: CH and CN lines appear remarkably stable in time, implying an upper limit δN/N ≤ 6% for CH and CN (3σ limit). The weak CH+λ4232 line shows a possible increase of 11% during the interval 2004-2007, which appears to be correlated with a comparable increase in the CH+ velocity dispersion over the same period. Conclusions: The excellent stability of CH and CN lines implies that these species are distributed uniformly to good accuracy within the cloud. The small size implied for the regions associated with the CH+ excess is consistent with scenarios in which this species is produced in very small (a few AU) localized active regions, possibly weakly magnetized shocks or turbulent vortices. Based on observations made at McDonald Observatory (USA) and Observatoire de Haute-Provence (France).
Alonso de Mezquia, David; Wang, Zilin; Lapeira, Estela; Klein, Michael; Wiegand, Simone; Mounir Bou-Ali, M
2014-11-01
In this study, the thermodiffusion, molecular diffusion, and Soret coefficients of 12 binary mixtures composed of toluene, n-hexane and n-dodecane in the whole range of concentrations at atmospheric pressure and temperatures of 298.15 K and 308.15 K have been determined. The experimental measurements have been carried out using the Thermogravitational Column, the Sliding Symmetric Tubes and the Thermal Diffusion Forced Rayleigh Scattering techniques. The results obtained using the different techniques show a maximum deviation of 9% for the thermodiffusion coefficient, 8% for the molecular diffusion coefficient and 2% for the Soret coefficient. For the first time we report a decrease of the thermodiffusion coefficient with increasing ratio of the thermal expansion coefficient and viscosity for a binary mixture of an organic ring compound with a short n-alkane. This observation is discussed in terms of interactions between the different components. Additionally, the thermogravitational technique has been used to measure the thermodiffusion coefficients of four ternary mixtures consisting of toluene, n-hexane and n-dodecane at 298.15 K. In order to complete the study, the values obtained for the molecular diffusion coefficient in binary mixtures, and the thermodiffusion coefficient of binary and ternary mixtures have been compared with recently derived correlations.
Microelectrode Studies of Seasonal Oxygen-Uptake in a Coastal Sediment - Role of Molecular-Diffusion
DEFF Research Database (Denmark)
RASMUSSEN, H.; JØRGENSEN, BB
1992-01-01
in the bay varied from 100 % air saturation during winter to 23 % during summer. The potentially higher O2 respiration during the summer months was counteracted by a lower O2 concentration in the bottom water, which led to a small seasonal variation in O2 uptake. Depth of the oxic sediment zone reached 5.1...... surface zone. The O2 consumption rates in the oxic surface layer, calculated from (b) and (c) using molecular diffusion coefficients of O2, closely agreed and accounted for 70 % of the total O2 uptake. The O2 uptake rates strongly depended on in situ O2 concentrations in the overlying seawater, which...... mm during winter, narrowed down rapidly to a few mm upon settling of a spring phytoplankton bloom, and was only 1.2 mm during summer. Modeling of O2 consumption from O2 microprofiles showed zero-order kinetics, i.e. constant O2 consumption rates throughout the oxic zone during winter. Enhanced O2...
Origin of CH+ in diffuse molecular clouds. Warm H2 and ion-neutral drift
Valdivia, Valeska; Godard, Benjamin; Hennebelle, Patrick; Gerin, Maryvonne; Lesaffre, Pierre; Le Bourlot, Jacques
2017-04-01
Context. Molecular clouds are known to be magnetised and to display a turbulent and complex structure where warm and cold phases are interwoven. The turbulent motions within molecular clouds transport molecules, and the presence of magnetic fields induces a relative velocity between neutrals and ions known as the ion-neutral drift (vd). These effects all together can influence the chemical evolution of the clouds. Aims: This paper assesses the roles of two physical phenomena which have previously been invoked to boost the production of CH+ under realistic physical conditions: the presence of warm H2 and the increased formation rate due to the ion-neutral drift. Methods: We performed ideal magnetohydrodynamical (MHD) simulations that include the heating and cooling of the multiphase interstellar medium (ISM), and where we treat dynamically the formation of the H2 molecule. In a post-processing step we compute the abundances of species at chemical equilibrium using a solver that we developed. The solver uses the physical conditions of the gas as input parameters, and can also prescribe the H2 fraction if needed. We validate our approach by showing that the H2 molecule generally has a much longer chemical evolution timescale compared to the other species. Results: We show that CH+ is efficiently formed at the edge of clumps, in regions where the H2 fraction is low (0.3-30%) but nevertheless higher than its equilibrium value, and where the gas temperature is high (≳ 300 K). We show that warm and out of equilibrium H2 increases the integrated column densities of CH+ by one order of magnitude up to values still 3-10 times lower than those observed in the diffuse ISM. We balance the Lorentz force with the ion-neutral drag to estimate the ion-drift velocities from our ideal MHD simulations. We find that the ion-neutral drift velocity distribution peaks around 0.04 km s-1, and that high drift velocities are too rare to have a significant statistical impact on the
International Nuclear Information System (INIS)
Ahmed, N.; Khan, G.
1990-09-01
In this report the author used of a very useful technique of simulation and applied it to successfully for determining the various properties of sodium, both in liquid and solid phase near transition point. As a first step the determination of specific heat and diffusion coefficient have been carried out. In liquid state the molecular dynamics (MD) values calculated matched the experimental data. But in solid state the diffusion coefficient obtained were not consistent with the one expected for a solid, rather the values obtained suggested that sodium remained in liquid state even below the melting point. (A.B.)
Mutoru, J W; Smith, W; O'Hern, C S; Firoozabadi, A
2013-01-14
Understanding the transport properties of molecular fluids in the critical region is important for a number of industrial and natural systems. In the literature, there are conflicting reports on the behavior of the self diffusion coefficient D(s) in the critical region of single-component molecular systems. For example, D(s) could decrease to zero, reach a maximum, or remain unchanged and finite at the critical point. Moreover, there is no molecular-scale understanding of the behavior of diffusion coefficients in molecular fluids in the critical regime. We perform extensive molecular dynamics simulations in the critical region of single-component fluids composed of medium-chain n-alkanes-n-pentane, n-decane, and n-dodecane-that interact via anisotropic united-atom potentials. For each system, we calculate D(s), and average molecular cluster sizes κ(cl) and numbers N(cl) at various cluster lifetimes τ, as a function of density ρ in the range 0.2ρ(c) ≤ ρ ≤ 2.0ρ(c) at the critical temperature T(c). We find that D(s) decreases with increasing ρ but remains finite at the critical point. Moreover, for any given τ critical point.
Nasrabad, Afshin Eskandari; Laghaei, Rozita; Eu, Byung Chan
2005-04-28
In previous work on the density fluctuation theory of transport coefficients of liquids, it was necessary to use empirical self-diffusion coefficients to calculate the transport coefficients (e.g., shear viscosity of carbon dioxide). In this work, the necessity of empirical input of the self-diffusion coefficients in the calculation of shear viscosity is removed, and the theory is thus made a self-contained molecular theory of transport coefficients of liquids, albeit it contains an empirical parameter in the subcritical regime. The required self-diffusion coefficients of liquid carbon dioxide are calculated by using the modified free volume theory for which the generic van der Waals equation of state and Monte Carlo simulations are combined to accurately compute the mean free volume by means of statistical mechanics. They have been computed as a function of density along four different isotherms and isobars. A Lennard-Jones site-site interaction potential was used to model the molecular carbon dioxide interaction. The density and temperature dependence of the theoretical self-diffusion coefficients are shown to be in excellent agreement with experimental data when the minimum critical free volume is identified with the molecular volume. The self-diffusion coefficients thus computed are then used to compute the density and temperature dependence of the shear viscosity of liquid carbon dioxide by employing the density fluctuation theory formula for shear viscosity as reported in an earlier paper (J. Chem. Phys. 2000, 112, 7118). The theoretical shear viscosity is shown to be robust and yields excellent density and temperature dependence for carbon dioxide. The pair correlation function appearing in the theory has been computed by Monte Carlo simulations.
DEFF Research Database (Denmark)
Hansen, Flemming Yssing; Criswell, L.; Fuhrmann, D
2004-01-01
Molecular dynamics simulations of a tetracosane (n-C24H50) monolayer adsorbed on a graphite basal-plane surface show that there are diffusive motions associated with the creation and annihilation of gauche defects occurring on a time scale of similar to0.1-4 ns. We present evidence...... that these relatively slow motions are observable by high-energy-resolution quasielastic neutron scattering (QNS) thus demonstrating QNS as a technique, complementary to nuclear magnetic resonance, for studying conformational dynamics on a nanosecond time scale in molecular monolayers....
Nagaoka, Katsumi; Yaginuma, Shin; Nakayama, Tomonobu
2018-02-01
We have discovered the condensation/diffusion phenomena of copper phthalocyanine (CuPc) molecules controlled with a pulsed electric field induced by the scanning tunneling microscope tip. This behavior is not explained by the conventional induced dipole model. In order to understand the mechanism, we have measured the electronic structure of the molecule by tunneling spectroscopy and also performed theoretical calculations on molecular orbitals. These data clearly indicate that the molecule is positively charged owing to charge transfer to the substrate, and that hydrogen bonding exists between CuPc molecules, which makes the molecular island stable.
Molecular Diffusion of Toluene through CaCO3-Filled Natural Rubber Composites
Directory of Open Access Journals (Sweden)
Hedayatollah Sadeghi Ghari
2012-12-01
Full Text Available The transport properties of liquids and gases through polymeric materialsplay a very important role in some areas of industrial applications. In thisstudy, natural rubber (NR/CaCO3 composites were prepared by melt mixingmethod. By equilibrium swelling test, the transport process of toluene in the prepared natural rubber composites was investigated. The diffusion and transport of toluene through calcium carbonate-filled natural rubber composites have been studied in the temperature range 25–45°C. The diffusion of toluene through these composites was studied with special reference to the effect of filler concentration and temperature.The transport coefficients such as diffusion, permeation and sorption coefficients were estimated from the swelling data. To find out the mechanism of diffusion in prepared composites, the results of swelling studies were applied to an empirical equation. In these composites, diffusion is approximately based on Fickian diffusion mechanism and by increases in temperature; diffusion mechanism is more close to Fickian mechanism. Increase of filler content in composite would result in decreased ultimateswelling and slower diffusion rate of solvent. The diffusion rate, diffusion coefficient and the permeability increased by temperature. The study of the diffusion of toluene through filled natural rubber indicated that the concentration of filler plays an important role in the diffusion, sorption and permeation coefficients. Also interfacial interactions in NR composites were checked by dynamic-mechanical analysis. The microstructure and dispersion of calcium carbonate particles in natural rubber matrix were studiedby field emission scanning electron microscopy (FE-SEM. In general, the results of swelling tests, dynamic-mechanical analysis and FE-SEM images show that the optimized value of filler in NR composites is equal to 10 phr calcium carbonate.
Zhang, Yong; Green, Christopher T.; Tick, Geoffrey R.
2015-01-01
This study evaluates the role of the Peclet number as affected by molecular diffusion in transient anomalous transport, which is one of the major knowledge gaps in anomalous transport, by combining Monte Carlo simulations and stochastic model analysis. Two alluvial settings containing either short- or long-connected hydrofacies are generated and used as media for flow and transport modeling. Numerical experiments show that 1) the Peclet number affects both the duration of the power-law segment of tracer breakthrough curves (BTCs) and the transition rate from anomalous to Fickian transport by determining the solute residence time for a given low-permeability layer, 2) mechanical dispersion has a limited contribution to the anomalous characteristics of late-time transport as compared to molecular diffusion due to an almost negligible velocity in floodplain deposits, and 3) the initial source dimensions only enhance the power-law tail of the BTCs at short travel distances. A tempered stable stochastic (TSS) model is then applied to analyze the modeled transport. Applications show that the time-nonlocal parameters in the TSS model relate to the Peclet number, Pe. In particular, the truncation parameter in the TSS model increases nonlinearly with a decrease in Pe due to the decrease of the mean residence time, and the capacity coefficient increases with an increase in molecular diffusion which is probably due to the increase in the number of immobile particles. The above numerical experiments and stochastic analysis therefore reveal that the Peclet number as affected by molecular diffusion controls transient anomalous transport in alluvial aquifer–aquitard complexes.
Turan, Meriç; Kuran, Mehmet Sukru; Yilmaz, H. Birkan; Demirkol, Ilker; Tugcu, Tuna
2018-01-01
By considering potential health problems that a fully covering receiver may cause in vessel-like environments, the implementation of a partially covering receiver is needed. To this end, distribution of hitting location of messenger molecules (MM) is analyzed within the context of molecular communication via diffusion with the aim of channel modeling. The distribution of these MMs for a fully covering receiver is analyzed in two parts: angular and radial dimensions. For the angular distributi...
Shen, Wenqing; Kumari, Niru; Gibson, Gary; Jeon, Yoocharn; Henze, Dick; Silverthorn, Sarah; Bash, Cullen; Kumar, Satish
2018-02-01
Non-volatile memory is a promising alternative to present memory technologies. Oxygen vacancy diffusion has been widely accepted as one of the reasons for the resistive switching mechanism of transition-metal-oxide based resistive random access memory. In this study, molecular dynamics simulation is applied to investigate the diffusion coefficient and activation energy of oxygen in amorphous hafnia. Two sets of empirical potential, Charge-Optimized Many-Body (COMB) and Morse-BKS (MBKS), were considered to investigate the structural and diffusion properties at different temperatures. COMB predicts the activation energy of 0.53 eV for the temperature range of 1000-2000 K, while MBKS predicts 2.2 eV at high temperature (1600-2000 K) and 0.36 eV at low temperature (1000-1600 K). Structural changes and appearance of nano-crystalline phases with increasing temperature might affect the activation energy of oxygen diffusion predicted by MBKS, which is evident from the change in coordination number distribution and radial distribution function. None of the potentials make predictions that are fully consistent with density functional theory simulations of both the structure and diffusion properties of HfO2. This suggests the necessity of developing a better multi-body potential that considers charge exchange.
Directory of Open Access Journals (Sweden)
D. J. Goossens
2015-01-01
Full Text Available Diffuse scattering from a crystal contains valuable information about the two-body correlations (related to the nanoscale order in the material. Despite years of development, the detailed analysis of single crystal diffuse scattering (SCDS has yet to become part of the everyday toolbox of the structural scientist. Recent decades have seen the pair distribution function approach to diffuse scattering (in fact, total scattering from powders become a relatively routine tool. However, analysing the detailed, complex, and often highly anisotropic three-dimensional distribution of SCDS remains valuable yet rare because there is no routine method for undertaking the analysis. At present, analysis requires significant investment of time to develop specialist expertise, which means that the analysis of diffuse scattering, which has much to offer, is not incorporated thorough studies of many compounds even though it has the potential to be a very useful adjunct to existing techniques. This article endeavours to outline in some detail how the diffuse scattering from a molecular crystal can be modelled relatively quickly and largely using existing software tools. It is hoped this will provide a template for other studies. To enable this, the entire simulation is included as deposited material.
Rossi, Mariana; Ceriotti, Michele; Manolopoulos, David
Diffusion of H+ and OH- along water wires provides an efficient mechanism for charge transport that is exploited by biological systems and shows promise in technological applications. However, what is lacking for a better control and design of these systems is a thorough theoretical understanding of the diffusion process at the atomic scale. Here we consider H+ and OH- in finite water wires using density functional theory. We employ machine learning techniques to identify the charged species, thus obtaining an agnostic definition of the charge. We employ thermostated ring polymer molecular dynamics and extract a ``universal'' diffusion coefficient from simulations with different wire sizes by considering Langevin dynamics on the potential of mean force of the charged species. In the classical case, diffusion coefficients depend significantly on the potential energy surface, in particular on how dispersion forces modulate O-O distances. NQEs, however, make the diffusion less sensitive to the underlying potential and geometry of the wire, presumably making them more robust to environment fluctuations.
Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A
2014-10-14
Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.
Samkoe, Kimberley S.; Davis, Scott C.; Srinivasan, Subhadra; O'Hara, Julia A.; Hasan, Tayyaba; Pogue, Brian W.
2009-06-01
Over the last several decades little progress has been made in the therapy and treatment monitoring of pancreas adenocarcinoma, a devastating and aggressive form of cancer that has a 5-year patient survival rate of 3%. Currently, investigations for the use of interstitial Verteporfin photodynamic therapy (PDT) are being undertaken in both orthotopic xenograft mouse models and in human clinical trials. In the mouse models, magnetic resonance (MR) imaging has been used as a measure of surrogate response to Verteporfin PDT; however, MR imaging alone lacks the molecular information required to assess the metabolic function and growth rates of the tumor immediately after treatment. We propose the implementation of MR-guided fluorescence tomography in conjunction with a fluorescently labeled (IR-Dye 800 CW, LI-COR) epidermal growth factor (EGF) as a molecular measure of surrogate response. To demonstrate the effectiveness of MR-guided diffuse fluorescence tomography for molecular imaging, we have used the AsPC-1 (+EGFR) human pancreatic adenocarcinoma in an orthotopic mouse model. EGF IRDye 800CW was injected 48 hours prior to imaging. MR image sequences were collected simultaneously with the fluorescence data using a MR-coupled diffuse optical tomography system. Image reconstruction was performed multiple times with varying abdominal organ segmentation in order to obtain a optimal tomographic image. It is shown that diffuse fluorescence tomography of the orthotopic pancreas model is feasible, with consideration of confounding fluorescence signals from the multiple organs and tissues surrounding the pancreas. MR-guided diffuse fluorescence tomography will be used to monitor EGF response after photodynamic therapy. Additionally, it provide the opportunity to individualize subsequent therapies based on response to PDT as well as to evaluate the success of combination therapies, such as PDT with chemotherapy, antibody therapy or even radiation.
Iqbal, Samina; Marchetti, Roberta; Aman, Afsheen; Silipo, Alba; Qader, Shah Ali Ul; Molinaro, Antonio
2017-10-01
Low molecular weight fractions were derived from native high molecular weight dextran produced by Leuconostoc mesenteroides KIBGE-IB26. Structural characterization of native and low molecular weight fractions obtained after acidic and enzymatic hydrolysis was done using FTIR and NMR spectroscopy. The molecular weight was estimated using Diffusion Ordered NMR spectroscopy. Native dextran (892kDa) is composed of α-(1→6) glycosidic linkage along with α-(1→3) branching. Major proportion of 528kDa dextran was obtained after prolong enzymatic hydrolysis however, an effective acidic treatment at pH-1.4 up to 02 and 04h of exposure resulted in the formation of 77kDa and 57kDa, respectively. The increment in pH from 1.4 to 1.8 lowered the hydrolysis efficiency and resulted in the formation of 270kDa dextran fraction. The results suggest that derived low molecular weight water soluble fractions can be utilized as a drug delivery carrier along with multiple application relating pharmaceutical industries. Copyright © 2017 Elsevier B.V. All rights reserved.
He, Ting; Fan, Ming; Zhang, Peng; Li, Hui; Zhang, Juan; Shao, Guoliang; Li, Lihua
2018-03-01
Breast cancer can be classified into four molecular subtypes of Luminal A, Luminal B, HER2 and Basal-like, which have significant differences in treatment and survival outcomes. We in this study aim to predict immunohistochemistry (IHC) determined molecular subtypes of breast cancer using image features derived from tumor and peritumoral stroma region based on diffusion weighted imaging (DWI). A dataset of 126 breast cancer patients were collected who underwent preoperative breast MRI with a 3T scanner. The apparent diffusion coefficients (ADCs) were recorded from DWI, and breast image was segmented into regions comprising the tumor and the surrounding stromal. Statistical characteristics in various breast tumor and peritumoral regions were computed, including mean, minimum, maximum, variance, interquartile range, range, skewness, and kurtosis of ADC values. Additionally, the difference of features between each two regions were also calculated. The univariate logistic based classifier was performed for evaluating the performance of the individual features for discriminating subtypes. For multi-class classification, multivariate logistic regression model was trained and validated. The results showed that the tumor boundary and proximal peritumoral stroma region derived features have a higher performance in classification compared to that of the other regions. Furthermore, the prediction model using statistical features, difference features and all the features combined from these regions generated AUC values of 0.774, 0.796 and 0.811, respectively. The results in this study indicate that ADC feature in tumor and peritumoral stromal region would be valuable for estimating the molecular subtype in breast cancer.
Danel, J.-F.; Kazandjian, L.; Zérah, G.
2012-06-01
Computations of the self-diffusion coefficient and viscosity in warm dense matter are presented with an emphasis on obtaining numerical convergence and a careful evaluation of the standard deviation. The transport coefficients are computed with the Green-Kubo relation and orbital-free molecular dynamics at the Thomas-Fermi-Dirac level. The numerical parameters are varied until the Green-Kubo integral is equal to a constant in the t→+∞ limit; the transport coefficients are deduced from this constant and not by extrapolation of the Green-Kubo integral. The latter method, which gives rise to an unknown error, is tested for the computation of viscosity; it appears that it should be used with caution. In the large domain of coupling constant considered, both the self-diffusion coefficient and viscosity turn out to be well approximated by simple analytical laws using a single effective atomic number calculated in the average-atom model.
Araf, Shamzah; Korfi, Koorosh; Rahim, Tahrima; Davies, Andrew; Fitzgibbon, Jude
2016-10-01
The adoption of high-throughput technologies has led to a transformation in our ability to classify diffuse large B-cell lymphoma (DLBCL) into unique molecular subtypes. In parallel, the expansion of agents targeting key genetic and gene expression signatures has led to an unprecedented opportunity to personalize cancer therapies, paving the way for precision medicine. Areas covered: This review summarizes the key molecular subtypes of DLBCL and outlines the novel technology platforms in development to discriminate clinically relevant subtypes. Expert commentary: The application of emerging diagnostic tests into routine clinical practise is gaining momentum following the demonstration of subtype specific activity by novel agents. Co-ordinated efforts are required to ensure that these state of the art technologies provide reliable and clinically meaningful results accessible to the wider haematology community.
Multi-charge-state molecular dynamics and self-diffusion coefficient in the warm dense matter regime
Fu, Yongsheng; Hou, Yong; Kang, Dongdong; Gao, Cheng; Jin, Fengtao; Yuan, Jianmin
2018-01-01
We present a multi-ion molecular dynamics (MIMD) simulation and apply it to calculating the self-diffusion coefficients of ions with different charge-states in the warm dense matter (WDM) regime. First, the method is used for the self-consistent calculation of electron structures of different charge-state ions in the ion sphere, with the ion-sphere radii being determined by the plasma density and the ion charges. The ionic fraction is then obtained by solving the Saha equation, taking account of interactions among different charge-state ions in the system, and ion-ion pair potentials are computed using the modified Gordon-Kim method in the framework of temperature-dependent density functional theory on the basis of the electron structures. Finally, MIMD is used to calculate ionic self-diffusion coefficients from the velocity correlation function according to the Green-Kubo relation. A comparison with the results of the average-atom model shows that different statistical processes will influence the ionic diffusion coefficient in the WDM regime.
GW-Bodies and P-Bodies Constitute Two Separate Pools of Sequestered Non-Translating RNAs.
Directory of Open Access Journals (Sweden)
Prajal H Patel
Full Text Available Non-translating RNAs that have undergone active translational repression are culled from the cytoplasm into P-bodies for decapping-dependent decay or for sequestration. Organisms that use microRNA-mediated RNA silencing have an additional pathway to remove RNAs from active translation. Consequently, proteins that govern microRNA-mediated silencing, such as GW182/Gw and AGO1, are often associated with the P-bodies of higher eukaryotic organisms. Due to the presence of Gw, these structures have been referred to as GW-bodies. However, several reports have indicated that GW-bodies have different dynamics to P-bodies. Here, we use live imaging to examine GW-body and P-body dynamics in the early Drosophila melanogaster embryo. While P-bodies are present throughout early embryonic development, cytoplasmic GW-bodies only form in significant numbers at the midblastula transition. Unlike P-bodies, which are predominantly cytoplasmic, GW-bodies are present in both nuclei and the cytoplasm. RNA decapping factors such as DCP1, Me31B, and Hpat are not associated with GW-bodies, indicating that P-bodies and GW-bodies are distinct structures. Furthermore, known Gw interactors such as AGO1 and the CCR4-NOT deadenylation complex, which have been shown to be important for Gw function, are also not present in GW-bodies. Use of translational inhibitors puromycin and cycloheximide, which respectively increase or decrease cellular pools of non-translating RNAs, alter GW-body size, underscoring that GW-bodies are composed of non-translating RNAs. Taken together, these data indicate that active translational silencing most likely does not occur in GW-bodies. Instead GW-bodies most likely function as repositories for translationally silenced RNAs. Finally, inhibition of zygotic gene transcription is unable to block the formation of either P-bodies or GW-bodies in the early embryo, suggesting that these structures are composed of maternal RNAs.
DEFF Research Database (Denmark)
Galliero, Guillaume; Medvedev, Oleg; Shapiro, Alexander
2005-01-01
A 322 (2004) 151). In the current study, a fast molecular dynamics scheme has been developed to determine the values of the penetration lengths in Lennard-Jones binary systems. Results deduced from computations provide a new insight into the concept of penetration lengths. It is shown for four different...... fluctuation theory and molecular dynamics scheme exhibit consistent trends and average deviations from experimental data around 10-20%. (c) 2004 Elsevier B.V. All rights reserved....
Di Rienzo, Carmine; Gratton, Enrico; Beltram, Fabio; Cardarelli, Francesco
2014-10-09
It has become increasingly evident that the spatial distribution and the motion of membrane components like lipids and proteins are key factors in the regulation of many cellular functions. However, due to the fast dynamics and the tiny structures involved, a very high spatio-temporal resolution is required to catch the real behavior of molecules. Here we present the experimental protocol for studying the dynamics of fluorescently-labeled plasma-membrane proteins and lipids in live cells with high spatiotemporal resolution. Notably, this approach doesn't need to track each molecule, but it calculates population behavior using all molecules in a given region of the membrane. The starting point is a fast imaging of a given region on the membrane. Afterwards, a complete spatio-temporal autocorrelation function is calculated correlating acquired images at increasing time delays, for example each 2, 3, n repetitions. It is possible to demonstrate that the width of the peak of the spatial autocorrelation function increases at increasing time delay as a function of particle movement due to diffusion. Therefore, fitting of the series of autocorrelation functions enables to extract the actual protein mean square displacement from imaging (iMSD), here presented in the form of apparent diffusivity vs average displacement. This yields a quantitative view of the average dynamics of single molecules with nanometer accuracy. By using a GFP-tagged variant of the Transferrin Receptor (TfR) and an ATTO488 labeled 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine (PPE) it is possible to observe the spatiotemporal regulation of protein and lipid diffusion on µm-sized membrane regions in the micro-to-milli-second time range.
A comparative molecular dynamics study of diffusion of n-decane ...
Indian Academy of Sciences (India)
Administrator
Abstract. Molecular dynamics simulations are reported on the structure and dynamics of n-decane and. 3-methylpentane in zeolite NaY. We have calculated several properties such as the center of mass-center of mass rdf, the end-end distance distribution, bond angle distribution and dihedral angle distribution. We.
Hyper alginate gel microbead formation by molecular diffusion at the hydrogel/droplet interface.
Hirama, Hirotada; Kambe, Taisuke; Aketagawa, Kyouhei; Ota, Taku; Moriguchi, Hiroyuki; Torii, Toru
2013-01-15
We report a simple method for forming monodispersed, uniformly shaped gel microbeads with precisely controlled sizes. The basis of our method is the placement of monodispersed sodium alginate droplets, formed by a microfluidic device, on an agarose slab gel containing a high-osmotic-pressure gelation agent (CaCl(2) aq.): (1) the droplets are cross-linked (gelated) due to the diffusion of the gelation agent from the agarose slab gel to the sodium alginate droplets and (2) the droplets simultaneously shrink to a fraction of their original size (slab gel. We verified the mass transfer mechanism between the droplet and the agarose slab gel. This method circumvents the limitations of gel microbead formation, such as the need to prepare microchannels of various sizes, microchannel clogging, and the deformation of the produced gel microbeads.
Surface morphology and molecular bonding of CaCO3 nanocrystallites by gas diffusion method
Sulimai, N. H.; Rani, Rozina Abdul; Khusaimi, Z.; Abdullah, S.; Salifairus, M. J.; Alrokayan, Salman; Khan, Haseeb; Rusop, M.
2018-05-01
Calcium carbonate with the chemical formula of (CaCO3) is the most abundant element in the world. Its usage on certain applications is largely affected by its properties. The best means to control its properties is through controlled preparation of CaCO3. This study uses diffusion method between the precursors Calcium Chloride and Ammonium Carbonate. Instead of using water, ethanol was used to prepare the salt. Reaction was done in room temperature (RT) for 6h-24h. Smallest average crystallite size measured by FESEM micrograph is 500nm produced by synthesis of CaCO3 reacted for 168 hours. From energy-dispersive X-ray spectrum also indicated the smallest particle size is by CaCO3 reacted for 168 hours. Changes was seen for element Ca at 3.7keV.
Delgado-López, P D; Corrales-García, E M; Martino, J; Lastra-Aras, E; Dueñas-Polo, M T
2017-08-01
The management of diffuse supratentorial WHO grade II glioma remains a challenge because of the infiltrative nature of the tumor, which precludes curative therapy after total or even supratotal resection. When possible, functional-guided resection is the preferred initial treatment. Total and subtotal resections correlate with increased overall survival. High-risk patients (age >40, partial resection), especially IDH-mutated and 1p19q-codeleted oligodendroglial lesions, benefit from surgery plus adjuvant chemoradiation. Under the new 2016 WHO brain tumor classification, which now incorporates molecular parameters, all diffusely infiltrating gliomas are grouped together since they share specific genetic mutations and prognostic factors. Although low-grade gliomas cannot be regarded as benign tumors, large observational studies have shown that median survival can actually be doubled if an early, aggressive, multi-stage and personalized therapy is applied, as compared to prior wait-and-see policy series. Patients need an honest long-term therapeutic strategy that should ideally anticipate neurological, cognitive and histopathologic worsening.
Energy Technology Data Exchange (ETDEWEB)
Tarancon, A. [M2E/XaRMAE/IREC, Department of Advanced Materials for Energy Applications, Catalonia Institute for Energy Research (IREC), Josep Pla 2, Torre 2, B2, 08019 Barcelona (Spain); Morata, A.; Peiro, F. [MIND/XaRMAE/IN2UB, Department of Electronics, University of Barcelona, Marti i Franques 1, 08028 Barcelona (Spain); Dezanneau, G. [Laboratoire Structures, Proprietes et Modelisation des Solides, Grande Voie des Vignes, Ecole Centrale Paris, F-92295 Chatenay-Malabry Cedex (France)
2011-02-15
The effect of the dopant distribution on the oxygen diffusion in doped fluorites typically used for solid oxide fuel cells electrolyte applications has been analysed by using molecular dynamics simulations. The oxygen mass transport in both yttria-stabilized zirconia (YSZ) and gadolinia-doped ceria has been studied and compared in the range of temperatures between 1,159 and 1,959 K. A new methodology based on the analysis of local environments is used to describe the diffusion process at an atomic scale. Preferred vacancy migration pathways, most suitable conduction models, energy landscapes and jump efficiency have been detailed for each material. Finally, a particular case of non-random distribution of dopants in YSZ is presented in order to quantitatively evaluate the effect of the dopant pattern on the mass transport properties and the potential of the methodology developed here for understanding and foreseeing real configurations at the nanoscale. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)
Molecular dynamics study of grain boundary diffusion of hydrogen in tungsten
International Nuclear Information System (INIS)
Von Toussaint, U; Gori, S; Manhard, A; Höschen, T; Höschen, C
2011-01-01
Understanding the influence of the microstructure of tungsten on hydrogen transport is crucial for the use of tungsten as first-wall material in fusion reactors. Here, we report the results of molecular dynamics and transition state studies on the influence of grain boundaries in tungsten on the transport of hydrogen. An exhaustive mapping of possible minimum activation energy migration trajectories for hydrogen as the trace impurity reveals a strongly modified activation energy distribution in the neighborhood of grain boundaries together with an altered connectivity matrix. The results indicate that grain boundaries in polycrystalline tungsten may provide an important transport channel, especially for neutron-damaged tungsten.
International Nuclear Information System (INIS)
Volino, F.
1976-01-01
After a short review of the main concepts concerning the neutron and its interaction with matter, the authors focus their attention on the study of molecular systems by means of neutron scattering. Instead of reviewing the subject yet again, they limit themselves to the new kind of work which can be done now, with the combined help of high flux reactors and novel instruments. As examples, a few experiments performed at the Institut Laue-Langevin in Grenoble are described: a neutron diffraction study of liquid acetonitrile using a powder diffractometer installed at the hot source; three high-resolution quasi-elastic studies of molecular motions - in an organic solid, (PAA), an organic liquid (C 3 H 6 ) and a liquid crystal (TBBA) - made by combining measurements with high and ultra-high energy resolution spectrometers installed at the cold source. The concept of elastic incoherent structure factor (EISF) is extensively used for the analysis. Finally some prospects on possible future developments are presented. (orig./HK) [de
Sheffer, Y.; Rogers, M.; Federman, S. R.; Abel, N. P.; Gredel, R.; Lambert, D. L.; Shaw, G.
2008-11-01
We carried out a comprehensive far-UV survey of 12CO and H2 column densities along diffuse molecular Galactic sight lines. This sample includes new measurements of CO from HST spectra along 62 sight lines and new measurements of H2 from FUSE data along 58 sight lines. In addition, high-resolution optical data were obtained at the McDonald and European Southern Observatories, yielding new abundances for CH, CH+, and CN along 42 sight lines to aid in interpreting the CO results. These new sight lines were selected according to detectable amounts of CO in their spectra and provide information on both lower density (production route for CO in higher density gas. Similar logarithmic plots among all five diatomic molecules reveal additional examples of dual slopes in the cases of CO versus CH (break at log N = 14.1, 13.0), CH+ versus H2 (13.1, 20.3), and CH+ versus CO (13.2, 14.1). We employ both analytical and numerical chemical schemes in order to derive details of the molecular environments. In the denser gas, where C2 and CN molecules also reside, reactions involving C+ and OH are the dominant factor leading to CO formation via equilibrium chemistry. In the low-density gas, where equilibrium chemistry studies have failed to reproduce the abundance of CH+, our numerical analysis shows that nonequilibrium chemistry must be employed for correctly predicting the abundances of both CH+ and CO.
Chapuy, Bjoern; Stewart, Chip; Dunford, Andrew J; Kim, Jaegil; Kamburov, Atanas; Redd, Robert A; Lawrence, Mike S; Roemer, Margaretha G M; Li, Amy J; Ziepert, Marita; Staiger, Annette M; Wala, Jeremiah A; Ducar, Matthew D; Leshchiner, Ignaty; Rheinbay, Ester; Taylor-Weiner, Amaro; Coughlin, Caroline A; Hess, Julian M; Pedamallu, Chandra S; Livitz, Dimitri; Rosebrock, Daniel; Rosenberg, Mara; Tracy, Adam A; Horn, Heike; van Hummelen, Paul; Feldman, Andrew L; Link, Brian K; Novak, Anne J; Cerhan, James R; Habermann, Thomas M; Siebert, Reiner; Rosenwald, Andreas; Thorner, Aaron R; Meyerson, Matthew L; Golub, Todd R; Beroukhim, Rameen; Wulf, Gerald G; Ott, German; Rodig, Scott J; Monti, Stefano; Neuberg, Donna S; Loeffler, Markus; Pfreundschuh, Michael; Trümper, Lorenz; Getz, Gad; Shipp, Margaret A
2018-04-30
Diffuse large B cell lymphoma (DLBCL), the most common lymphoid malignancy in adults, is a clinically and genetically heterogeneous disease that is further classified into transcriptionally defined activated B cell (ABC) and germinal center B cell (GCB) subtypes. We carried out a comprehensive genetic analysis of 304 primary DLBCLs and identified low-frequency alterations, captured recurrent mutations, somatic copy number alterations, and structural variants, and defined coordinate signatures in patients with available outcome data. We integrated these genetic drivers using consensus clustering and identified five robust DLBCL subsets, including a previously unrecognized group of low-risk ABC-DLBCLs of extrafollicular/marginal zone origin; two distinct subsets of GCB-DLBCLs with different outcomes and targetable alterations; and an ABC/GCB-independent group with biallelic inactivation of TP53, CDKN2A loss, and associated genomic instability. The genetic features of the newly characterized subsets, their mutational signatures, and the temporal ordering of identified alterations provide new insights into DLBCL pathogenesis. The coordinate genetic signatures also predict outcome independent of the clinical International Prognostic Index and suggest new combination treatment strategies. More broadly, our results provide a roadmap for an actionable DLBCL classification.
Molecular dynamics simulations of oxygen vacancy diffusion in SrTiO3
International Nuclear Information System (INIS)
Schie, Marcel; Marchewka, Astrid; Waser, Rainer; Müller, Thomas; De Souza, Roger A
2012-01-01
A classical force-field model with partial ionic charges was applied to study the behaviour of oxygen vacancies in the perovskite oxide strontium titanate (SrTiO 3 ). The dynamical behaviour of these point defects was investigated as a function of temperature and defect concentration by means of molecular dynamics (MD) simulations. The interaction between oxygen vacancies and an extended defect, here a Σ3(111) grain boundary, was also examined by means of MD simulations. Analysis of the vacancy distribution revealed considerable accumulation of vacancies in the envelope of the grain boundary. The possible clustering of oxygen vacancies in bulk SrTiO 3 was studied by means of static lattice calculations within the Mott-Littleton approach. All binary vacancy-vacancy configurations were found to be energetically unfavourable.
Molecular dynamics simulations of oxygen vacancy diffusion in SrTiO3.
Schie, Marcel; Marchewka, Astrid; Müller, Thomas; De Souza, Roger A; Waser, Rainer
2012-12-05
A classical force-field model with partial ionic charges was applied to study the behaviour of oxygen vacancies in the perovskite oxide strontium titanate (SrTiO(3)). The dynamical behaviour of these point defects was investigated as a function of temperature and defect concentration by means of molecular dynamics (MD) simulations. The interaction between oxygen vacancies and an extended defect, here a Σ3(111) grain boundary, was also examined by means of MD simulations. Analysis of the vacancy distribution revealed considerable accumulation of vacancies in the envelope of the grain boundary. The possible clustering of oxygen vacancies in bulk SrTiO(3) was studied by means of static lattice calculations within the Mott-Littleton approach. All binary vacancy-vacancy configurations were found to be energetically unfavourable.
Directory of Open Access Journals (Sweden)
Carmen Bellas
Full Text Available Diffuse large B-cell lymphoma (DLBCL is an aggressive non-Hodgkin lymphoma with marked biologic heterogeneity. We analyzed 100 cases of DLBCL to evaluate the prognostic value of immunohistochemical markers derived from the gene expression profiling-defined cell origin signature, including MYC, BCL2, BCL6, and FOXP1 protein expression. We also investigated genetic alterations in BCL2, BCL6, MYC and FOXP1 using fluorescence in situ hybridization and assessed their prognostic significance. BCL6 rearrangements were detected in 29% of cases, and BCL6 gene alteration (rearrangement and/or amplification was associated with the non-germinal center B subtype (non-GCB. BCL2 translocation was associated with the GCB phenotype, and BCL2 protein expression was associated with the translocation and/or amplification of 18q21. MYC rearrangements were detected in 15% of cases, and MYC protein expression was observed in 29% of cases. FOXP1 expression, mainly of the non-GCB subtype, was demonstrated in 37% of cases. Co-expression of the MYC and BCL2 proteins, with non-GCB subtype predominance, was observed in 21% of cases. We detected an association between high FOXP1 expression and a high proliferation rate as well as a significant positive correlation between MYC overexpression and FOXP1 overexpression. MYC, BCL2 and FOXP1 expression were significant predictors of overall survival. The co-expression of MYC and BCL2 confers a poorer clinical outcome than MYC or BCL2 expression alone, whereas cases negative for both markers had the best outcomes. Our study confirms that DLBCL, characterized by the co-expression of MYC and BCL2 proteins, has a poor prognosis and establishes a significant positive correlation with MYC and FOXP1 over-expression in this entity.
An analysis of hydrated proton diffusion in ab initio molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Tse, Ying-Lung Steve; Voth, Gregory A., E-mail: gavoth@uchicago.edu [Department of Chemistry, James Franck Institute, and Computation Institute, University of Chicago, Chicago, Illinois 60637 (United States); Knight, Chris [Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439 (United States)
2015-01-07
A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ∼2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP–D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300–330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions
Energy Technology Data Exchange (ETDEWEB)
Stone, Kevin H.
2014-07-14
Some polymer properties, such as conductivity, are very sensitive to short- and intermediate-range orientational and positional ordering of anisotropic molecular functional groups, and yet means to characterize orientational order in disordered systems are very limited. We demonstrate that resonant scattering at the carbon K-edge is uniquely sensitive to short-range orientation correlations in polymers through depolarized scattering at high momentum transfers, using atactic polystyrene as a well-characterized test system. Depolarized scattering is found to coexist with unpolarized fluorescence, and to exhibit pronounced anisotropy. We also quantify the spatially averaged optical anisotropy from low-angle reflectivity measurements, finding anisotropy consistent with prior visible, x-ray absorption, and theoretical studies. The average anisotropy is much smaller than that in the depolarized scattering and the two have different character. Both measurements exhibit clear spectral signatures from the phenyl rings and the polyethylene-like backbone. Discussion focuses on analysis considerations and prospects for using this depolarized scattering for studies of disorder in soft condensed matter.
Emission from small dust particles in diffuse and molecular cloud medium
International Nuclear Information System (INIS)
Bernard, J.P.; Desert, X.
1990-01-01
Infrared Astronomy Satellite (IRAS) observations of the whole galaxy has shown that long wavelength emission (100 and 60 micron bands) can be explained by thermal emission from big grains (approx 0.1 micron) radiating at their equilibrium temperature when heated by the InterStellar Radiation Field (ISRF). This conclusion has been confirmed by continuum sub-millimeter observations of the galactic plane made by the EMILIE experiment at 870 microns (Pajot et al. 1986). Nevertheless, shorter wavelength observations like 12 and 25 micron IRAS bands, show an emission from the galactic plane in excess with the long wavelength measurements which can only be explained by a much hotter particles population. Because dust at equilibrium cannot easily reach high temperatures required to explain this excess, this component is thought to be composed of very small dust grains or big molecules encompassing thermal fluctuations. Researchers present here a numerical model that computes emission, from Near Infrared Radiation (NIR) to Sub-mm wavelengths, from a non-homogeneous spherical cloud heated by the ISRF. This model fully takes into account the heating of dust by multi-photon processes and back-heating of dust in the Visual/Infrared Radiation (VIS-IR) so that it is likely to describe correctly emission from molecular clouds up to large A sub v and emission from dust experiencing temperature fluctuations. The dust is a three component mixture of polycyclic aromatic hydrocarbons, very small grains, and classical big grains with independent size distributions (cut-off and power law index) and abundances
Energy Technology Data Exchange (ETDEWEB)
Du, Jincheng
2018-03-16
This NEUP Project aimed to generate accurate atomic structural models of nuclear waste glasses by using large-scale molecular dynamics-based computer simulations and to use these models to investigate self-diffusion behaviors, interfacial structures, and hydrated gel structures formed during dissolution of these glasses. The goal was to obtain realistic and accurate short and medium range structures of these complex oxide glasses, to provide a mechanistic understanding of the dissolution behaviors, and to generate reliable information with predictive power in designing nuclear waste glasses for long-term geological storage. Looking back of the research accomplishments of this project, most of the scientific goals initially proposed have been achieved through intensive research in the three and a half year period of the project. This project has also generated a wealth of scientific data and vibrant discussions with various groups through collaborations within and outside of this project. Throughout the project one book chapter and 14 peer reviewed journal publications have been generated (including one under review) and 16 presentations (including 8 invited talks) have been made to disseminate the results of this project in national and international conference. Furthermore, this project has trained several outstanding graduate students and young researchers for future workforce in nuclear related field, especially on nuclear waste immobilization. One postdoc and four PhD students have been fully or partially supported through the project with intensive training in the field material science and engineering with expertise on glass science and nuclear waste disposal
Bonhommeau, David A; Perret, Alexandre; Nuzillard, Jean-Marc; Cilindre, Clara; Cours, Thibaud; Alijah, Alexander; Liger-Belair, Gérard
2014-12-18
The diffusion coefficients of carbon dioxide (CO2) and ethanol (EtOH) in carbonated hydroalcoholic solutions and Champagne wines are evaluated as a function of temperature by classical molecular dynamics (MD) simulations and (13)C NMR spectroscopy measurements. The excellent agreement between theoretical and experimental diffusion coefficients suggest that ethanol is the main molecule, apart from water, responsible for the value of the CO2 diffusion coefficients in typical Champagne wines, a result that could likely be extended to most sparkling wines with alike ethanol concentrations. CO2 and EtOH hydrodynamical radii deduced from viscometry measurements by applying the Stokes-Einstein relationship are found to be mostly constant and in close agreement with MD predictions. The reliability of our approach should be of interest to physical chemists aiming to model transport phenomena in supersaturated aqueous solutions or water/alcohol mixtures.
Chen, Chunyan; Wang, Jie; Loch, Cheryl L; Ahn, Dongchan; Chen, Zhan
2004-02-04
In this paper, the feasibility of monitoring molecular structures at a moving polymer/liquid interface by sum frequency generation (SFG) vibrational spectroscopy has been demonstrated. N-(2-Aminoethyl)-3-aminopropyltrimethoxysilane (AATM, NH2(CH2)2NH(CH2)3Si(OCH3)3) has been brought into contact with a deuterated poly(methyl methacrylate) (d-PMMA) film, and the interfacial silane structure has been monitored using SFG. Upon initial contact, the SFG spectra can be detected, but as time progresses, the spectral intensity changes and finally disappears. Additional experiments indicate that these silane molecules can diffuse into the polymer film and the detected SFG signals are actually from the moving polymer/silane interface. Our results show that the molecular order of the polymer/silane interface exists during the entire diffusion process and is lost when the silane molecules traverse through the thickness of the d-PMMA film. The loss of the SFG signal is due to the formation of a new disordered substrate/silane interface, which contributes no detectable SFG signal. The kinetics of the diffusion of the silane into the polymer have been deduced from the time-dependent SFG signals detected from the AATM molecules as they diffuse through polymer films of different thickness.
Salles, Fabrice; Jobic, Hervé; Devic, Thomas; Llewellyn, Philip L; Serre, Christian; Férey, Gérard; Maurin, Guillaume
2010-01-26
Quasi-elastic neutron scattering measurements are combined with molecular dynamics simulations to determine the self-diffusivity, corrected diffusivity, and transport diffusivity of CO(2) in the metal-organic framework MIL-47(V) (MIL = Materials Institut Lavoisier) over a wide range of loading. The force field used for describing the host/guest interactions is first validated on the thermodynamics of the MIL-47(V)/CO(2) system, prior to being transferred to the investigations of the dynamics. A decreasing profile is then deduced for D(s) and D(o) whereas D(t) presents a non monotonous evolution with a slight decrease at low loading followed by a sharp increase at higher loading. Such decrease of D(t) which has never been evidenced in any microporous systems comes from the atypical evolution of the thermodynamic correction factor that reaches values below 1 at low loading. This implies that, due to intermolecular interactions, the CO(2) molecules in MIL-47(V) do not behave like an ideal gas. Further, molecular simulations enabled us to elucidate unambiguously a 3D diffusion mechanism within the pores of MIL-47(V).
Energy Technology Data Exchange (ETDEWEB)
Andriyevsky, B., E-mail: bohdan.andriyevskyy@tu.koszalin.pl [Faculty of Electronics and Computer Sciences, Koszalin University of Technology, 2 Śniadeckich Str., PL-75-453, Koszalin (Poland); Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, D-89069, Ulm (Germany); Doll, K. [Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, D-89069, Ulm (Germany); Institute of Theoretical Chemistry, Pfaffenwaldring 55, D-70569, Stuttgart (Germany); Jacob, T. [Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, D-89069, Ulm (Germany); Helmholtz Institute Ulm (HIU) for Electrochemical Energy Storage, Albert-Einstein-Allee 11, D-89081, Ulm (Germany)
2017-01-01
Using ab initio density functional theory the thermally-stimulated migration of lithium ions in the garnet-type material Li{sub 7}La{sub 3}Zr{sub 2}O{sub 12} is investigated. The methods of ab initio molecular dynamics have been applied to calculate the lithium ion self-diffusion coefficient and the diffusion barriers as function of lithium ion concentration. The concentration of lithium in the initial Li{sub 7}La{sub 3}Zr{sub 2}O{sub 12} crystal unit cell is varied from 53 to 59 atoms, where 56 lithium atoms represent the stoichiometric concentration. Almost monotonous dependencies of the main characteristics on the number of lithium atoms N{sup (Li)} have been found, except for a non-monotonous peculiarity of the stoichiometric compound (N{sup (Li)} = 56). Finally, the influence of the unit cell volume change on lithium ion diffusion parameters as well as lithium ion hopping rates has been studied. - Highlights: • Partial lithium atoms subtraction from LLZO increases diffusion coefficient D{sup (Li)}. • Partial subtraction of lithium atoms from LLZO decreases activation energy E{sub a}{sup (Li)}. • Activation energy E{sub a}{sup (Li)} is the smallest for tetrahedral oxygen surrounding. • Compression of LLZO leads to a decrease of lithium ion diffusion coefficient D{sup (Li)}.
Chen, Gong; Kong, Xian; Lu, Diannan; Wu, Jianzhong; Liu, Zheng
2017-05-10
Molecular dynamics (MD) simulations, in combination with the Markov-state model (MSM), were applied to probe CO 2 diffusion from an aqueous solution into the active site of human carbonic anhydrase II (hCA-II), an enzyme useful for enhanced CO 2 capture and utilization. The diffusion process in the hydrophobic pocket of hCA-II was illustrated in terms of a two-dimensional free-energy landscape. We found that CO 2 diffusion in hCA-II is a rate-limiting step in the CO 2 diffusion-binding-reaction process. The equilibrium distribution of CO 2 shows its preferential accumulation within a hydrophobic domain in the protein core region. An analysis of the committors and reactive fluxes indicates that the main pathway for CO 2 diffusion into the active site of hCA-II is through a binding pocket where residue Gln 136 contributes to the maximal flux. The simulation results offer a new perspective on the CO 2 hydration kinetics and useful insights toward the development of novel biochemical processes for more efficient CO 2 sequestration and utilization.
Li, Li; Yang, Deshuai; Fisher, Trevor R; Qiao, Qi; Yang, Zhen; Hu, Na; Chen, Xiangshu; Huang, Liangliang
2017-10-24
The loading-dependent diffusion behavior of CH 4 , CO 2 , SO 2 , and their binary mixtures in ZIF-10 has been investigated in detail by using classical molecular dynamics simulations. Our simulation results demonstrate that the self-diffusion coefficient D i of CH 4 molecules decreases sharply and monotonically with the loading while those of both CO 2 and SO 2 molecules initially display a slight increase at low uptakes and follow a slow decrease at high uptakes. Accordingly, the interaction energies between CH 4 molecules and ZIF-10 remain nearly constant regardless of the loading due to the absence of hydrogen bonds (HBs), while the interaction energies between CO 2 (or SO 2 ) and ZIF-10 decease rapidly with the loading, especially at small amounts of gas molecules. Such different loading-dependent diffusion and interaction mechanisms can be attributed to the relevant HB behavior between gas molecules and ZIF-10. At low loadings, both the number and strength of HBs between CO 2 (or SO 2 ) molecules and ZIF-10 decrease obviously as the loading increases, which is responsible for the slight increase of their diffusion coefficients. However, at high loadings, their HB strength increases with the loading. Similar loading-dependent phenomena of diffusion, interaction, and HB behavior can be observed for CH 4, CO 2 , and SO 2 binary mixtures in ZIF-10, only associated with some HB competition between CO 2 and SO 2 molecules in the case of the CO 2 /SO 2 mixture.
Directory of Open Access Journals (Sweden)
Georg Lenz
2015-05-01
Full Text Available Within the last couple of years, the understanding of the molecular mechanisms that drive the pathogenesis of diffuse large B-cell lymphoma (DLBCL has significantly improved. Large-scale gene expression profiling studies have led to the discovery of several molecularly defined subtypes that are characterized by specific oncogene addictions and significant differences in their outcome. Next generation sequencing efforts combined with RNA interference screens frequently identify crucial oncogenes that lead to constitutive activation of various signaling pathways that drive lymphomagenesis. This review summarizes our current understanding of the molecular pathogenesis of the activated B-cell-like (ABC DLBCL subtype that is characterized by poor prognosis. A special emphasis is put on findings that might impact therapeutic strategies of affected patients.
Energy Technology Data Exchange (ETDEWEB)
Lenz, Georg [Translational Oncology, Department of Medicine A, Albert-Schweitzer Campus 1, University Hospital Münster, 48149 Münster (Germany); Cluster of Excellence EXC 1003, Cells in Motion, 48149 Münster (Germany)
2015-05-22
Within the last couple of years, the understanding of the molecular mechanisms that drive the pathogenesis of diffuse large B-cell lymphoma (DLBCL) has significantly improved. Large-scale gene expression profiling studies have led to the discovery of several molecularly defined subtypes that are characterized by specific oncogene addictions and significant differences in their outcome. Next generation sequencing efforts combined with RNA interference screens frequently identify crucial oncogenes that lead to constitutive activation of various signaling pathways that drive lymphomagenesis. This review summarizes our current understanding of the molecular pathogenesis of the activated B-cell-like (ABC) DLBCL subtype that is characterized by poor prognosis. A special emphasis is put on findings that might impact therapeutic strategies of affected patients.
Le Gall, O; Candresse, T; Dunez, J
1995-05-01
In grapevine chrome mosaic and tomato black ring viruses (GCMV and TBRV), as in many other nepoviruses, the 3' non-translated regions (3'NTR) are identical between the two genomic RNAs. We have investigated the structure of the 3'NTR of two recombinant isolates which contain GCMV RNA-1 and TBRV RNA-2. In these isolates, the 3'NTR of RNA-1 was transferred to RNA-2, thus restoring the 3' identity. The transfer occurred within three passages, and probably contributes to the spread of randomly appearing mutations from one genomic RNA to the other. The site of recombination is near the 3' end of the open reading frame.
Uekawa, Ken; Nakamura, Hideo; Shinojima, Naoki; Takezaki, Tatsuya; Yano, Shigetoshi; Kuratsu, Jun-Ichi
2016-04-01
Unlike in children, brain stem gliomas in adult are rare and still poorly understood. In addition, most adult brain stem gliomas result predominantly in the pons and are less often found in the medulla oblongata. Here, we report a case of an adult glioma in the medulla oblongata and its molecular biological features. A 46-year-old male presented with gait disturbance, paresthesia, and dysphagia. Magnetic resonance imaging (MRI) showed a diffuse hyper-intensive lesion in the medulla oblongata on a T 2 -weighted image without gadolinium contrast enhancement. We performed an open biopsy and the lesion was pathologically diagnosed as a diffuse astrocytoma. Molecular biological analyses revealed the absence of histone H3.3 mutation (H3F3A K27M), and presence of methylation of O-6-methylguanine-DNA methyltransferase (MGMT) promoter and a mutation in isocitrate dehydrogenase 1 (IDH-1). The patient received local radiotherapy and temozolomide chemotherapy. The patient's symptoms were ameliorated, and MRI showed no tumor growth at 6 months after the initial treatment. Biopsy for brain stem lesions is generally thought to have risk of complications, but if performed minimally, it is useful to diagnose and determine treatment strategy. Obtaining patient characteristics and molecular biological features will provide insight towards therapeutic treatment for adult brain stem gliomas.
High-precision molecular dynamics simulation of UO2–PuO2: Anion self-diffusion in UO2
International Nuclear Information System (INIS)
Potashnikov, S.I.; Boyarchenkov, A.S.; Nekrasov, K.A.; Kupryazhkin, A.Ya.
2013-01-01
Highlights: ► We perform MD simulation of oxygen diffusion in UO2 (up to 50 000 ions and 1 μs time). ► We reached 1400 K and 10 −12 cm 2 /sec, which allowed direct comparison to experiments. ► S-shaped T-dependence of activation energy and λ-peak of its derivative were obtained. ► Continual superionic phase transition (rather than first or second order) was proved. ► Activation energy of exchange diffusion equals anti-Frenkel defect formation energy. -- Abstract: Our series of articles is devoted to high-precision molecular dynamics simulation of mixed actinide-oxide (MOX) fuel in the approximation of rigid ions and pair interactions (RIPI) using high-performance graphics processors (GPU). In this article we study self-diffusion mechanisms of oxygen anions in uranium dioxide (UO 2 ) with the 10 recent and widely used sets of interatomic pair potentials (SPP) under periodic (PBC) and isolated (IBC) boundary conditions. Wide range of measured diffusion coefficients (from 10 −3 cm 2 /s at melting point down to 10 −12 cm 2 /s at 1400 K) made possible a direct comparison (without extrapolation) of the simulation results with the experimental data, which have been known only at low temperatures (T < 1500 K). A highly detailed (with the temperature step of 1 K) calculation of the diffusion coefficient allowed us to plot temperature dependences of the diffusion activation energy and its derivative, both of which show a wide (∼1000 K) superionic transition region confirming the broad λ-peaks of heat capacity obtained by us earlier. It is shown that regardless of SPP the anion self-diffusion in model crystals without surface or artificially embedded defects goes on via exchange mechanism, rather than interstitial or vacancy mechanisms suggested by the previous works. The activation energy of exchange diffusion turned out to coincide with the anti-Frenkel defect formation energy calculated by the lattice statics
Energy Technology Data Exchange (ETDEWEB)
Karakasidis, T
1995-11-13
In the first part, we present a model of variable cationic charges based on a rigid ion potential. In order to implement the model we performed static and dynamic simulations in calcium fluoride. The structural properties do not depend on the way the model is adjusted but the anion diffusion and the high frequency dielectric constant do. These results allowed to specify the criteria to adjust the variable charge model. As indicated by the behaviour of optical phonons this model introduced a supplementary polarisation mechanism to the rigid ion model. In the second part of this work, we studied the structural and diffusional behaviour of a high angle tilt grain boundary in NiO by molecular dynamics, using a usual rigid ion model. We examined structures with and without point defects between 0 K and 2500 K. The structure without defects presents always the lowest potential energy. In the others structures the defects can cluster and sometimes cause local changes in the boundary. Computer simulated images of high resolution electron microscopy, produced using these structures, present a similarity with the experimental ones. We calculated in the same boundary the diffusion coefficient of a doubly charged nickel vacancy between 2250 k and 2650 K. The atomic trajectories reveal the existence of preferential migration paths for the vacancy. The grain boundary diffusion is slightly anisotropic which is in agreement with an extrapolation of experimental results. A similar study in the volume reveals a migration energy higher than in the grain boundary. The calculated quantities allow for an estimation of the nickel diffusion acceleration due to the boundary. This acceleration is significant, but lower than the one measured by certain authors in polycrystalline, NiO; other authors studying bicrystals have not observed any certain authors in polycrystalline, NiO; other authors studying bicrystals have not observed any acceleration. (author) 118 refs.
International Nuclear Information System (INIS)
Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge
2014-01-01
The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results
International Nuclear Information System (INIS)
Hermichen, W.D.; Schuetze, H.
1987-01-01
Investigations at natural gas fields as well as modelling experiments have pointed out that changes of the chemical and isotopic composition occur in the course of migration, accumulation and dispersion of natural gas. Dissolution and sorption processes as well as in particular the diffusion process are considered to be the elementary separation processes. The influences on dissolved and freely flowing gases and on stationary gas accumulation are described by differential equations. The simulation of the following phenomena is shown: (1) immigration of gas into the pore space which is hydrodynamically passive, (2) diffusive migration of gas into the environment of the accumulation, and (3) diffusive 'decompression' into the roof and the floor of a gas bed and a gas containing subsoil water stratum, respectively. (author)
Energy Technology Data Exchange (ETDEWEB)
Gao, Wei; Jiao, Yang; Dai, Lenore L., E-mail: Lenore.Dai@asu.edu [Arizona State University, School of Engineering of Matter, Transport, and Energy (United States)
2016-04-15
We have employed molecular dynamics simulations to systematically investigate the effects of nanoparticles’ structural and chemical properties on their diffusive behaviors at/across the water–benzene interface. Four different nanoparticles were studied: modified hydrocarbon nanoparticles with a mean diameter of 1.2 nm (1.2HCPs), modified hydrocarbon nanoparticles with a mean diameter of 0.6 nm (0.6HCPs), single-walled carbon nanotubes (SWCNTs), and buckyballs. We found that the diffusion coefficients of 0.6 and 1.2HCP were larger than the corresponding values predicted using the Stokes–Einstein (SE) equation and attributed this deviation to the small particle size and the anisotropy of the interface system. In addition, the observed directional diffusive behaviors for various particles were well-correlated with the derivative of the potential of mean force (PMF), which might indicate an effective driving force for the particles along the direction perpendicular to the interface. We also found that nanoparticles with isotropic shape and uniform surface, e.g., buckyballs, tend to have smaller diffusion coefficients than those of nanoparticles with comparable dimensions but anisotropic shapes and non-uniform surface composition, e.g., SWCNT and 0.6HCP. One possible hypothesis for this behavior is that the “perfect” isotropic shape and uniform surface of buckyballs result in a better-defined “solvation shell” (i.e., a shell of solution molecules), which leads to a larger “effective radius” of the particle, and thus, a reduced diffusion coefficient.
Molecular dynamics simulations using AMB06C, an in-house carbohydrate force field, (NPT ensembles, 1atm) were carried out on a periodic cell that contained a cyclic-DP-240 amylose fragment and TIP3P water molecules. Molecular conformation and movement of the amylose fragment and water molecules at ...
International Nuclear Information System (INIS)
Gupta, A.; Hong, S.; Moacanin, J.
1981-01-01
A method and apparatus for measuring thermal diffusivity and molecular relaxation processes in a sample material utilizing two light beams, one being a pulsed laser light beam for forming a thermal lens in the sample material, and the other being a relatively low power probe light beam for measuring changes in the refractive index of the sample material during formation and dissipation of the thermal lens. More specifically, a sample material is irradiated by relatively high power, short pulses from a dye laser. Energy from the pulses is absorbed by the sample material, thereby forming a thermal lens in the area of absorption. The pulse repetition rate is chosen so that the thermal lens is substantially dissipated by the time the next pulse reaches the sample material. A probe light beam, which in a specific embodiment is a relatively low power, continuous wave (Cw) laser beam, irradiates the thermal lens formed in the sample material. The intensity characteristics of the probe light beam subsequent to irradiation of the thermal lens is related to changes in the refractive index of the sample material as the thermal lens is formed and dissipated. A plot of the changes in refractive index as a function of time during formation of the thermal lens as reflected by changes in intensity of the probe beam, provides a curve related to molecular relaxation characteristics of the material, and a plot during dissipation of the thermal lens provides a curve related to the thermal diffusivity of the sample material
Energy Technology Data Exchange (ETDEWEB)
Kimmich, R; Nusser, W; Gneiting, T [Ulm Universitaet (Federal Republic of Germany). Sektion Kernresonanzspektroskopie
1990-04-01
A model theory is presented explaining a series of striking phenomena observed with nuclear magnetic relaxation in protein systems such as solutions or tissue. The frequency, concentration and temperature dependences of proton or deuteron relaxation times of protein solutions and tissue are explained. It is concluded that the translational diffusion of water molecules along the rugged surfaces of proteins and, to a minor degree, protein backbone fluctuations are crucial processes. The rate limiting factor of macromolecular tumbling is assumed to be given by the free water content in a certain analogy to the free-volume model of Cohen ad Turnbull. There are two characteristic water mass fractions indicating the saturation of the hydration shells and the onset of protein tumbling. A closed and relatively simple set of relaxation formulas is presented. The potentially fractal nature of the diffusion of water molecules on the protein surface is discussed. (author). 43 refs.; 4 figs.
Energy Technology Data Exchange (ETDEWEB)
Okuchi, T. [Okayama Univ., Misasa, Tottori (Japan); Moudrakovski, I.L.; Ripmeester, J.A. [National Research Council of Canada, Ottawa, ON (Canada). Steacie Inst. for Molecular Sciences
2008-07-01
The challenge of storing high-density hydrogen into compact host media was investigated. The conventional storage scheme where an aqueous solution is frozen with hydrogen gas is too slow for practical use in a hydrogen-based society. Therefore, the authors developed a faster method whereby hydrogen was stored into gas hydrates. The hydrogen gas was directly charged into hydrogen-free, crystalline hydrate powders with partly empty lattices. The storage kinetics and hydrogen diffusion into the hydrate was observed in situ by nuclear magnetic resonance (NMR) in a pressurized tube cell. At pressures up to 20 MPa, the storage was complete within 80 minutes, as observed by growth of stored-hydrogen peak into the hydrate. Hydrogen diffusion within the crystalline hydrate media is the rate-determining step of current storage scheme. Therefore, the authors measured the diffusion coefficient of hydrogen molecules using the pulsed field gradient NMR method. The results show that the stored hydrogen is very mobile at temperatures down to 250 K. As such, the powdered hydrate media should work well even in cold environments. Compared with more prevailing hydrogen storage media such as metal hydrides, clathrate hydrates have the advantage of being free from hydrogen embrittlement, more chemically durable, more environmentally sound, and economically affordable. It was concluded that the powdered clathrate hydrate is suitable as a hydrogen storage media. 22 refs., 4 figs.
International Nuclear Information System (INIS)
Roux, B.
1993-01-01
Superconducting radiofrequency cavities were chosen for most of the future particle accelerators. In the case of pure niobium cavities, several laboratories have observed degradation of superconducting properties related to the conditions of the cooling down process. This effect seems to stem from hydrogen contamination which occurs during surface treatments. With the aim to study the influence of different surface treatments on the hydrogen contamination depth concentration profiling of the near surface region (the first 200 nm) was first carried out by the classical ERDA technique with 30 nm depth resolution. In order to better localize hydrogen, the initial particle selecting device (Teflon foil) was replaced by an electromagnetic (ExB) filter improving then the depth resolution by a factor three. This study reveals an hydrogen segregation at the niobium surface. Such a result is in contradiction with the relative high experimental value of the hydrogen diffusion coefficient given by the literature. To understand the trapping mechanism of hydrogen, a simulation by molecular dynamics of this impurity diffusion process was performed. This approach requires the knowledge of the interatomic potential. The potential parameters were fitted with static and dynamic tests. Nb-Nb interaction is based on many body potential. Nb-H is represented by two body potential. The Arrhenius diagram of the diffusion coefficient achieved by dynamic for a single crystal provides too small activation energy in comparison with experimental results. However, in presence of defects, a simulation proves a large increase of these values. It is only around 1000 K that the diffusion of hydrogen is not altered by defects. This conclusion confirms the experimental results concerning a good characteristic of superconducting cavities after thermal treatments. (orig.)
Directory of Open Access Journals (Sweden)
Murat Kuscu
Full Text Available We consider a microfluidic molecular communication (MC system, where the concentration-encoded molecular messages are transported via fluid flow-induced convection and diffusion, and detected by a surface-based MC receiver with ligand receptors placed at the bottom of the microfluidic channel. The overall system is a convection-diffusion-reaction system that can only be solved by numerical methods, e.g., finite element analysis (FEA. However, analytical models are key for the information and communication technology (ICT, as they enable an optimisation framework to develop advanced communication techniques, such as optimum detection methods and reliable transmission schemes. In this direction, we develop an analytical model to approximate the expected time course of bound receptor concentration, i.e., the received signal used to decode the transmitted messages. The model obviates the need for computationally expensive numerical methods by capturing the nonlinearities caused by laminar flow resulting in parabolic velocity profile, and finite number of ligand receptors leading to receiver saturation. The model also captures the effects of reactive surface depletion layer resulting from the mass transport limitations and moving reaction boundary originated from the passage of finite-duration molecular concentration pulse over the receiver surface. Based on the proposed model, we derive closed form analytical expressions that approximate the received pulse width, pulse delay and pulse amplitude, which can be used to optimize the system from an ICT perspective. We evaluate the accuracy of the proposed model by comparing model-based analytical results to the numerical results obtained by solving the exact system model with COMSOL Multiphysics.
Fan, Ming
2017-12-16
Breast cancer heterogeneity is the main obstacle preventing the identification of patients with breast cancer with poor prognoses and treatment responses; however, such heterogeneity has not been well characterized. The purpose of this retrospective study was to reveal heterogeneous patterns in the apparent diffusion coefficient (ADC) signals in tumours and the surrounding stroma to predict molecular subtypes of breast cancer. A dataset of 126 patients with breast cancer, who underwent preoperative diffusion-weighted imaging (DWI) on a 3.0-T image system, was collected. Breast images were segmented into regions comprising the tumour and surrounding stromal shells in which features that reflect heterogeneous ADC signal distribution were extracted. For each region, imaging features were computed, including the mean, minimum, variance, interquartile range (IQR), range, skewness, kurtosis and entropy of ADC values. Univariate and stepwise multivariate logistic regression modelling was performed to identify the magnetic resonance imaging features that optimally discriminate luminal A, luminal B, human epidermal growth factor 2 (HER2)-enriched and basal-like molecular subtypes. The performance of the predictive models was evaluated using the area under the receiver operating characteristic curve (AUC). Univariate logistic regression analysis showed that the skewness in the tumour boundary achieved an AUC of 0.718 for discrimination between luminal A and non-luminal A tumours, whereas the IQR of the ADC value in the tumour boundary had an AUC of 0.703 for classification of the HER2-enriched subtype. Imaging features in the tumour boundary and the proximal peritumoral stroma corresponded to a higher overall prediction performance than those in other regions. A multivariate logistic regression model combining features in all the regions achieved an overall AUC of 0.800 for the classification of the four tumour subtypes. These findings suggest that features in the tumour
Fan, Ming; He, Ting; Zhang, Peng; Cheng, Hu; Zhang, Juan; Gao, Xin; Li, Lihua
2017-01-01
Breast cancer heterogeneity is the main obstacle preventing the identification of patients with breast cancer with poor prognoses and treatment responses; however, such heterogeneity has not been well characterized. The purpose of this retrospective study was to reveal heterogeneous patterns in the apparent diffusion coefficient (ADC) signals in tumours and the surrounding stroma to predict molecular subtypes of breast cancer. A dataset of 126 patients with breast cancer, who underwent preoperative diffusion-weighted imaging (DWI) on a 3.0-T image system, was collected. Breast images were segmented into regions comprising the tumour and surrounding stromal shells in which features that reflect heterogeneous ADC signal distribution were extracted. For each region, imaging features were computed, including the mean, minimum, variance, interquartile range (IQR), range, skewness, kurtosis and entropy of ADC values. Univariate and stepwise multivariate logistic regression modelling was performed to identify the magnetic resonance imaging features that optimally discriminate luminal A, luminal B, human epidermal growth factor 2 (HER2)-enriched and basal-like molecular subtypes. The performance of the predictive models was evaluated using the area under the receiver operating characteristic curve (AUC). Univariate logistic regression analysis showed that the skewness in the tumour boundary achieved an AUC of 0.718 for discrimination between luminal A and non-luminal A tumours, whereas the IQR of the ADC value in the tumour boundary had an AUC of 0.703 for classification of the HER2-enriched subtype. Imaging features in the tumour boundary and the proximal peritumoral stroma corresponded to a higher overall prediction performance than those in other regions. A multivariate logistic regression model combining features in all the regions achieved an overall AUC of 0.800 for the classification of the four tumour subtypes. These findings suggest that features in the tumour
Kuscu, Murat; Akan, Ozgur B
2018-01-01
We consider a microfluidic molecular communication (MC) system, where the concentration-encoded molecular messages are transported via fluid flow-induced convection and diffusion, and detected by a surface-based MC receiver with ligand receptors placed at the bottom of the microfluidic channel. The overall system is a convection-diffusion-reaction system that can only be solved by numerical methods, e.g., finite element analysis (FEA). However, analytical models are key for the information and communication technology (ICT), as they enable an optimisation framework to develop advanced communication techniques, such as optimum detection methods and reliable transmission schemes. In this direction, we develop an analytical model to approximate the expected time course of bound receptor concentration, i.e., the received signal used to decode the transmitted messages. The model obviates the need for computationally expensive numerical methods by capturing the nonlinearities caused by laminar flow resulting in parabolic velocity profile, and finite number of ligand receptors leading to receiver saturation. The model also captures the effects of reactive surface depletion layer resulting from the mass transport limitations and moving reaction boundary originated from the passage of finite-duration molecular concentration pulse over the receiver surface. Based on the proposed model, we derive closed form analytical expressions that approximate the received pulse width, pulse delay and pulse amplitude, which can be used to optimize the system from an ICT perspective. We evaluate the accuracy of the proposed model by comparing model-based analytical results to the numerical results obtained by solving the exact system model with COMSOL Multiphysics.
Directory of Open Access Journals (Sweden)
Ee-Cheng Khor
Full Text Available Prader-Willi Syndrome (PWS, a maternally imprinted disorder and leading cause of obesity, is characterised by insatiable appetite, poor muscle development, cognitive impairment, endocrine disturbance, short stature and osteoporosis. A number of causative loci have been located within the imprinted Prader-Willi Critical Region (PWCR, including a set of small non-translated nucleolar RNA's (snoRNA. Recently, micro-deletions in humans identified the snoRNA Snord116 as a critical contributor to the development of PWS exhibiting many of the classical symptoms of PWS. Here we show that loss of the PWCR which includes Snord116 in mice leads to a reduced bone mass phenotype, similar to that observed in humans. Consistent with reduced stature in PWS, PWCR KO mice showed delayed skeletal development, with shorter femurs and vertebrae, reduced bone size and mass in both sexes. The reduction in bone mass in PWCR KO mice was associated with deficiencies in cortical bone volume and cortical mineral apposition rate, with no change in cancellous bone. Importantly, while the length difference was corrected in aged mice, consistent with continued growth in rodents, reduced cortical bone formation was still evident, indicating continued osteoblastic suppression by loss of PWCR expression in skeletally mature mice. Interestingly, deletion of this region included deletion of the exclusively brain expressed Snord116 cluster and resulted in an upregulation in expression of both NPY and POMC mRNA in the arcuate nucleus. Importantly, the selective deletion of the PWCR only in NPY expressing neurons replicated the bone phenotype of PWCR KO mice. Taken together, PWCR deletion in mice, and specifically in NPY neurons, recapitulates the short stature and low BMD and aspects of the hormonal imbalance of PWS individuals. Moreover, it demonstrates for the first time, that a region encoding non-translated RNAs, expressed solely within the brain, can regulate bone mass in health
Li, Qi; Tan, Jonathan C.; Christie, Duncan; Bisbas, Thomas G.; Wu, Benjamin
2018-01-01
We present a series of adaptive mesh refinement hydrodynamic simulations of flat rotation curve galactic gas disks, with a detailed treatment of the interstellar medium (ISM) physics of the atomic to molecular phase transition under the influence of diffuse far-ultraviolet (FUV) radiation fields and cosmic-ray backgrounds. We explore the effects of different FUV intensities, including a model with a radial gradient designed to mimic the Milky Way. The effects of cosmic rays, including radial gradients in their heating and ionization rates, are also explored. The final simulations in this series achieve 4 pc resolution across the ˜20 kpc global disk diameter, with heating and cooling followed down to temperatures of ˜10 K. The disks are evolved for 300 Myr, which is enough time for the ISM to achieve a quasi-statistical equilibrium. In particular, the mass fraction of molecular gas is stabilized by ˜200 Myr. Additional global ISM properties are analyzed. Giant molecular clouds (GMCs) are also identified and the statistical properties of their populations are examined. GMCs are tracked as the disks evolve. GMC collisions, which may be a means of triggering star cluster formation, are counted and their rates are compared with analytic models. Relatively frequent GMC collision rates are seen in these simulations, and their implications for understanding GMC properties, including the driving of internal turbulence, are discussed.
Großerueschkamp, Frederik; Bracht, Thilo; Diehl, Hanna C.; Kuepper, Claus; Ahrens, Maike; Kallenbach-Thieltges, Angela; Mosig, Axel; Eisenacher, Martin; Marcus, Katrin; Behrens, Thomas; Brüning, Thomas; Theegarten, Dirk; Sitek, Barbara; Gerwert, Klaus
2017-03-01
Diffuse malignant mesothelioma (DMM) is a heterogeneous malignant neoplasia manifesting with three subtypes: epithelioid, sarcomatoid and biphasic. DMM exhibit a high degree of spatial heterogeneity that complicates a thorough understanding of the underlying different molecular processes in each subtype. We present a novel approach to spatially resolve the heterogeneity of a tumour in a label-free manner by integrating FTIR imaging and laser capture microdissection (LCM). Subsequent proteome analysis of the dissected homogenous samples provides in addition molecular resolution. FTIR imaging resolves tumour subtypes within tissue thin-sections in an automated and label-free manner with accuracy of about 85% for DMM subtypes. Even in highly heterogeneous tissue structures, our label-free approach can identify small regions of interest, which can be dissected as homogeneous samples using LCM. Subsequent proteome analysis provides a location specific molecular characterization. Applied to DMM subtypes, we identify 142 differentially expressed proteins, including five protein biomarkers commonly used in DMM immunohistochemistry panels. Thus, FTIR imaging resolves not only morphological alteration within tissue but it resolves even alterations at the level of single proteins in tumour subtypes. Our fully automated workflow FTIR-guided LCM opens new avenues collecting homogeneous samples for precise and predictive biomarkers from omics studies.
Li, Qi; Tan, Jonathan C.; Christie, Duncan; Bisbas, Thomas G.; Wu, Benjamin
2018-05-01
We present a series of adaptive mesh refinement hydrodynamic simulations of flat rotation curve galactic gas disks, with a detailed treatment of the interstellar medium (ISM) physics of the atomic to molecular phase transition under the influence of diffuse far-ultraviolet (FUV) radiation fields and cosmic-ray backgrounds. We explore the effects of different FUV intensities, including a model with a radial gradient designed to mimic the Milky Way. The effects of cosmic rays, including radial gradients in their heating and ionization rates, are also explored. The final simulations in this series achieve 4 pc resolution across the ˜20 kpc global disk diameter, with heating and cooling followed down to temperatures of ˜10 K. The disks are evolved for 300 Myr, which is enough time for the ISM to achieve a quasi-statistical equilibrium. In particular, the mass fraction of molecular gas is stabilized by ˜200 Myr. Additional global ISM properties are analyzed. Giant molecular clouds (GMCs) are also identified and the statistical properties of their populations are examined. GMCs are tracked as the disks evolve. GMC collisions, which may be a means of triggering star cluster formation, are counted and their rates are compared with analytic models. Relatively frequent GMC collision rates are seen in these simulations, and their implications for understanding GMC properties, including the driving of internal turbulence, are discussed.
Jarošová, Marie; Kučerová, Jana; Flodr, Patrik; Mikešová, Michaela; Procházka, Vít; Papajík, Tomáš
2014-04-01
The currently valid molecular genetic subclassification of patients with diffuse large B-cell lymphoma (DLBCL) into three prognostic subgroups based on expression profiling has been the objective of numerous genetic studies. In routine clinical practice, however, expression profiling technology remains unavailable for the most of centers. Apart from the technology, in some cases molecular genetic laboratories have problems obtaining high-quality material, i.e. fresh tissues, for RNA isolation to determine gene expression. One possibility is to determine the gene expression from RNA obtained by isolation from formalin-fixed, paraffin-embedded (FFPE) tissue. This pilot study aimed at isolating RNA from FFPE in patients diagnosed with DLBCL and verifying the potential use of such RNA for the expression analysis of 7 selected genes. Although the study showed that it is possible to isolate RNA and determine the expression of the selected genes from archival material, the values of relative expression of some genes in the set were too variable to be used for unambiguous prognostic classification. It was confirmed that retrospective analyses of selected genes may be performed with sufficient material obtained, and that properly archived blocks may be used for molecular biology analyses even after 8 years.
Energy Technology Data Exchange (ETDEWEB)
Indriolo, Nick; Neufeld, D. A. [Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218 (United States); Gerin, M. [LERMA, CNRS, Observatoire de Paris and ENS, F-75231 Paris Cedex 05 (France); Geballe, T. R. [Gemini Observatory, Hilo, HI 96720 (United States); Black, J. H. [Department of Earth and Space Sciences, Chalmers University of Technology, Onsala Space Observatory, SE-43992 Onsala (Sweden); Menten, K. M. [MPI fuer Radioastronomie, D-53121 Bonn (Germany); Goicoechea, J. R. [Departamento de Astrofisica, Centro de Astrobiologia (CSIC-INTA), E-28850 Madrid (Spain)
2012-10-20
Absorption lines from the molecules OH{sup +}, H{sub 2}O{sup +}, and H{sup +} {sub 3} have been observed in a diffuse molecular cloud along a line of sight near W51 IRS2. We present the first chemical analysis that combines the information provided by all three of these species. Together, OH{sup +} and H{sub 2}O{sup +} are used to determine the molecular hydrogen fraction in the outskirts of the observed cloud, as well as the cosmic-ray ionization rate of atomic hydrogen. H{sup +} {sub 3} is used to infer the cosmic-ray ionization rate of H{sub 2} in the molecular interior of the cloud, which we find to be {zeta}{sub 2} = (4.8 {+-} 3.4) Multiplication-Sign 10{sup -16} s{sup -1}. Combining the results from all three species we find an efficiency factor-defined as the ratio of the formation rate of OH{sup +} to the cosmic-ray ionization rate of H-of {epsilon} = 0.07 {+-} 0.04, much lower than predicted by chemical models. This is an important step in the future use of OH{sup +} and H{sub 2}O{sup +} on their own as tracers of the cosmic-ray ionization rate.
Czech Academy of Sciences Publication Activity Database
Lísal, Martin; Předota, Milan; Brennan, J.K.
2013-01-01
Roč. 39, č. 13 (2013), s. 1103-1120 ISSN 0892-7022 R&D Projects: GA ČR GA13-09914S Grant - others:GA ČR(CZ) GA13-08651S Institutional support: RVO:67985858 Keywords : molecular dynamics * reaction ensemble Monte Carlo * slit and cylindrical nanopores Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.119, year: 2013
Directory of Open Access Journals (Sweden)
Jörg Kärger
2013-07-01
Full Text Available The presence of mesopores in the interior of microporous particles may significantly improve their transport properties. Complementing previous macroscopic transient sorption experiments and pulsed field gradient NMR self-diffusion studies with such materials, the present study is dedicated to an in-depth study of molecular uptake and release on the individual particles of mesoporous zeolitic specimens, notably with samples of the narrow-pore structure types, CHA and LTA. The investigations are focused on determining the time constants and functional dependences of uptake and release. They include a systematic variation of the architecture of the mesopores and of the guest molecules under study as well as a comparison of transient uptake with blocked and un-blocked mesopores. In addition to accelerating intracrystalline mass transfer, transport enhancement by mesopores is found to be, possibly, also caused by a reduction of transport resistances on the particle surfaces.
van der Post, Rachel S; Gullo, Irene; Oliveira, Carla; Tang, Laura H; Grabsch, Heike I; O'Donovan, Maria; Fitzgerald, Rebecca C; van Krieken, Han; Carneiro, Fátima
Familial clustering is seen in 10 % of gastric cancer cases and approximately 1-3 % of gastric cancer arises in the setting of hereditary diffuse gastric cancer (HDGC). In families with HDGC, gastric cancer presents at young age. HDGC is predominantly caused by germline mutations in CDH1 and in a minority by mutations in other genes, including CTNNA1. Early stage HDGC is characterized by a few, up to dozens of intramucosal foci of signet ring cell carcinoma and its precursor lesions. These include in situ signet ring cell carcinoma and pagetoid spread of signet ring cells. Advanced HDGC presents as poorly cohesive/diffuse type carcinoma, normally with very few typical signet ring cells, and has a poor prognosis. Currently, it is unknown which factors drive the progression towards aggressive disease, but it is clear that most intramucosal lesions will not have such progression.Immunohistochemical profile of early and advanced HDGC is often characterized by abnormal E-cadherin immunoexpression, including absent or reduced membranous expression, as well as "dotted" or cytoplasmic expression. However, membranous expression of E-cadherin does not exclude HDGC. Intramucosal HDGC (pT1a) presents with an "indolent" phenotype, characterized by typical signet ring cells without immunoexpression of Ki-67 and p53, while advanced carcinomas (pT > 1) display an "aggressive" phenotype with pleomorphic cells, that are immunoreactive for Ki-67 and p53. These features show that the IHC profile is different between intramucosal and more advanced HDGC, providing evidence of phenotypic heterogeneity, and may help to define predictive biomarkers of progression from indolent to aggressive, widely invasive carcinomas.
Directory of Open Access Journals (Sweden)
Haiyan Wang
2014-01-01
Full Text Available Based on silsesquioxanes (SSO derived from the hydrolytic condensation of (γ-glycidyloxypropyltrimethoxysilane (GPMS and titanium tetrabutoxide (TTB, hybrid films on aluminum alloy (AA, film-GPMS-SSO (f-GS and f-GS-TTBi% (f-GSTT5%–25%, i = 5, 10, 15, 20 and 25 wt%, were prepared and tested by electrochemical measurements with typical potentiodynamic polarization curves. The Icorr values of the samples were significantly lower, comparing with the Icorr values of the f-GS, AA and f-GS modified tetraethoxysilane (TEOS in the previous study, which implies that the TTB5%–25% (TiO2 additions in the coatings indeed enhance the electrochemical corrosion resistance. Correlations between the film structures and anticorrosion properties were discussed. To validate the corresponding anticorrosion experiment results, different 3D-amorphous cubic unit cells were employed as models to investigate the self-diffusion coefficient (SDC for SO2, NO2 and H2O molecules by molecular dynamics (MD simulation. All of the SDCs calculated for SO2, NO2 and H2O diffusing in f-GSTT5%–25% cells were less than the SDCs in f-GS. These results validated the corresponding anticorrosion experiment results.
International Nuclear Information System (INIS)
Lemarechal, A.
1963-01-01
This report brings together the essential principles of thermal diffusion in the liquid and gaseous phases. The macroscopic and molecular aspects of the thermal diffusion constant are reviewed, as well as the various measurement method; the most important developments however concern the operation of the CLUSIUS and DICKEL thermo-gravitational column and its applications. (author) [fr
DEFF Research Database (Denmark)
Huang, Ru-Jin; Hou, Xiaolin; Hoffmann, Thorsten
2010-01-01
In this paper we present the evaluation and optimization of a new approach for the quantification of gaseous molecular iodine (I2) for laboratory- and field-based studies and its novel application for the measurement of radioactive molecular iodine. α-Cyclodextrin (α-CD) in combination with 129I......, and condition of release and derivatization of iodine, is extensively evaluated and optimized. The collection efficiency is larger than 98% and the limit of detection (LOD) obtained is 0.17 parts-per-trillion-by-volume (pptv) for a sampling duration of 30 min at 500 mL min−1. Furthermore, the potential use...... of this protocol for the determination of radioactive I2 at ultra trace level is also demonstrated when 129I− used in the coating is replaced by 127I− and a multiple denuder system is used. Using the present method we observed 25.7−108.6 pptv 127I2 at Mweenish Bay, Ireland and 108 molecule m−3 129I2 at Mainz...
Salinas, Octavio
2016-01-05
Fine-tuning the microporosity of PIM-1 by heat treatment was applied to develop a suitable carbon molecular sieve membrane for ethylene/ethane separation. Pristine PIM-1 films were heated from 400 to 800 °C under inert N2 atmosphere (< 2 ppm O2). At 400 °C, PIM-1 self-cross-linked and developed polar carbonyl and hydroxyl groups due to partial dioxane splitting in the polymer backbone. Significant degradation occurred at 600 °C due to carbonization of PIM-1 and resulted in 30% increase in cumulative surface area compared to its cross-linked predecessor. In addition, PIM-1-based CMS developed smaller ultramicropores with increasing pyrolysis temperature, which enhanced their molecular sieving capability by restricted diffusion of ethylene and ethane through the matrix due to microstructural carbon densification. Consequently, the pure-gas ethylene permeability (measured at 35 °C and 2 bar) decreased from 1600 Barrer for the pristine PIM-1 to 1.3 Barrer for the amorphous carbon generated at 800 °C, whereas the ethylene/ethane pure-gas selectivity increased significantly from 1.8 to 13.
Faussillon, Marine; Murakami, Ichiro; Bichat, Magalie; Telvi, Louise; Jeanpierre, Cécile; Nezelof, Christian; Jaubert, Francis; Gogusev, Jean
2008-07-01
The novel continuous cell line WT-Pe.1 was established in vitro from Wilms tumor with histological features of diffuse anaplasia. The cultures grew as poorly differentiated epithelial-like cells with pleomorphic polygonal shapes and formation of typical monolayers. WT-Pe.1 cells were immunoreactive for cytokeratin, vimentin, laminin, villin, CD10, and CD24 proteins. Conventional cytogenetic analysis by RHG-banding revealed a hypotriploid karyotype with numerous abnormalities including ring chromosomes, double-minutes, homogeneous staining regions, radial structures, dicentrics, and several marker chromosomes. Comparative genomic hybridization analysis revealed DNA copy numbers losses on chromosome segments 1p, 3p, 6q, 9q34.1 approximately q34.3, 11q24 approximately q25, 14q12 approximately qter, 16q, 18q, and 22q11 approximately q13; gain of genomic material was localized on chromosome arms 1q, 4p, 6q, and 7p and the entire chromosome 12. With DNA from the original tumor, copy number losses were detected on chromosomes 1p, 14q, 16q, 17q, and 22q and gains were observed on 1q, 4p, 8q, 12p, 12q, and chromosome 14p. Copy number amplifications of distinct loci were found on 1q21.1 and 4p15.3, as well as an elevated copy number of cyclin D2 (CCND2) and cyclin D associated kinase (CDK4) genes on chromosome 12 (confirmed by fluorescence in situ hybridization).
Energy Technology Data Exchange (ETDEWEB)
Liu, Jinchen; Keskin, Seda; Sholl, David S; Johnson, J. Karl
2011-05-01
Adsorption and diffusion of CO{sub 2}/CH{sub 4} and CH{sub 4}/H{sub 2} mixtures were computed in zeolite imidazolate frameworks (ZIFs), ZIF-68 and ZIF-70, using atomically detailed simulations. Adsorption selectivity, diffusion selectivity, and membrane selectivity of ZIFs were calculated based on the results of atomistic simulations. Mixture adsorption isotherms predicted by the ideal adsorbed solution theory agree well with the results of molecular simulations for both ZIFs. Mixture diffusivity calculations indicate that diffusion of CH{sub 4} is increased with increasing concentration of H{sub 2} in the CH{sub 4}/H{sub 2} mixture, while the diffusivity of H{sub 2} decreases with increasing CH{sub 4} concentration. In contrast, the diffusivity of CH{sub 4} is essentially independent of the concentration of CO{sub 2} in the CO{sub 2}/CH{sub 4} mixture, while CO{sub 2} diffusivity decreases with increased CH{sub 4} loading, even though the diffusivity of CH{sub 4} is substantially larger than that of CO{sub 2}. This unusual behavior can be explained in terms of differences in adsorption site preferences due to charge–quadrupole interactions.
DEFF Research Database (Denmark)
Visco, Carlo; Wang, Jinfen; Tisi, Maria Chiara
2017-01-01
apoptotic pathways, have higher proliferative index, and lack BCL2 translocations. CONCLUSIONS: HCV-positive DLBCL have distinct molecular and pathological features compared to the HCV-negative counterparts.British Journal of Cancer advance online publication, 26 September 2017; doi:10.1038/bjc.2017.345 www.bjcancer.com....... in lymphomagenesis, as witnessed by the curative potential of antiviral therapy in HCV-related low-grade B-cell lymphomas. METHODS: We performed a case-control study including 44 HCV-positive cases of de novo DLBCL, comparing them with 132 HCV-negative patients as controls (ratio 3 to 1). Cases and controls were...... for MYC, BCL2 and BCL6, TP53 mutations, and diagnostic specimens reviewed to exclude transformation from low-grade lymphoma. RESULTS: Compared to the HCV-negative controls, patients with HCV-positive de novo DLBCL had differential expression of genes that regulate innate immune response and modulate...
Directory of Open Access Journals (Sweden)
Alexander E. Kobryn
2016-04-01
Full Text Available Although better means to model the properties of bulk heterojunction molecular blends are much needed in the field of organic optoelectronics, only a small subset of methods based on molecular dynamics- and Monte Carlo-based approaches have been hitherto employed to guide or replace empirical characterization and testing. Here, we present the first use of the integral equation theory of molecular liquids in modelling the structural properties of blends of phenyl-C61-butyric acid methyl ester (PCBM with poly(3-hexylthiophene (P3HT and a carboxylated poly(3-butylthiophene (P3BT, respectively. For this, we use the Reference Interaction Site Model (RISM with the Universal Force Field (UFF to compute the microscopic structure of blends and obtain insight into the miscibility of its components. Input parameters for RISM, such as optimized molecular geometries and charge distribution of interaction sites, are derived by the Density Functional Theory (DFT methods. We also run Molecular Dynamics (MD simulation to compare the diffusivity of the PCBM in binary blends with P3HT and P3BT, respectively. A remarkably good agreement with available experimental data and results of alternative modelling/simulation is observed for PCBM in the P3HT system. We interpret this as a step in the validation of the use of our approach for organic photovoltaics and support of its results for new systems that do not have reference data for comparison or calibration. In particular, for the less-studied P3BT, our results show that expectations about its performance in binary blends with PCBM may be overestimated, as it does not demonstrate the required level of miscibility and short-range structural organization. In addition, the simulated mobility of PCBM in P3BT is somewhat higher than what is expected for polymer blends and falls into a range typical for fluids. The significance of our predictive multi-scale modelling lies in the insights it offers into nanoscale
Directory of Open Access Journals (Sweden)
Lucy C. Fox
2018-06-01
Full Text Available Primary cutaneous diffuse large B-cell lymphoma, leg type (PCDLBCL-LT is one of the well-recognized extranodal lymphomas commonly addicted to the B-cell receptor-MYD88 superpathway. We aimed to describe the genomic changes in a patient who progressed through treatment with ibrutinib, a Bruton’s tyrosine kinase (BTK inhibitor. An 80-year-old woman presented with multiply relapsed PCDLBCL-LT after multiple lines of chemoimmunotherapy and radiotherapy. Pre-treatment testing of the localized cutaneous tumor lesion on a lymphoid amplicon panel demonstrated an MYD88 p.L265P mutation. Ibrutinib therapy was subsequently commenced, resulting in complete resolution of the skin disease. Despite an ongoing skin response, the patient developed progressive nodal disease at two months. Genomic analysis of the cutaneous tumor sample at baseline was compared to that of the inguinal lymph node upon progression, and revealed the acquisition of multiple genomic changes. These included several aberrations expected to bypass BTK inhibition, including two CARD11-activating mutations, and a deleterious mutation in the nuclear factor kappa B (NF-κB negative regulator, NFKBIE. In addition, an IgH-IRF8 translocation was detected (which brings the IRF8 transcription factor under control of the immunoglobulin heavy chain locus, representing a third plausible mechanism contributing to ibrutinib resistance. Several copy-number changes occurred in both samples, including an amplification of 18q, which encodes the anti-apoptotic protein BCL2. We describe the first case of novel genomic changes of PCDLBCL-LT that occurred while on ibrutinib, providing important mechanistic insights into both pathogenesis and drug resistance.
Directory of Open Access Journals (Sweden)
Anil Babu Korrapati
Full Text Available BACKGROUND: Dengue is a mosquito-borne viral disease caused by four closely related serotypes of Dengue viruses (DENVs. This disease whose symptoms range from mild fever to potentially fatal haemorrhagic fever and hypovolemic shock, threatens nearly half the global population. There is neither a preventive vaccine nor an effective antiviral therapy against dengue disease. The difference between severe and mild disease appears to be dependent on the viral load. Early diagnosis may enable timely therapeutic intervention to blunt disease severity by reducing the viral load. Harnessing the therapeutic potential of RNA interference (RNAi to attenuate DENV replication may offer one approach to dengue therapy. METHODOLOGY/PRINCIPAL FINDINGS: We screened the non-translated regions (NTRs of the RNA genomes of representative members of the four DENV serotypes for putative siRNA targets mapping to known transcription/translation regulatory elements. We identified a target site in the 5' NTR that maps to the 5' upstream AUG region, a highly conserved cis-acting element essential for viral replication. We used a replication-defective human adenovirus type 5 (AdV5 vector to deliver a short-hairpin RNA (shRNA targeting this site into cells. We show that this shRNA matures to the cognate siRNA and is able to inhibit effectively antigen secretion, viral RNA replication and infectious virus production by all four DENV serotypes. CONCLUSION/SIGNIFICANCE: The data demonstrate the feasibility of using AdV5-mediated delivery of shRNAs targeting conserved sites in the viral genome to achieve inhibition of all four DENV serotypes. This paves the way towards exploration of RNAi as a possible therapeutic strategy to curtail DENV infection.
Directory of Open Access Journals (Sweden)
Matthew A. Brodsky
2012-08-01
Full Text Available Background: It is generally agreed that diffusion of botulinum toxin occurs, but the extent of the spread and its clinical importance are disputed. Many factors have been suggested to play a role but which have the most clinical relevance is a subject of much discussion.Methods: This review discusses the variables affecting diffusion, including protein composition and molecular size as well as injection factors (e.g., volume, dose, injection method. It also discusses data on diffusion from comparative studies in animal models and human clinical trials that illustrate differences between the available botulinum toxin products (onabotulinumtoxinA, abobotulinumtoxinA, incobotulinumtoxinA, and rimabotulinumtoxinB.Results: Neither molecular weight nor the presence of complexing proteins appears to affect diffusion; however, injection volume, concentration, and dose all play roles and are modifiable. Both animal and human studies show that botulinum toxin products are not interchangeable, and that some products are associated with greater diffusion and higher rates of diffusion-related adverse events than others.Discussion: Each of the botulinum toxins is a unique pharmacologic entity. A working knowledge of the different serotypes is essential to avoid unwanted diffusion-related adverse events. In addition, clinicians should be aware that the factors influencing diffusion may range from properties intrinsic to the drug to accurate muscle selection as well as dilution, volume, and dose injected.
Thermal diffusion (1963); Diffusion thermique (1963)
Energy Technology Data Exchange (ETDEWEB)
Lemarechal, A [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires
1963-07-01
This report brings together the essential principles of thermal diffusion in the liquid and gaseous phases. The macroscopic and molecular aspects of the thermal diffusion constant are reviewed, as well as the various measurement method; the most important developments however concern the operation of the CLUSIUS and DICKEL thermo-gravitational column and its applications. (author) [French] Ce rapport rassemble les principes essentiels de la diffusion thermique en phase liquide et en phase gazeuse. Les aspects macroscopique et moleculaire de la constante de diffusion thermique sont passes en revue ainsi que ses differentes methodes de mesure; mais les developpements les plus importants concernent le fonctionnement de ls colonne thermogravitationnelle de CLUSIUS et DICKEL et ses applications. (auteur)
Diffusion in Coulomb crystals.
Hughto, J; Schneider, A S; Horowitz, C J; Berry, D K
2011-07-01
Diffusion in Coulomb crystals can be important for the structure of neutron star crusts. We determine diffusion constants D from molecular dynamics simulations. We find that D for Coulomb crystals with relatively soft-core 1/r interactions may be larger than D for Lennard-Jones or other solids with harder-core interactions. Diffusion, for simulations of nearly perfect body-centered-cubic lattices, involves the exchange of ions in ringlike configurations. Here ions "hop" in unison without the formation of long lived vacancies. Diffusion, for imperfect crystals, involves the motion of defects. Finally, we find that diffusion, for an amorphous system rapidly quenched from Coulomb parameter Γ=175 to Coulomb parameters up to Γ=1750, is fast enough that the system starts to crystalize during long simulation runs. These results strongly suggest that Coulomb solids in cold white dwarf stars, and the crust of neutron stars, will be crystalline and not amorphous.
International Nuclear Information System (INIS)
Black, J.H.
1987-01-01
The author defines and discusses the nature of diffuse interstellar clouds. He discusses how they contribute to the general extinction of starlight. The atomic and molecular species that have been identified in the ultraviolet, visible, and near infrared regions of the spectrum of a diffuse cloud are presented. The author illustrates some of the practical considerations that affect absorption line observations of interstellar atoms and molecules. Various aspects of the theoretical description of diffuse clouds required for a full interpretation of the observations are discussed
Infrared diffuse interstellar bands
Galazutdinov, G. A.; Lee, Jae-Joon; Han, Inwoo; Lee, Byeong-Cheol; Valyavin, G.; Krełowski, J.
2017-05-01
We present high-resolution (R ˜ 45 000) profiles of 14 diffuse interstellar bands in the ˜1.45 to ˜2.45 μm range based on spectra obtained with the Immersion Grating INfrared Spectrograph at the McDonald Observatory. The revised list of diffuse bands with accurately estimated rest wavelengths includes six new features. The diffuse band at 15 268.2 Å demonstrates a very symmetric profile shape and thus can serve as a reference for finding the 'interstellar correction' to the rest wavelength frame in the H range, which suffers from a lack of known atomic/molecular lines.
International Nuclear Information System (INIS)
Wold, S.; Eriksen, Trygve E.
2000-09-01
Diffusion of radionuclides in compacted bentonite can be affected by inorganic and organic colloids if the radionuclides form complexes with the colloids. Formation and mobility of the colloid-radionuclide complexes will be governed by the properties of the colloids as well as the competition between complexation and sorption of the radionuclides on bentonite. This report presents the results of experiments with organic colloids humic acid (HA) and lignosulfonate (LS). The aim of the experiments has been to describe the HA and LS properties: size distribution, acidity, sorption on bentonite, diffusivity in compacted bentonite, complexation with strontium, and diffusion of strontium in bentonite in the presence of HA. This study indicates that the diffusion of cationic radionuclides like Sr 2+ is not affected by the presence of HA in high ionic strength solution. In 0.1 M NaClO 4 solution, HA is most probably not available for complexation due to coiling and shielding of the negative sites
Energy Technology Data Exchange (ETDEWEB)
Moultos, Othonas A.; Economou, Ioannis G. [Chemical Engineering Program, Texas A& M University at Qatar, P.O. Box 23847, Doha (Qatar); Zhang, Yong; Maginn, Edward J., E-mail: ed@nd.edu [Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556 (United States); Tsimpanogiannis, Ioannis N. [Chemical Engineering Program, Texas A& M University at Qatar, P.O. Box 23847, Doha (Qatar); Environmental Research Laboratory, National Center for Scientific Research “Demokritos,” 15310 Aghia Paraskevi Attikis (Greece)
2016-08-21
Molecular dynamics simulations were carried out to study the self-diffusion coefficients of CO{sub 2}, methane, propane, n-hexane, n-hexadecane, and various poly(ethylene glycol) dimethyl ethers (glymes in short, CH{sub 3}O–(CH{sub 2}CH{sub 2}O){sub n}–CH{sub 3} with n = 1, 2, 3, and 4, labeled as G1, G2, G3, and G4, respectively) at different conditions. Various system sizes were examined. The widely used Yeh and Hummer [J. Phys. Chem. B 108, 15873 (2004)] correction for the prediction of diffusion coefficient at the thermodynamic limit was applied and shown to be accurate in all cases compared to extrapolated values at infinite system size. The magnitude of correction, in all cases examined, is significant, with the smallest systems examined giving for some cases a self-diffusion coefficient approximately 15% lower than the infinite system-size extrapolated value. The results suggest that finite size corrections to computed self-diffusivities must be used in order to obtain accurate results.
Cho, S. Y.; Yetter, R. A.; Dryer, F. L.
1992-01-01
Various chemically reacting flow problems highlighting chemical and physical fundamentals rather than flow geometry are presently investigated by means of a comprehensive mathematical model that incorporates multicomponent molecular diffusion, complex chemistry, and heterogeneous processes, in the interest of obtaining sensitivity-related information. The sensitivity equations were decoupled from those of the model, and then integrated one time-step behind the integration of the model equations, and analytical Jacobian matrices were applied to improve the accuracy of sensitivity coefficients that are calculated together with model solutions.
International Nuclear Information System (INIS)
Malek, Kourosh; Coppens, Marc-Olivier
2008-01-01
The analysis in Hu and Jiang's Comment to our paper cannot reveal long-time diffusion, and incorrectly led the authors to conclude that the diffusion in beta-lactoglobuline is anomalous. In this context, the limitations of applying a mean-square displacement analysis to short, heterogeneous pore channels are discussed. A more appropriate approach based on first-passage time analysis is illustrated by a detailed analysis of water motion in a natural membrane protein channel. The partitioning and the motion of water molecules between core and surface hydration layers is discussed. Finally, the calculation of the water density profile is commented upon. (reply)
Czech Academy of Sciences Publication Activity Database
Svoboda, Martin; Brennan, J. K.; Lísal, Martin
2015-01-01
Roč. 113, 9-10 (2015), s. 1124-1136 ISSN 0026-8976 R&D Projects: GA ČR(CZ) GA13-02938S Institutional support: RVO:67985858 Keywords : carbon dioxide separation * density profiles * self-diffusion coefficients Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.837, year: 2015
Corby, J. F.; McGuire, B. A.; Herbst, E.; Remijan, A. J.
2018-02-01
The 1-50 GHz PRebiotic Interstellar MOlecular Survey (PRIMOS) contains 50 molecular absorption lines observed in clouds located in the line-of-sight to Sgr B2(N). The line-of-sight material is associated with diffuse and translucent clouds located in the Galactic center, bar, and spiral arms in the disk. We measured the column densities and estimate abundances, relative to H2, of 11 molecules and additional isotopologues observed in this material. We used absorption by optically thin transitions of c-C3H2 to estimate the molecular hydrogen columns, and argue that this method is preferable to more commonly used methods. We discuss the kinematic structure and abundance patterns of small molecules including the sulfur-bearing species CS, SO, CCS, H2CS, and HCS+; oxygen-bearing molecules OH, SiO, and H2CO; and simple hydrocarbon molecules c-C3H2, l-C3H, and l-C3H+. Finally, we discuss the implications of the observed chemistry for the structure of the gas and dust in the ISM. Highlighted results include the following. First, whereas gas in the disk has a molecular hydrogen fraction of 0.65, clouds on the outer edge of the Galactic bar and in or near the Galactic center have molecular fractions of 0.85 and >0.9, respectively. Second, we observe trends in isotope ratios with Galactocentric distance; while carbon and silicon show enhancement of the rare isotopes at low Galactocentric distances, sulfur exhibits no trend with Galactocentric distance. We also determine that the ratio of c-C3H2/c-H13CCCH provides a good estimate of the 12C/13C ratio, whereas H2CO/H213CO exhibits fractionation. Third, we report the presence of l-C3H+ in diffuse clouds for the first time. Finally, we suggest that CS has an enhanced abundance within higher density clumps of material in the disk, and therefore may be diagnostic of cloud conditions. If this holds, the diffuse clouds in the Galactic disk contain multiple embedded hyperdensities in a clumpy structure, and the density profile is not
International Nuclear Information System (INIS)
Carlen, E.A.
1984-01-01
In Nelson's stochastic mechanics, quantum phenomena are described in terms of diffusions instead of wave functions. These diffusions are formally given by stochastic differential equations with extremely singular coefficients. Using PDE methods, we prove the existence of solutions. This reult provides a rigorous basis for stochastic mechanics. (orig.)
Shetty, Anil N; Chiang, Sharon; Maletic-Savatic, Mirjana; Kasprian, Gregor; Vannucci, Marina; Lee, Wesley
2014-01-01
In this article, we discuss the theoretical background for diffusion weighted imaging and diffusion tensor imaging. Molecular diffusion is a random process involving thermal Brownian motion. In biological tissues, the underlying microstructures restrict the diffusion of water molecules, making diffusion directionally dependent. Water diffusion in tissue is mathematically characterized by the diffusion tensor, the elements of which contain information about the magnitude and direction of diffusion and is a function of the coordinate system. Thus, it is possible to generate contrast in tissue based primarily on diffusion effects. Expressing diffusion in terms of the measured diffusion coefficient (eigenvalue) in any one direction can lead to errors. Nowhere is this more evident than in white matter, due to the preferential orientation of myelin fibers. The directional dependency is removed by diagonalization of the diffusion tensor, which then yields a set of three eigenvalues and eigenvectors, representing the magnitude and direction of the three orthogonal axes of the diffusion ellipsoid, respectively. For example, the eigenvalue corresponding to the eigenvector along the long axis of the fiber corresponds qualitatively to diffusion with least restriction. Determination of the principal values of the diffusion tensor and various anisotropic indices provides structural information. We review the use of diffusion measurements using the modified Stejskal-Tanner diffusion equation. The anisotropy is analyzed by decomposing the diffusion tensor based on symmetrical properties describing the geometry of diffusion tensor. We further describe diffusion tensor properties in visualizing fiber tract organization of the human brain.
Directory of Open Access Journals (Sweden)
Etienne CanouÃ¯
2017-11-01
Full Text Available An unusual case of pleural empyema related to Nocardia farcinica and Ureaplasma urealyticum, occurring after autologous haematopoietic stem cell transplantation in a 30-year-old patient with lymphoma, is reported. This case illustrates the role of repeated and comprehensive microbiological investigations and the contribution of molecular techniques in reaching the aetiological diagnosis. Keywords: Nocardia farcinica, Ureaplasma urealyticum, Pleuropneumonia, Immunocompromised patient, Molecular microbiological diagnosis
Golubev, V. A.; Kumeev, R. S.; Gurina, D. L.; Nikiforov, M. Yu.
2017-05-01
The effect of concentration on the self-diffusion coefficients of acetylsalicylic acid and methyl salicylate in methanol- d4 is investigated in the temperature range of 278-318 K using NMR. It is found that the self-diffusion coefficients increase along with temperature and fall as concentration rises. Within the limit of an infinitely dilute solution, the effective radii of solute molecules, calculated using the Stokes-Einstein equation shrink as the temperature grows. It is shown that the observed reduction of effective radii is associated with an increase in the fraction of solute monomers as the temperature rises. The physicochemical parameters of heteroassociation of acetylsalicylic acid and methyl salicylate with methanol are determined.
Diffusion Influenced Adsorption Kinetics.
Miura, Toshiaki; Seki, Kazuhiko
2015-08-27
When the kinetics of adsorption is influenced by the diffusive flow of solutes, the solute concentration at the surface is influenced by the surface coverage of solutes, which is given by the Langmuir-Hinshelwood adsorption equation. The diffusion equation with the boundary condition given by the Langmuir-Hinshelwood adsorption equation leads to the nonlinear integro-differential equation for the surface coverage. In this paper, we solved the nonlinear integro-differential equation using the Grünwald-Letnikov formula developed to solve fractional kinetics. Guided by the numerical results, analytical expressions for the upper and lower bounds of the exact numerical results were obtained. The upper and lower bounds were close to the exact numerical results in the diffusion- and reaction-controlled limits, respectively. We examined the validity of the two simple analytical expressions obtained in the diffusion-controlled limit. The results were generalized to include the effect of dispersive diffusion. We also investigated the effect of molecular rearrangement of anisotropic molecules on surface coverage.
Salinas, Octavio; Ma, Xiaohua; Litwiller, Eric; Pinnau, Ingo
2016-01-01
Fine-tuning the microporosity of PIM-1 by heat treatment was applied to develop a suitable carbon molecular sieve membrane for ethylene/ethane separation. Pristine PIM-1 films were heated from 400 to 800 °C under inert N2 atmosphere (< 2 ppm O2
Anomalous diffusion in chaotic scattering
International Nuclear Information System (INIS)
Srokowski, T.; Ploszajczak, M.
1994-01-01
The anomalous diffusion is found for peripheral collision of atomic nuclei described in the framework of the molecular dynamics. Similarly as for chaotic billiards, the long free paths are the source of the long-time correlations and the anomalous diffusion. Consequences of this finding for the energy dissipation in deep-inelastic collisions and the dynamics of fission in hot nuclei are discussed (authors). 30 refs., 2 figs
Fractional Diffusion Equations and Anomalous Diffusion
Evangelista, Luiz Roberto; Kaminski Lenzi, Ervin
2018-01-01
Preface; 1. Mathematical preliminaries; 2. A survey of the fractional calculus; 3. From normal to anomalous diffusion; 4. Fractional diffusion equations: elementary applications; 5. Fractional diffusion equations: surface effects; 6. Fractional nonlinear diffusion equation; 7. Anomalous diffusion: anisotropic case; 8. Fractional Schrödinger equations; 9. Anomalous diffusion and impedance spectroscopy; 10. The Poisson–Nernst–Planck anomalous (PNPA) models; References; Index.
Diffusion in membranes: Toward a two-dimensional diffusion map
Directory of Open Access Journals (Sweden)
Toppozini Laura
2015-01-01
Full Text Available For decades, quasi-elastic neutron scattering has been the prime tool for studying molecular diffusion in membranes over relevant nanometer distances. These experiments are essential to our current understanding of molecular dynamics of lipids, proteins and membrane-active molecules. Recently, we presented experimental evidence from X-ray diffraction and quasi-elastic neutron scattering demonstrating that ethanol enhances the permeability of membranes. At the QENS 2014/WINS 2014 conference we presented a novel technique to measure diffusion across membranes employing 2-dimensional quasi-elastic neutron scattering. We present results from our preliminary analysis of an experiment on the cold neutron multi-chopper spectrometer LET at ISIS, where we studied the self-diffusion of water molecules along lipid membranes and have the possibility of studying the diffusion in membranes. By preparing highly oriented membrane stacks and aligning them horizontally in the spectrometer, our aim is to distinguish between lateral and transmembrane diffusion. Diffusion may also be measured at different locations in the membranes, such as the water layer and the hydrocarbon membrane core. With a complete analysis of the data, 2-dimensional mapping will enable us to determine diffusion channels of water and ethanol molecules to quantitatively determine nanoscale membrane permeability.
International Nuclear Information System (INIS)
Lee, Gun Do; Wang, C. Z.; Lu, Z. Y.; Ho, K. M.
1999-01-01
The diffusion pathways along the trough and between the trough and the dimer row on the Si(100) surface are investigated by tight-binding molecular dynamics calculations using the environment dependent tight-binding silicon potential and by ab initio calculations using the Car-Parrinello method. The studies discover new diffusion pathways consisting of rotation of addimer. The calculated energy barrier are in excellent agreement with experiment. The rotational diffusion pathway between the trough and the dimer row is much more energetically favorable than other diffusion pathways by parallel and perpendicular addimer. The new pathway along the trough is nearly same as the energy barrier of the diffusion pathway by dissociation of the addimer
Energy Technology Data Exchange (ETDEWEB)
Slama, L [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires
1963-07-01
The experiments of the molecular scattering of light have been repeated using a ruby laser as a light source. The angular distribution of the scattered light intensity has been measured when the electric vector of the incident beam is either in the plane of observation or perpendicular to that plane. In the first case a good agreement with the Rayleigh theory has been found but this is not true in the second case. The differential cross sections for scattering have been measured for various gases. The values found are two or three times larger than the ones deduced from the classical theory. The possible effect of a variation of the beam intensity upon the linearity of the scattering process has been looked for. (author) [French] Les experiences sur la diffusion moleculaire de la lumiere ont ete reprises en utilisant un laser a rubis comme source lumineuse. La distribution angulaire de l'intensite diffusee a ete mesuree dans le cas ou le vecteur electrique de l'onde lumineuse incidente est soit dans le plan, soit perpendiculaire a ce plan. Dans le premier cas un bon accord est observe avec la theorie de Rayleigh, ce qui n'est plus vrai dans le second cas. Des sections efficaces differentielles de diffusion ont ete mesurees pour differents gaz. Les valeurs trouvees sont 2 a 3 fois plus grandes que celles prevues par la theorie classique. On a recherche enfin l'effet d'une variation d'intensite du faisceau du laser sur la linearite du phenomene de diffusion. (auteur)
Diffusivities and Viscosities of Poly(ethylene oxide) Oligomers †
Hong, Bingbing; Escobedo, Fernando; Panagiotopoulos, Athanassios Z.
2010-01-01
Diffusivities and viscosities of poly(ethylene oxide) (PEO) oligomer melts with 1 to 12 repeat units have been obtained from equilibrium molecular dynamics simulations using the TraPPE-UA force field. The simulations generated diffusion coefficients
Breuer, Tobias; Witte, Gregor
2013-10-09
A variety of low dimensional C60 structures has been grown on supporting pentacene multilayers. By choice of substrate temperature during growth the effective diffusion length of evaporated fullerenes and their nucleation at terraces or step edges can be precisely controlled. AFM and SEM measurements show that this enables the fabrication of either 2D adlayers or solely 1D chains decorating substrate steps, while at elevated growth temperature continuous wetting of step edges is prohibited and instead the formation of separated C60 clusters pinned at the pentacene step edges occurs. Remarkably, all structures remain thermally stable at room temperature once they are formed. In addition the various fullerene structures have been overgrown by an additional pentacene capping layer. Utilizing the different probe depth of XRD and NEXAFS, we found that no contiguous pentacene film is formed on the 2D C60 structure, whereas an encapsulation of the 1D and 0D structures with uniformly upright oriented pentacene is achieved, hence allowing the fabrication of low dimensional buried organic heterostructures.
International Nuclear Information System (INIS)
Anderson, R.C.
1976-01-01
A method is described for joining beryllium to beryllium by diffusion bonding. At least one surface portion of at least two beryllium pieces is coated with nickel. A coated surface portion is positioned in a contiguous relationship with another surface portion and subjected to an environment having an atmosphere at a pressure lower than ambient pressure. A force is applied on the beryllium pieces for causing the contiguous surface portions to abut against each other. The contiguous surface portions are heated to a maximum temperature less than the melting temperature of the beryllium, and the applied force is decreased while increasing the temperature after attaining a temperature substantially above room temperature. A portion of the applied force is maintained at a temperature corresponding to about maximum temperature for a duration sufficient to effect the diffusion bond between the contiguous surface portions
International Nuclear Information System (INIS)
Lalis, A.; Rouviere, R.; Simon, G.
1976-01-01
A multipassage diffuser having 2p passages comprises a leak-tight cylindrical enclosure closed by a top cover and a bottom end-wall, parallel porous tubes which are rigidly assembled in sectors between tube plates and through which the gas mixture flows, the tube sectors being disposed at uniform intervals on the periphery of the enclosure. The top tube plates are rigidly fixed to an annular header having the shape of a half-torus and adapted to communicate with the tubes of the corresponding sector. Each passage is constituted by a plurality of juxtaposed sectors in which the mixture circulates in the same direction, the header being divided into p portions limited by radial partition-walls and each constituting two adjacent passages. The diffuser is provided beneath the bottom end-wall with p-1 leak-tight chambers each adapted to open into two different portions of the header, and with two collector-chambers each fitted with a nozzle for introducing the gas mixture and discharging the fraction of the undiffused mixture. By means of a central orifice formed in the bottom end-wall the enclosure communicates with a shaft for discharging the diffused fraction of the gas mixture
Pham-Ledard, Anne; Prochazkova-Carlotti, Martina; Deveza, Mélanie; Laforet, Marie-Pierre; Beylot-Barry, Marie; Vergier, Béatrice; Parrens, Marie; Feuillard, Jean; Merlio, Jean-Philippe; Gachard, Nathalie
2017-11-01
Immunophenotype of primary cutaneous diffuse large B-cell lymphoma, leg-type (PCLBCL-LT) suggests a germinal center-experienced B lymphocyte (BCL2+ MUM1+ BCL6+/-). As maturation history of B-cell is "imprinted" during B-cell development on the immunoglobulin gene sequence, we studied the structure and sequence of the variable part of the genes (IGHV, IGLV, IGKV), immunoglobulin surface expression and features of class switching in order to determine the PCLBCL-LT cell of origin. Clonality analysis with BIOMED2 protocol and VH leader primers was done on DNA extracted from frozen skin biopsies on retrospective samples from 14 patients. The clonal DNA IGHV sequence of the tumor was aligned and compared with the closest germline sequence and homology percentage was calculated. Superantigen binding sites were studied. Features of selection pressure were evaluated with the multinomial Lossos model. A functional monoclonal sequence was observed in 14 cases as determined for IGHV (10), IGLV (2) or IGKV (3). IGV mutation rates were high (>5%) in all cases but one (median:15.5%), with superantigen binding sites conservation. Features of selection pressure were identified in 11/12 interpretable cases, more frequently negative (75%) than positive (25%). Intraclonal variation was detected in 3 of 8 tumor specimens with a low rate of mutations. Surface immunoglobulin was an IgM in 12/12 cases. FISH analysis of IGHM locus, deleted during class switching, showed heterozygous IGHM gene deletion in half of cases. The genomic PCR analysis confirmed the deletions within the switch μ region. IGV sequences were highly mutated but functional, with negative features of selection pressure suggesting one or more germinal center passage(s) with somatic hypermutation, but superantigen (SpA) binding sites conservation. Genetic features of class switch were observed, but on the non functional allele and co-existing with primary isotype IgM expression. These data suggest that cell-of origin is
International Nuclear Information System (INIS)
Habib, S.
1994-01-01
We consider a simple quantum system subjected to a classical random force. Under certain conditions it is shown that the noise-averaged Wigner function of the system follows an integro-differential stochastic Liouville equation. In the simple case of polynomial noise-couplings this equation reduces to a generalized Fokker-Planck form. With nonlinear noise injection new ''quantum diffusion'' terms rise that have no counterpart in the classical case. Two special examples that are not of a Fokker-Planck form are discussed: the first with a localized noise source and the other with a spatially modulated noise source
Hereditary Diffuse Gastric Cancer
... Hereditary Diffuse Gastric Cancer Request Permissions Hereditary Diffuse Gastric Cancer Approved by the Cancer.Net Editorial Board , 10/2017 What is hereditary diffuse gastric cancer? Hereditary diffuse gastric cancer (HDGC) is a rare ...
Some basic mathematical methods of diffusion theory. [emphasis on atmospheric applications
Giere, A. C.
1977-01-01
An introductory treatment of the fundamentals of diffusion theory is presented, starting with molecular diffusion and leading up to the statistical methods of turbulent diffusion. A multilayer diffusion model, designed to permit concentration and dosage calculations downwind of toxic clouds from rocket vehicles, is described. The concepts and equations of diffusion are developed on an elementary level, with emphasis on atmospheric applications.
Iotov, Mihail S.
The goals of this research are twofold: First, to develop methods and tools for studying problems in chemistry, material science and biology, as well as accurate prediction of the properties of structures and materials of importance to those fields. Second, use those tools to apply the methods to practical problems. In terms of methodology development this thesis focuses on two topics: One: Development of a massively parallel computer program to perform electronic, atomic, molecular levels simulations of problems in chemistry, material science and biology. This computer program uses existing and emerging hardware platforms and parallel tools and is based on decades long research in computer modeling and algorithms. We report on that development in Chapter 3. Two: Development of tools for Molecular Dynamics simulation and methods and tools for course-grained meso-scale modeling of transport properties and especially diffusion of gas penetrants in polymers. We have formulated a new method for extracting coarse-grained information from short (0.2-0.5 nanoseconds [ns]) MD simulations and use this in a meso-scale simulation to calculate diffusion constants in polymer matrices. This is a grid-based method, which calculates the average probability of each grid point of being a void and performs constrained and biased Monte Carlo (MC) dynamics to reach much longer time regimes than possible in MD. The MC method mimics the three regimes of mean square deviation (MSD) behavior seen in MD, thus accounting for the proper mobility of the voids and the compressibility of the polymer matrix. Theoretical discussions and justification for the method is presented in chapter 6. Initial results on He diffusion in a low-density polyethylene (PE) matrix are presented in chapter 7. The behavior at different temperatures follows closely the trend observed from calibrating long term MD for this particular system.
Mechanism for hydrogen diffusion in amorphous silicon
International Nuclear Information System (INIS)
Biswas, R.; Li, Q.; Pan, B.C.; Yoon, Y.
1998-01-01
Tight-binding molecular-dynamics calculations reveal a mechanism for hydrogen diffusion in hydrogenated amorphous silicon. Hydrogen diffuses through the network by successively bonding with nearby silicons and breaking their Si endash Si bonds. The diffusing hydrogen carries with it a newly created dangling bond. These intermediate transporting states are densely populated in the network, have lower energies than H at the center of stretched Si endash Si bonds, and can play a crucial role in hydrogen diffusion. copyright 1998 The American Physical Society
In situ measurement of diffusivity
International Nuclear Information System (INIS)
Berne, F.; Pocachard, J.
2004-01-01
The mechanism of molecular diffusion controls the migration of contaminants in very low-permeability porous media, like underground facilities for the storage of hazardous waste. Determining of relevant diffusion coefficients is therefore of prime importance. A few techniques exist for in situ measurement of the quantity, but they suffer from many handicaps (duration, complexity and cost of the experiments). We propose here two innovative methods that have some potential to improve the situation. So far, we have found them feasible on the basis of design calculations and laboratory experiments. This work is presently protected by a patent. (author)
In situ measurement of diffusivity
International Nuclear Information System (INIS)
Berne, Ph.; Pocachard, J.
2005-01-01
The mechanism of molecular diffusion controls the migration of contaminants in very low-permeability porous media, like underground facilities for the storage of hazardous waste. Determining the relevant diffusion coefficients is, therefore, of prime importance. A few techniques exist for the in situ measurement of that quantity, but they suffer from many handicaps (duration, complexity and cost of the experiments). We propose here two innovative methods that have some potential to improve this situation. So far, we have found them feasible on the basis of design calculations and laboratory experiments. This work is presently protected by a patent. (author)
Diffusion archeology for diffusion progression history reconstruction.
Sefer, Emre; Kingsford, Carl
2016-11-01
Diffusion through graphs can be used to model many real-world processes, such as the spread of diseases, social network memes, computer viruses, or water contaminants. Often, a real-world diffusion cannot be directly observed while it is occurring - perhaps it is not noticed until some time has passed, continuous monitoring is too costly, or privacy concerns limit data access. This leads to the need to reconstruct how the present state of the diffusion came to be from partial diffusion data. Here, we tackle the problem of reconstructing a diffusion history from one or more snapshots of the diffusion state. This ability can be invaluable to learn when certain computer nodes are infected or which people are the initial disease spreaders to control future diffusions. We formulate this problem over discrete-time SEIRS-type diffusion models in terms of maximum likelihood. We design methods that are based on submodularity and a novel prize-collecting dominating-set vertex cover (PCDSVC) relaxation that can identify likely diffusion steps with some provable performance guarantees. Our methods are the first to be able to reconstruct complete diffusion histories accurately in real and simulated situations. As a special case, they can also identify the initial spreaders better than the existing methods for that problem. Our results for both meme and contaminant diffusion show that the partial diffusion data problem can be overcome with proper modeling and methods, and that hidden temporal characteristics of diffusion can be predicted from limited data.
Single Crystal Diffuse Neutron Scattering
Directory of Open Access Journals (Sweden)
Richard Welberry
2018-01-01
Full Text Available Diffuse neutron scattering has become a valuable tool for investigating local structure in materials ranging from organic molecular crystals containing only light atoms to piezo-ceramics that frequently contain heavy elements. Although neutron sources will never be able to compete with X-rays in terms of the available flux the special properties of neutrons, viz. the ability to explore inelastic scattering events, the fact that scattering lengths do not vary systematically with atomic number and their ability to scatter from magnetic moments, provides strong motivation for developing neutron diffuse scattering methods. In this paper, we compare three different instruments that have been used by us to collect neutron diffuse scattering data. Two of these are on a spallation source and one on a reactor source.
Huang, Ru-Jin; Hoffmann, Thorsten
2009-03-01
This study concerns the development of a coupled diffusion denuder system capable of separating and quantifying gaseous molecular iodine (I(2)) and two other highly reactive iodine species, ICl and HOI, which are collectively named activated iodine compounds (AIC). Both I(2) and AIC are key species in the atmospheric chemistry of iodine. 1,3,5-Trimethoxybenzene (1,3,5-TMB)- and alpha-cyclodextrin/(129)I(-) (alpha-CD/(129)I(-))-coated denuders proved to be suitable for the collection of gaseous AIC and I(2), respectively. The experimental collection efficiencies for AIC (tested as ICl) and I(2) agreed well with the theoretical values for gas flow rates in the range between 300 and 1800 mL min(-1). The coupled denuder system (1,3,5-TMB-coated denuder as front-denuder coupled upstream of an alpha-CD/(129)I(-)-coated denuder) was applied successfully to separate test gas mixtures of ICl and I(2) at various mixing ratios in the laboratory. The operation of both denuder systems was demonstrated to be independent of relative humidity (0-100%) and storage period (at least 2 weeks prior to and after sampling). Detection limits were achieved at sub-parts-per-trillion-by-volume (sub-pptv) level. The presented method provides a reliable and practical approach for the speciation of gaseous iodine compounds. In addition, we report for the first time ambient air measurements of AIC mixing ratios, carried out at the atmospheric research station in Mace Head, Ireland. A maximum concentration of AIC of 30.2 pptv was observed for nighttime measurements and 6.0 pptv for daytime measurements. A similar diurnal pattern was found for I(2) with an average concentration level of 23.2 pptv during daytime and 85.1 pptv during nighttime, indicating a strong correlation with AIC.
Imaging and assessment of diffusion coefficients by magnetic resonance
International Nuclear Information System (INIS)
Tintera, J.; Dezortova, M.; Hajek, M.; Fitzek, C.
1999-01-01
The problem of assessment of molecular diffusion by magnetic resonance is highlighted and some typical applications of diffusion imaging in the diagnosis, e.g., of cerebral ischemia, changes in patients with phenylketonuria or multiple sclerosis are discussed. The images were obtained by using diffusion weighted spin echo Echo-Planar Imaging sequence with subsequent correction of the geometrical distortion of the images and calculation of the Apparent Diffusion Coefficient map
Diffusion and particle mobility in 1D system
International Nuclear Information System (INIS)
Borman, V.D.; Johansson, B.; Skorodumova, N.V.; Tronin, I.V.; Tronin, V.N.; Troyan, V.I.
2006-01-01
The transport properties of one-dimensional (1D) systems have been studied theoretically. Contradictory experimental results on molecular transport in quasi-1D systems, such as zeolite structures, when both diffusion transport acceleration and the existence of the diffusion mode with lower particle mobility (single-file diffusion ( 2 >∼t 1/2 )) have been reported, are consolidated in a consistent model. Transition from the single-file diffusion mode to an Einstein-like diffusion 2 >∼t with diffusion coefficient increasing with the density has been predicted to occur at large observation times
Excess Entropy and Diffusivity
Indian Academy of Sciences (India)
First page Back Continue Last page Graphics. Excess Entropy and Diffusivity. Excess entropy scaling of diffusivity (Rosenfeld,1977). Analogous relationships also exist for viscosity and thermal conductivity.
Ion diffusion in compacted bentonite
Energy Technology Data Exchange (ETDEWEB)
Lehikoinen, J. [VTT Chemical Technology, Espoo (Finland)
1999-03-01
In the study, a two-dimensional molecular-level diffusion model, based on a modified form of the Gouy-Chapman (GC) theory of the electrical double layers, for hydrated ionic species in compacted bentonite was developed. The modifications to the GC theory, which forms the very kernel of the diffusion model, stem from various non-conventional features: ionic hydration, dielectric saturation, finite ion-sizes and specific adsorption. The principal objectives of the study were met. With the aid of the consistent diffusion model, it is a relatively simple matter to explain the experimentally observed macroscopic exclusion for anions as well as the postulated, but greatly controversial, surface diffusion for cations. From purely theoretical grounds, it was possible to show that the apparent diffusivities of cations, anions and neutral molecules (i) do not exhibit order-or-magnitude differences, and (ii) are practically independent of the solution ionic strength used and, consequently, of the distribution coefficient, K{sub d}, unless they experience specific binding onto the substrate surface. It was also of interest to investigate the equilibrium anionic concentration distribution in the pore geometry of the GMM model as a function of the solution ionic strength, and to briefly speculate its consequences to diffusion. An explicit account of the filter-plate effect was taken by developing a computerised macroscopic diffusion model, which is based upon the very robust and efficient Laplace Transform Finite-Difference technique. Finally, the inherent limitations as well as the potential fields of applications of the models were addressed. (orig.) 45 refs.
Ion diffusion in compacted bentonite
International Nuclear Information System (INIS)
Lehikoinen, J.
1999-03-01
In the study, a two-dimensional molecular-level diffusion model, based on a modified form of the Gouy-Chapman (GC) theory of the electrical double layers, for hydrated ionic species in compacted bentonite was developed. The modifications to the GC theory, which forms the very kernel of the diffusion model, stem from various non-conventional features: ionic hydration, dielectric saturation, finite ion-sizes and specific adsorption. The principal objectives of the study were met. With the aid of the consistent diffusion model, it is a relatively simple matter to explain the experimentally observed macroscopic exclusion for anions as well as the postulated, but greatly controversial, surface diffusion for cations. From purely theoretical grounds, it was possible to show that the apparent diffusivities of cations, anions and neutral molecules (i) do not exhibit order-or-magnitude differences, and (ii) are practically independent of the solution ionic strength used and, consequently, of the distribution coefficient, K d , unless they experience specific binding onto the substrate surface. It was also of interest to investigate the equilibrium anionic concentration distribution in the pore geometry of the GMM model as a function of the solution ionic strength, and to briefly speculate its consequences to diffusion. An explicit account of the filter-plate effect was taken by developing a computerised macroscopic diffusion model, which is based upon the very robust and efficient Laplace Transform Finite-Difference technique. Finally, the inherent limitations as well as the potential fields of applications of the models were addressed. (orig.)
Stochastic models for surface diffusion of molecules
Energy Technology Data Exchange (ETDEWEB)
Shea, Patrick, E-mail: patrick.shea@dal.ca; Kreuzer, Hans Jürgen [Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Nova Scotia B3H 3J5 (Canada)
2014-07-28
We derive a stochastic model for the surface diffusion of molecules, starting from the classical equations of motion for an N-atom molecule on a surface. The equation of motion becomes a generalized Langevin equation for the center of mass of the molecule, with a non-Markovian friction kernel. In the Markov approximation, a standard Langevin equation is recovered, and the effect of the molecular vibrations on the diffusion is seen to lead to an increase in the friction for center of mass motion. This effective friction has a simple form that depends on the curvature of the lowest energy diffusion path in the 3N-dimensional coordinate space. We also find that so long as the intramolecular forces are sufficiently strong, memory effects are usually not significant and the Markov approximation can be employed, resulting in a simple one-dimensional model that can account for the effect of the dynamics of the molecular vibrations on the diffusive motion.
Protein diffusion in photopolymerized poly(ethylene glycol) hydrogel networks
International Nuclear Information System (INIS)
Engberg, Kristin; Frank, Curtis W
2011-01-01
In this study, protein diffusion through swollen hydrogel networks prepared from end-linked poly(ethylene glycol)-diacrylate (PEG-DA) was investigated. Hydrogels were prepared via photopolymerization from PEG-DA macromonomer solutions of two molecular weights, 4600 Da and 8000 Da, with three initial solid contents: 20, 33 and 50 wt/wt% PEG. Diffusion coefficients for myoglobin traveling across the hydrogel membrane were determined for all PEG network compositions. The diffusion coefficient depended on PEG molecular weight and initial solid content, with the slowest diffusion occurring through lower molecular weight, high-solid-content networks (D gel = 0.16 ± 0.02 x 10 -8 cm 2 s -1 ) and the fastest diffusion occurring through higher molecular weight, low-solid-content networks (D gel = 11.05 ± 0.43 x 10 -8 cm 2 s -1 ). Myoglobin diffusion coefficients increased linearly with the increase of water content within the hydrogels. The permeability of three larger model proteins (horseradish peroxidase, bovine serum albumin and immunoglobulin G) through PEG(8000) hydrogel membranes was also examined, with the observation that globular molecules as large as 10.7 nm in hydrodynamic diameter can diffuse through the PEG network. Protein diffusion coefficients within the PEG hydrogels ranged from one to two orders of magnitude lower than the diffusion coefficients in free water. Network defects were determined to be a significant contributing factor to the observed protein diffusion.
Diffusion weighted imaging by MR method
International Nuclear Information System (INIS)
Horikawa, Yoshiharu; Naruse, Shoji; Ebisu, Toshihiko; Tokumitsu, Takuaki; Ueda, Satoshi; Tanaka, Chuzo; Higuchi, Toshihiro; Umeda, Masahiro.
1993-01-01
Diffusion weighted magnetic resonance imaging is a recently developed technique used to examine the micromovement of water molecules in vivo. We have applied this technique to examine various kinds of brain diseases, both experimentally and clinically. The calculated apparent diffusion coefficient (ADC) in vivo showed reliable values. In experimentally induced brain edema in rats, the pathophysiological difference of the type of edema (such as cytotoxic, and vasogenic) could be differentiated on the diffusion weighted MR images. Cytotoxic brain edema showed high intensity (slower diffusion) on the diffusion weighted images. On the other hand, vasogenic brain edema showed a low intensity image (faster diffusion). Diffusion anisotropy was demonstrated according to the direction of myelinated fibers and applied motion proving gradient (MPG). This anisotropy was also demonstrated in human brain tissue along the course of the corpus callosum, pyramidal tract and optic radiation. In brain ischemia cases, lesions were detected as high signal intensity areas, even one hour after the onset of ischemia. Diffusion was faster in brain tumor compared with normal brain. Histological differences were not clearly reflected by the ADC value. In epidermoid tumor cases, the intensity was characteristically high, was demonstrated, and the cerebrospinal fluid border was clearly demonstrated. New clinical information obtainable with this molecular diffusion method will prove to be useful in various clinical studies. (author)
Diffusing diffusivity: Rotational diffusion in two and three dimensions
Jain, Rohit; Sebastian, K. L.
2017-06-01
We consider the problem of calculating the probability distribution function (pdf) of angular displacement for rotational diffusion in a crowded, rearranging medium. We use the diffusing diffusivity model and following our previous work on translational diffusion [R. Jain and K. L. Sebastian, J. Phys. Chem. B 120, 3988 (2016)], we show that the problem can be reduced to that of calculating the survival probability of a particle undergoing Brownian motion, in the presence of a sink. We use the approach to calculate the pdf for the rotational motion in two and three dimensions. We also propose new dimensionless, time dependent parameters, αr o t ,2 D and αr o t ,3 D, which can be used to analyze the experimental/simulation data to find the extent of deviation from the normal behavior, i.e., constant diffusivity, and obtain explicit analytical expressions for them, within our model.
International Nuclear Information System (INIS)
Tiwari, G.P.; Kale, G.B.; Patil, R.V.
1999-01-01
The article presents a brief survey of process of diffusion in solids. It is emphasised that the essence of diffusion is the mass transfer through the atomic jumps. To begin with formal equations for diffusion coefficient are presented. This is followed by discussions on mechanisms of diffusion. Except for solutes which form interstitial solid solution, diffusion in majority of cases is mediated through exchange of sites between an atom and its neighbouring vacancy. Various vacancy parameters such as activation volume, correlation factor, mass effect etc are discussed and their role in establishing the mode of diffusion is delineated. The contribution of dislocations and grain boundaries in diffusion process is brought out. The experimental determination of different types of diffusion coefficients are described. Finally, the pervasive nature of diffusion process in number of commercial processes is outlined to show the importance of diffusion studies in materials science and technology. (author)
Diffusion coefficients of paracetamol in aqueous solutions
International Nuclear Information System (INIS)
Ribeiro, Ana C.F.; Barros, Marisa C.F.; Veríssimo, Luís M.P.; Santos, Cecilia I.A.V.; Cabral, Ana M.T.D.P.V.; Gaspar, Gualter D.; Esteso, Miguel A.
2012-01-01
Highlights: ► Mutual diffusion coefficients of paracetamol in aqueous dilute solutions. ► Influence of the thermodynamic factors on the variation of their mutual diffusion coefficients. ► Estimation of the mutual limiting diffusion coefficients of the molecular, D m 0 , and ionized forms, D ± 0 , of this drug. - Abstract: Binary mutual diffusion coefficients measured by the Taylor dispersion method, for aqueous solutions of paracetamol (PA) at concentrations from (0.001 to 0.050) mol·dm −3 at T = 298.15 K, are reported. From the Nernst–Hartley equation and our experimental results, the limiting diffusion coefficient of this drug and its thermodynamic factors are estimated, thereby contributing in this way to a better understanding of the structure of such systems and of their thermodynamic behaviour in aqueous solution at different concentrations.
Diffusion archeology for diffusion progression history reconstruction
Sefer, Emre; Kingsford, Carl
2015-01-01
Diffusion through graphs can be used to model many real-world processes, such as the spread of diseases, social network memes, computer viruses, or water contaminants. Often, a real-world diffusion cannot be directly observed while it is occurring — perhaps it is not noticed until some time has passed, continuous monitoring is too costly, or privacy concerns limit data access. This leads to the need to reconstruct how the present state of the diffusion came to be from partial d...
Bois, Pierre-Antoine
Under realistic assumptions, we propose a thermodynamical formalism providing, for the moist-saturated air (cloudy air), a generalized Fick's law. This Fick's law leads to a double diffusive rheology with Dufour effect. The form taken by the energy equation is slightly different from the classical form used in convection problems. We compare the equations with those of the convection in moist unsaturated air (the Dufour effect and all double diffusive effects disappear in this case). As application we demonstrate some consequences of this diffusion in cloudy convection. To cite this article: P.A. Bois, C. R. Mecanique 330 (2002) 627-632.
Diffusion imaging and tractography of congenital brain malformations
International Nuclear Information System (INIS)
Wahl, Michael; Barkovich, A.J.; Mukherjee, Pratik
2010-01-01
Diffusion imaging is an MRI modality that measures the microscopic molecular motion of water in order to investigate white matter microstructure. The modality has been used extensively in recent years to investigate the neuroanatomical basis of congenital brain malformations. We review the basic principles of diffusion imaging and of specific techniques, including diffusion tensor imaging (DTI) and high angular resolution diffusion imaging (HARDI). We show how DTI and HARDI, and their application to fiber tractography, has elucidated the aberrant connectivity underlying a number of congenital brain malformations. Finally, we discuss potential uses for diffusion imaging of developmental disorders in the clinical and research realms. (orig.)
Diffusion of tritiated water (HTO) in dextran+water mixtures
International Nuclear Information System (INIS)
Comper, W.D.; Van Damme, M.P.I.; Preston, B.N.
1982-01-01
The diffusion of HTO has been measured in dextran solutions using an open-ended capillary technique and a newly developed Sundeloef diffusion cell. HTO diffusion has been examined as a function of dextran concentration and molecular weight. These results, together with our previous results on the intradiffusion and mutual-diffusion coefficients of dextrans, now provide a complete set of conventional translational diffusion coefficients for both components in this binary system. Various assumptions associated with the theoretical description of polymer translational motion can now be examined. (author)
New diffusion mechanism for high temperature diffusion in solids
International Nuclear Information System (INIS)
Doan, N.V.; Adda, Y.
1986-09-01
A new atomic transport mechanism in solids at high temperatures has been discovered by Molecular Dynamics computer simulation. It can be described as a ring sequence of atomic replacements induced by unstable Frenkel pairs. This transport process takes place without stable defects, the atomic migration occurring indeed by simultaneous creation and migration of unstable defects. Starting from the analysis of this mechanism in different solids at high temperature (CaF 2 , Na, Ar) and in irradiated copper by subthreshold collisions, we discuss the role of this mechanism on various diffusion controlled phenomena and also on the atomic processes of defect creation
Diffusion in reactor materials
International Nuclear Information System (INIS)
Fedorov, G.B.; Smirnov, E.A.
1984-01-01
The monograph contains a brief description of the principles underlying the theory of diffusion, as well as modern methods of studying diffusion. Data on self-diffusion and diffusion of impurities in a nuclear fuel and fissionable materials (uranium, plutonium, thorium, zirconium, titanium, hafnium, niobium, molybdenum, tungsten, beryllium, etc.) is presented. Anomalous diffusion, diffusion of components, and interdiffusion in binary and ternary alloys were examined. The monograph presents the most recent reference material on diffusion. It is intended for a wide range of researchers working in the field of diffusion in metals and alloys and attempting to discover new materials for application in nuclear engineering. It will also be useful for teachers, research scholars and students of physical metallurgy
International Nuclear Information System (INIS)
Reus, K.W.
1979-01-01
This thesis is concerned with the back-diffusion method of calculating the mutual diffusion coefficient of two gases. The applicability of this method for measuring diffusion coefficients at temperatures up to 1300 K is considered. A further aim of the work was to make a contribution to the description of the interatomic potential energy of noble gases at higher energies as a function of the internuclear distance. This was achieved with the measured diffusion coefficients, especially with those for high temperatures. (Auth.)
Diffusion Under Geometrical Constraint
Ogawa, Naohisa
2014-01-01
Here we discus the diffusion of particles in a curved tube. This kind of transport phenomenon is observed in biological cells and porous media. To solve such a problem, we discuss the three dimensional diffusion equation with a confining wall forming a thinner tube. We find that the curvature appears in a effective diffusion coefficient for such a quasi-one-dimensional system. As an application to higher dimensional case, we discuss the diffusion in a curved surface with ...
DEFF Research Database (Denmark)
Zhang, Chen
Diffuse ceiling ventilation is an innovative ventilation concept where the suspended ceiling serves as air diffuser to supply fresh air into the room. Compared with conventional ventilation systems, diffuse ceiling ventilation can significantly reduce or even eliminate draught risk due to the low...
Genetics and pharmacogenomics of diffuse gliomas
van Thuijl, H. F.; Ylstra, B.; Würdinger, T.; van Nieuwenhuizen, D.; Heimans, J. J.; Wesseling, P.; Reijneveld, J. C.
2013-01-01
Rapidly evolving techniques for analysis of the genome provide new opportunities for cancer therapy. For diffuse gliomas this has resulted in molecular markers with potential for personalized therapy. Some drugs that utilize pharmacogenomics are currently being tested in clinical trials. In
Molecular motion in restricted geometries
Indian Academy of Sciences (India)
Molecular dynamics in restricted geometries is known to exhibit anomalous behaviour. Diffusion, translational or rotational, of molecules is altered significantly on confinement in restricted geometries. Quasielastic neutron scattering (QENS) offers a unique possibility of studying molecular motion in such systems. Both time ...
Gas-induced friction and diffusion of rigid rotors
Martinetz, Lukas; Hornberger, Klaus; Stickler, Benjamin A.
2018-05-01
We derive the Boltzmann equation for the rotranslational dynamics of an arbitrary convex rigid body in a rarefied gas. It yields as a limiting case the Fokker-Planck equation accounting for friction, diffusion, and nonconservative drift forces and torques. We provide the rotranslational friction and diffusion tensors for specular and diffuse reflection off particles with spherical, cylindrical, and cuboidal shape, and show that the theory describes thermalization, photophoresis, and the inverse Magnus effect in the free molecular regime.
Fractional diffusion equations and anomalous diffusion
Evangelista, Luiz Roberto
2018-01-01
Anomalous diffusion has been detected in a wide variety of scenarios, from fractal media, systems with memory, transport processes in porous media, to fluctuations of financial markets, tumour growth, and complex fluids. Providing a contemporary treatment of this process, this book examines the recent literature on anomalous diffusion and covers a rich class of problems in which surface effects are important, offering detailed mathematical tools of usual and fractional calculus for a wide audience of scientists and graduate students in physics, mathematics, chemistry and engineering. Including the basic mathematical tools needed to understand the rules for operating with the fractional derivatives and fractional differential equations, this self-contained text presents the possibility of using fractional diffusion equations with anomalous diffusion phenomena to propose powerful mathematical models for a large variety of fundamental and practical problems in a fast-growing field of research.
Friction and diffusion dynamics of adsorbates at surfaces
Fusco, C.
2005-01-01
A theoretical study of the motion of adsorbates (e. g. atoms, molecules or clusters) on solid surfaces is presented, with a focus on surface diffusion and atomic-scale friction. These two phenomena are inextricably linked, because when an atomic or molecular adsorbate diffuses, or is pulled, it
Temperature dependence of Self-diffusion coefficient (SDC) of liquid ...
African Journals Online (AJOL)
PROF HORSFALL
2018-04-09
Apr 9, 2018 ... inverse square relationship between the natural logarithm of self-diffusion ... using the Equilibrium Molecular Dynamics (MD) and ..... Density, and Viscosity of Liquid Aluminum and. Iron. J. Phys. Chem. Ref. Data 35 ... Atomic Diffusion in Condensed Matter. Nature. 381: 137. Einstein, A (1905). Annalen der ...
A Simple Refraction Experiment for Probing Diffusion in Ternary Mixtures
Coutinho, Cecil A.; Mankidy, Bijith D.; Gupta, Vinay K.
2010-01-01
Diffusion is a fundamental phenomenon that is vital in many chemical processes such as mass transport in living cells, corrosion, and separations. We describe a simple undergraduate-level experiment based on Weiner's Method to probe diffusion in a ternary aqueous mixture of small molecular-weight molecules. As an illustration, the experiment…
Magnetic resonance temporal diffusion tensor spectroscopy of disordered anisotropic tissue
DEFF Research Database (Denmark)
Nielsen, Jonathan Scharff; Dyrby, Tim B; Lundell, Henrik
2018-01-01
Molecular diffusion measured with diffusion weighted MRI (DWI) offers a probe for tissue microstructure. However, inferring microstructural properties from conventional DWI data is a complex inverse problem and has to account for heterogeneity in sizes, shapes and orientations of the tissue...
Basic consideration of diffusion/perfusion imaging
International Nuclear Information System (INIS)
Tamagawa, Yoichi; Kimura, Hirohiko; Matsuda, Tsuyoshi; Kawamura, Yasutaka; Nakatsugawa, Shigekazu; Ishii, Yasushi; Sakuma, Hajime; Tsukamoto, Tetsuji.
1990-01-01
In magnetic resonance imaging (MRI), microscopic motion of biological system such as molecular diffusion of water and microcirculation of blood in the capillary network (perfusion) has been proposed to cause signal attenuation as an intravoxel incoherent motion (IVIM). Quantitative imaging of the IVIM phenomenon was attempted to generate from a set of spin-echo (SE) sequences with or without sensitization by motion probing gradient (MPG). The IVIM imaging is characterized by a parameter, apparent diffusion coefficient (ADC), which is an integration of both the diffusion and the perfusion factor on voxel-by-voxel basis. Hard ware was adjusted to avoid image artifact mainly produced by eddy current. Feasibility of the method was tested using bottle phantom filled with water at different temperature and acetone, and the calculated ADC values of these media corresponded well with accepted values of diffusion. The method was then applied to biological system to investigate mutual participation of diffusion/perfusion on the ADC value. The result of tumor model born on nude mouse suggested considerable participation of perfusion factor which immediately disappeared after sacrificing the animal. Meanwhile, lower value of sacrificed tissue without microcirculation was suggested to have some restriction of diffusion factor by biological tissue. To substantiate the restriction effect on the diffusion, a series of observation have made on a fiber phantom, stalk of celory with botanical fibers and human brain with nerve fibers, in applying unidirectional MPG along the course of these banch of fiber system. The directional restriction effect of diffusion along the course of fiber (diffusion anisotrophy) was clearly visualized as directional change of ADC value. The present method for tissue characterization by diffusion/perfusion on microscopic level will provide a new insight for evaluation of functional derangement in human brain and other organs. (author)
Stable isotope separation by thermal diffusion
International Nuclear Information System (INIS)
Vasaru, Gheorghe
2001-01-01
Thermal diffusion in both gaseous and liquid phase has been subject of extensive experimental and theoretical investigations, especially after the invention of K. Clusius and G. Dickel of the thermal diffusion column, sixty three years ago. This paper gives a brief overview of the most important research and developments performed during the time at the National Institute for Research and Development for Isotopic and Molecular Technology (ITIM) at Cluj - Napoca, Romania in the field of separation of stable isotopes by thermal diffusion. An retrospective analysis of the research and results concerning isotope separation by thermal diffusion entails the following conclusions: - thermal diffusion is an adequate method for hydrogen isotope separation (deuterium and tritium) and for noble gas isotope separation (He, Ne, Ar, Kr, Xe); - thermal diffusion is attractive also for 13 C enrichment using methane as raw material for separation, when annual yields of up to 100 g are envisaged; - lately, the thermal diffusion appears to be chosen as a final enrichment step for 17 O. An obvious advantage of this method is its non-specificity, i.e. the implied equipment can be utilized for isotope separation of other chemical elements too. Having in view the low investment costs for thermal diffusion cascades the method appears economically attractive for obtaining low-scale, laboratory isotope production. The paper has the following content: 1. The principle of method; 2. The method's application; 3. Research in the field of thermal diffusion at ITIM; 4. Thermal diffusion cascades for N, C, Ne, Ar and Kr isotope separation; 5. Conclusion
Diffusion in molybdenum disilicide
International Nuclear Information System (INIS)
Salamon, M.; Mehrer, H.
2005-01-01
The diffusion behaviour of the high-temperature material molybdenum disilicide (MoSi 2 ) was completely unknown until recently. In this paper we present studies of Mo self-diffusion and compare our present results with our already published studies of Si and Ge diffusion in MoSi 2 . Self-diffusion of molybdenum in monocrystalline MoSi 2 was studied by the radiotracer technique using the radioisotope 99 Mo. Deposition of the radiotracer and serial sectioning after the diffusion anneals to determine the concentration-depth profiles was performed using a sputtering device. Diffusion of Mo is a very slow process. In the entire temperature region investigated (1437 to 2173 K), the 99 Mo diffusivities in both principal directions of the tetragonal MoSi 2 crystals obey Arrhenius laws, where the diffusion perpendicular to the tetragonal axis is faster by two to three orders of magnitude than parallel to it. The activation enthalpies for diffusion perpendicular and parallel to the tetragonal axis are Q perpendicular to = 468 kJ mol -1 (4.85 eV) and Q parallel = 586 kJ mol -1 (6.07 eV), respectively. Diffusion of Si and its homologous element Ge is fast and is mediated by thermal vacancies of the Si sublattice of MoSi 2 . The diffusion of Mo is by several orders of magnitude slower than the diffusion of Si and Ge. This large difference suggests that Si and Mo diffusion are decoupled and that the diffusion of Mo likely takes place via vacancies on the Mo sublattice. (orig.)
Mechanism and kinetics of hydrated electron diffusion
International Nuclear Information System (INIS)
Tay, Kafui A.; Coudert, Francois-Xavier; Boutin, Anne
2008-01-01
Molecular dynamics simulations are used to study the mechanism and kinetics of hydrated electron diffusion. The electron center of mass is found to exhibit Brownian-type behavior with a diffusion coefficient considerably greater than that of the solvent. As previously postulated by both experimental and theoretical works, the instantaneous response of the electron to the librational motions of surrounding water molecules constitutes the principal mode of motion. The diffusive mechanism can be understood within the traditional framework of transfer diffusion processes, where the diffusive step is akin to the exchange of an extramolecular electron between neighboring water molecules. This is a second-order process with a computed rate constant of 5.0 ps -1 at 298 K. In agreement with experiment the electron diffusion exhibits Arrhenius behavior over the temperature range of 298-400 K. We compute an activation energy of 8.9 kJ mol -1 . Through analysis of Arrhenius plots and the application of a simple random walk model it is demonstrated that the computed rate constant for exchange of an excess electron is indeed the phenomenological rate constant associated with the diffusive process
Metric diffusion along foliations
Walczak, Szymon M
2017-01-01
Up-to-date research in metric diffusion along compact foliations is presented in this book. Beginning with fundamentals from the optimal transportation theory and the theory of foliations; this book moves on to cover Wasserstein distance, Kantorovich Duality Theorem, and the metrization of the weak topology by the Wasserstein distance. Metric diffusion is defined, the topology of the metric space is studied and the limits of diffused metrics along compact foliations are discussed. Essentials on foliations, holonomy, heat diffusion, and compact foliations are detailed and vital technical lemmas are proved to aide understanding. Graduate students and researchers in geometry, topology and dynamics of foliations and laminations will find this supplement useful as it presents facts about the metric diffusion along non-compact foliation and provides a full description of the limit for metrics diffused along foliation with at least one compact leaf on the two dimensions.
International Nuclear Information System (INIS)
Wong, Alexander; Glaister, Jeffrey; Cameron, Andrew; Haider, Masoom
2013-01-01
Prostate cancer is one of the leading causes of cancer death in the male population. Fortunately, the prognosis is excellent if detected at an early stage. Hence, the detection and localization of prostate cancer is crucial for diagnosis, as well as treatment via targeted focal therapy. New imaging techniques can potentially be invaluable tools for improving prostate cancer detection and localization. In this study, we introduce a new form of diffusion magnetic resonance imaging called correlated diffusion imaging, where the tissue being imaged is characterized by the joint correlation of diffusion signal attenuation across multiple gradient pulse strengths and timings. By taking into account signal attenuation at different water diffusion motion sensitivities, correlated diffusion imaging can provide improved delineation between cancerous tissue and healthy tissue when compared to existing diffusion imaging modalities. Quantitative evaluation using receiver operating characteristic (ROC) curve analysis, tissue class separability analysis, and visual assessment by an expert radiologist were performed to study correlated diffusion imaging for the task of prostate cancer diagnosis. These results are compared with that obtained using T2-weighted imaging and standard diffusion imaging (via the apparent diffusion coefficient (ADC)). Experimental results suggest that correlated diffusion imaging provide improved delineation between healthy and cancerous tissue and may have potential as a diagnostic tool for cancer detection and localization in the prostate gland. A new form of diffusion magnetic resonance imaging called correlated diffusion imaging (CDI) was developed for the purpose of aiding radiologists in cancer detection and localization in the prostate gland. Preliminary results show CDI shows considerable promise as a diagnostic aid for radiologists in the detection and localization of prostate cancer
International Nuclear Information System (INIS)
Garrett, G.A.; Shacter, J.
1978-01-01
A gaseous diffusion system is described comprising a plurality of diffusers connected in cascade to form a series of stages, each of the diffusers having a porous partition dividing it into a high pressure chamber and a low pressure chamber, and means for combining a portion of the enriched gas from a succeeding stage with a portion of the enriched gas from the low pressure chamber of each stage and feeding it into one extremity of the high pressure chamber thereof
Inpainting using airy diffusion
Lorduy Hernandez, Sara
2015-09-01
One inpainting procedure based on Airy diffusion is proposed, implemented via Maple and applied to some digital images. Airy diffusion is a partial differential equation with spatial derivatives of third order in contrast with the usual diffusion with spatial derivatives of second order. Airy diffusion generates the Airy semigroup in terms of the Airy functions which can be rewritten in terms of Bessel functions. The Airy diffusion can be used to smooth an image with the corresponding noise elimination via convolution. Also the Airy diffusion can be used to erase objects from an image. We build an algorithm using the Maple package ImageTools and such algorithm is tested using some images. Our results using Airy diffusion are compared with the similar results using standard diffusion. We observe that Airy diffusion generates powerful filters for image processing which could be incorporated in the usual packages for image processing such as ImageJ and Photoshop. Also is interesting to consider the possibility to incorporate the Airy filters as applications for smartphones and smart-glasses.
Diffusion in compacted betonite
International Nuclear Information System (INIS)
Muurinen, A.; Rantanen, J.
1985-01-01
The objective of this report is to collect the literature bearing on the diffusion in compacted betonite, which has been suggested as possible buffer material for the disposal of spent fuel. Diffusion in a porous, water-saturated material is usually described as diffusion in the pore-water where sorption on the solid matter can delay the migration in the instationary state. There are also models which take into consideration that the sorbed molecules can also move while being sorbed. Diffusion experiments in compacted bentonite have been reported by many authors. Gases, anions, cations and actinides have been used as diffusing molecules. The report collects the results and the information on the measurement methods. On the basis of the results can be concluded that different particles possibly follow different diffusion mechanisms. The parameters which affect the diffusion seem to be for example the size, the electric charge and the sorption properties of the diffusing molecule. The report also suggest the parameters to be used in the diffusion calculation of the safety analyses of spent fuel disposal. (author)
Diffusion of Hydrogen and Helium in Inconel 625
Palosz, W.; Gillies, D.; Lehoczky, S.
2006-01-01
Diffusion parameters for hydrogen and helium in Inconel 625 were investigated. The dependence of permeability of hydrogen in the temperature range 310 - 750 C is given. Solubility of hydrogen at 1 atm in the range 640 - 860 C was determined and diffusivity of the gas was calculated. Experiments with diffusion and solubility at 0.09 atm suggest a molecular mechanism of solution of hydrogen in the material. Diffusivity of helium was estimated at less than 10(exp -18) sq cm/s (at 1040 C).
Diffusion measurements in binary liquid mixtures by Raman spectroscopy
DEFF Research Database (Denmark)
Berg, Rolf W.; Hansen, Susanne Brunsgaard; Shapiro, Alexander
2007-01-01
It is shown that Raman spectroscopy allows determination of the molar fractions in mixtures subjected to molecular diffusion. Spectra of three binary systems, benzene/n-hexane, benzene/cyclohexane, and benzene/ acetone, were obtained during vertical (exchange) diffusion at several different heights...... in the literature were found, even in a thermostatically controlled diffusion cell, recording spectra through circulating water. For the system benzene/acetone, the determined diffusion coefficients were in good agreement with the literature data. The limitations of the Raman method are discussed...
Water vapor permeabilities through polymers: diffusivities from experiments and simulations
International Nuclear Information System (INIS)
Seethamraju, Sindhu; Ramamurthy, Praveen Chandrashekarapura; Madras, Giridhar
2014-01-01
This study experimentally determines water vapor permeabilities, which are subsequently correlated with the diffusivities obtained from simulations. Molecular dynamics (MD) simulations were used for determining the diffusion of water vapor in various polymeric systems such as polyethylene, polypropylene, poly (vinyl alcohol), poly (vinyl acetate), poly (vinyl butyral), poly (vinylidene chloride), poly (vinyl chloride) and poly (methyl methacrylate). Cavity ring down spectroscopy (CRDS) based methodology has been used to determine the water vapor transmission rates. These values were then used to calculate the diffusion coefficients for water vapor through these polymers. A comparative analysis is provided for diffusivities calculated from CRDS and MD based results by correlating the free volumes. (paper)
Diffusion quantum Monte Carlo for molecules
International Nuclear Information System (INIS)
Lester, W.A. Jr.
1986-07-01
A quantum mechanical Monte Carlo method has been used for the treatment of molecular problems. The imaginary-time Schroedinger equation written with a shift in zero energy [E/sub T/ - V(R)] can be interpreted as a generalized diffusion equation with a position-dependent rate or branching term. Since diffusion is the continuum limit of a random walk, one may simulate the Schroedinger equation with a function psi (note, not psi 2 ) as a density of ''walks.'' The walks undergo an exponential birth and death as given by the rate term. 16 refs., 2 tabs
New diffusion imaging method with a single acquisition sequence
International Nuclear Information System (INIS)
Melki, Ph.S.; Bittoun, J.; Lefevre, J.E.
1987-01-01
The apparent diffusion coefficient (ADC) is related to the molecular diffusion coefficient and to physiologic information: microcirculation in the capillary network, incoherent slow flow, and restricted diffusion. The authors present a new MR imaging sequence that yields computed ADC images in only one acquisition of 9-minutes with a 1.5-T imager (GE Signa). Compared to the previous method, this sequence is at least two times faster and thus can be used as a routine examination to supplement T1-, T2-, and density-weighted images. The method was assessed by measurement of the molecular diffusion in liquids, and the first clinical images obtained in neurologic diseases demonstrate its efficiency for clinical investigation. The possibility of separately imaging diffusion and perfusion is supported by an algorithm
Relativistic collective diffusion in one-dimensional systems
Lin, Gui-Wu; Lam, Yu-Yiu; Zheng, Dong-Qin; Zhong, Wei-Rong
2018-05-01
The relativistic collective diffusion in one-dimensional molecular system is investigated through nonequilibrium molecular dynamics with Monte Carlo methods. We have proposed the relationship among the speed, the temperature, the density distribution and the collective diffusion coefficient of particles in a relativistic moving system. It is found that the relativistic speed of the system has no effect on the temperature, but the collective diffusion coefficient decreases to zero as the velocity of the system approaches to the speed of light. The collective diffusion coefficient is modified as D‧ = D(1 ‑w2 c2 )3 2 for satisfying the relativistic circumstances. The present results may contribute to the understanding of the behavior of the particles transport diffusion in a high speed system, as well as enlighten the study of biological metabolism at relativistic high speed situation.
Predicting diffusivities in dense fluid mixtures
Directory of Open Access Journals (Sweden)
C. DARIVA
1999-09-01
Full Text Available In this work the Enskog solution of the Boltzmann equation, as corrected by Speedy, together with the Weeks-Chandler-Andersen (WCA perturbation theory of liquids is employed in correlating and predicting self-diffusivities of dense fluids. Afterwards this theory is used to estimate mutual diffusion coefficients of solutes at infinite dilution in sub and supercritical solvents. We have also investigated the behavior of Fick diffusion coefficients in the proximity of a binary vapor-liquid critical point since this subject is of great interest for extraction purposes. The approach presented here, which makes use of a density and temperature dependent hard-sphere diameter, is shown to be excellent for predicting diffusivities in dense pure fluids and fluid mixtures. The calculations involved highly nonideal mixtures as well as systems with high molecular asymmetry. The predicted diffusivities are in good agreement with the experimental data for the pure and binary systems. The methodology proposed here makes only use of pure component information and density of mixtures. The simple algebraic relations are proposed without any binary adjustable parameters and can be readily used for estimating diffusivities in multicomponent mixtures.
Concentration dependent hydrogen diffusion in tungsten
Energy Technology Data Exchange (ETDEWEB)
Ahlgren, T., E-mail: tommy.ahlgren@helsinki.fi; Bukonte, L.
2016-10-15
The diffusion of hydrogen in tungsten is studied as a function of temperature, hydrogen concentration and pressure using Molecular Dynamics technique. A new analysis method to determine diffusion coefficients that accounts for the random oscillation of atoms around the equilibrium position is presented. The results indicate that the hydrogen migration barrier of 0.25 eV should be used instead of the presently recommended value of 0.39 eV. This conclusion is supported by both experiments and density functional theory calculations. Moreover, the migration volume at the saddle point for H in W is found to be positive: ΔV{sub m} ≈ 0.488 Å{sup 3}, leading to a decrease in the diffusivity at high pressures. At high H concentrations, a dramatic reduction in the diffusion coefficient is observed, due to site blocking and the repulsive H-H interaction. The results of this study indicates that high flux hydrogen irradiation leads to much higher H concentrations in tungsten than expected. - Highlights: • The recommended value of 0.39 eV for the H in W migration barrier should be changed to 0.25 eV. • The random oscillation of atoms around the equilibrium position can be dealt with in diffusion simulations. • Hydrogen diffusion in tungsten is highly concentration dependent.
Discrimination of thermal diffusivity
Bergmann Tiest, W.M.; Kappers, A.M.L.
2009-01-01
Materials such as wood or metal which are at equal temperatures are perceived to be of different ‘coldness’ due to differences in thermal properties, such as the thermal diffusivity. The thermal diffusivity of a material is a parameter that controls the rate with which heat is extracted from the
Diffusion Based Photon Mapping
DEFF Research Database (Denmark)
Schjøth, Lars; Fogh Olsen, Ole; Sporring, Jon
2007-01-01
. To address this problem we introduce a novel photon mapping algorithm based on nonlinear anisotropic diffusion. Our algorithm adapts according to the structure of the photon map such that smoothing occurs along edges and structures and not across. In this way we preserve the important illumination features......, while eliminating noise. We call our method diffusion based photon mapping....
Diffusion Based Photon Mapping
DEFF Research Database (Denmark)
Schjøth, Lars; Olsen, Ole Fogh; Sporring, Jon
2006-01-01
. To address this problem we introduce a novel photon mapping algorithm based on nonlinear anisotropic diffusion. Our algorithm adapts according to the structure of the photon map such that smoothing occurs along edges and structures and not across. In this way we preserve the important illumination features......, while eliminating noise. We call our method diffusion based photon mapping....
Adaptation and Cultural Diffusion.
Ormrod, Richard K.
1992-01-01
Explores the role of adaptation in cultural diffusion. Explains that adaptation theory recognizes the lack of independence between innovations and their environmental settings. Discusses testing and selection, modification, motivation, and cognition. Suggests that adaptation effects are pervasive in cultural diffusion but require a broader, more…
Modelling of Innovation Diffusion
Directory of Open Access Journals (Sweden)
Arkadiusz Kijek
2010-01-01
Full Text Available Since the publication of the Bass model in 1969, research on the modelling of the diffusion of innovation resulted in a vast body of scientific literature consisting of articles, books, and studies of real-world applications of this model. The main objective of the diffusion model is to describe a pattern of spread of innovation among potential adopters in terms of a mathematical function of time. This paper assesses the state-of-the-art in mathematical models of innovation diffusion and procedures for estimating their parameters. Moreover, theoretical issues related to the models presented are supplemented with empirical research. The purpose of the research is to explore the extent to which the diffusion of broadband Internet users in 29 OECD countries can be adequately described by three diffusion models, i.e. the Bass model, logistic model and dynamic model. The results of this research are ambiguous and do not indicate which model best describes the diffusion pattern of broadband Internet users but in terms of the results presented, in most cases the dynamic model is inappropriate for describing the diffusion pattern. Issues related to the further development of innovation diffusion models are discussed and some recommendations are given. (original abstract
Energy Technology Data Exchange (ETDEWEB)
Cavillon, F
2004-10-15
This work presents a methodology for the analysis of the scattering spectra of neutrons on molecular liquids. This method is based on the adjustment of the molecular form factor concerning great momentum transfer. The subtraction of the intra-molecular contributions gives access to information on inter-molecular interactions such as the hydrogen bond. 3 systems with increasing levels of difficulty have been studied: the ammonia molecule, the N-methyl-formamide (NMF) and the N-methyl-acetamide (NMA). The value we get for the N-D intermolecular distance of the liquid ammonia molecule is 1.7 angstrom, this value is different from the value generally admitted (2.3 angstrom) but we have validated it by studying the isotopic substitution N{sup 14}/N{sup 15}. The adjustment to the NMF is obtained with a good accuracy but the characterization of the hydrogen bound is more delicate to infer. A preliminary study of the NMA molecule shows that this method can give relevant results on complex molecules.
Alignment dynamics of diffusive scalar gradient in a two-dimensional model flow
Gonzalez, M.
2018-04-01
The Lagrangian two-dimensional approach of scalar gradient kinematics is revisited accounting for molecular diffusion. Numerical simulations are performed in an analytic, parameterized model flow, which enables considering different regimes of scalar gradient dynamics. Attention is especially focused on the influence of molecular diffusion on Lagrangian statistical orientations and on the dynamics of scalar gradient alignment.
Michaud, Georges; Richer, Jacques
2015-01-01
This book gives an overview of atomic diffusion, a fundamental physical process, as applied to all types of stars, from the main sequence to neutron stars. The superficial abundances of stars as well as their evolution can be significantly affected. The authors show where atomic diffusion plays an essential role and how it can be implemented in modelling. In Part I, the authors describe the tools that are required to include atomic diffusion in models of stellar interiors and atmospheres. An important role is played by the gradient of partial radiative pressure, or radiative acceleration, which is usually neglected in stellar evolution. In Part II, the authors systematically review the contribution of atomic diffusion to each evolutionary step. The dominant effects of atomic diffusion are accompanied by more subtle effects on a large number of structural properties throughout evolution. One of the goals of this book is to provide the means for the astrophysicist or graduate student to evaluate the importanc...
Degenerate nonlinear diffusion equations
Favini, Angelo
2012-01-01
The aim of these notes is to include in a uniform presentation style several topics related to the theory of degenerate nonlinear diffusion equations, treated in the mathematical framework of evolution equations with multivalued m-accretive operators in Hilbert spaces. The problems concern nonlinear parabolic equations involving two cases of degeneracy. More precisely, one case is due to the vanishing of the time derivative coefficient and the other is provided by the vanishing of the diffusion coefficient on subsets of positive measure of the domain. From the mathematical point of view the results presented in these notes can be considered as general results in the theory of degenerate nonlinear diffusion equations. However, this work does not seek to present an exhaustive study of degenerate diffusion equations, but rather to emphasize some rigorous and efficient techniques for approaching various problems involving degenerate nonlinear diffusion equations, such as well-posedness, periodic solutions, asympt...
Cherniak, D. J.; Zhang, X. Y.; Nakamura, M.; Watson, E. B.
2004-09-01
We report measurements of oxygen diffusion in natural monazites under both dry, 1-atm conditions and hydrothermal conditions. For dry experiments, 18O-enriched CePO4 powder and monazite crystals were sealed in Ag-Pd capsules with a solid buffer (to buffer at NNO) and annealed in 1-atm furnaces. Hydrothermal runs were conducted in cold-seal pressure vessels, where monazite grains were encapsulated with 18O-enriched water. Following the diffusion anneals, oxygen concentration profiles were measured with Nuclear Reaction Analysis (NRA) using the reaction 18O(p,α)15N. Over the temperature range 850-1100 °C, the Arrhenius relation determined for dry diffusion experiments on monazite is given by: Under wet conditions at 100 MPa water pressure, over the temperature range 700-880 °C, oxygen diffusion can be described by the Arrhenius relationship: Oxygen diffusion under hydrothermal conditions has a significantly lower activation energy for diffusion than under dry conditions, as has been found the case for many other minerals, both silicate and nonsilicate. Given these differences in activation energies, the differences between dry and wet diffusion rates increase with lower temperatures; for example, at 600 °C, dry diffusion will be more than 4 orders of magnitude slower than diffusion under hydrothermal conditions. These disparate diffusivities will result in pronounced differences in the degree of retentivity of oxygen isotope signatures. For instance, under dry conditions (presumably rare in the crust) and high lower-crustal temperatures (∼800 °C), monazite cores of 70-μm radii will preserve O isotope ratios for about 500,000 years; by comparison, they would be retained at this temperature under wet conditions for about 15,000 years.
Diffusion of protein through the human cornea.
Charalel, Resmi A; Engberg, Kristin; Noolandi, Jaan; Cochran, Jennifer R; Frank, Curtis; Ta, Christopher N
2012-01-01
To determine the rate of diffusion of myoglobin and bovine serum albumin (BSA) through the human cornea. These small proteins have hydrodynamic diameters of approximately 4.4 and 7.2 nm, and molecular weights of 16.7 and 66 kDa, for myoglobin and BSA, respectively. Diffusion coefficients were measured using a diffusion chamber where the protein of interest and balanced salt solution were in different chambers separated by an ex vivo human cornea. Protein concentrations in the balanced salt solution chamber were measured over time. Diffusion coefficients were calculated using equations derived from Fick's law and conservation of mass in a closed system. Our experiments demonstrate that the diffusion coefficient of myoglobin is 5.5 ± 0.9 × 10(-8) cm(2)/s (n = 8; SD = 1.3 × 10(-8) cm(2)/s; 95% CI: 4.6 × 10(-8) to 6.4 × 10(-8) cm(2)/s) and the diffusion coefficient of BSA is 3.1 ± 1.0 × 10(-8) cm(2)/s (n = 8; SD = 1.4 × 10(-8) cm(2)/s; 95% CI: 2.1 × 10(-8) to 4.1 × 10(-8) cm(2)/s). Our study suggests that molecules as large as 7.2 nm may be able to passively diffuse through the human cornea. With applications in pharmacotherapy and the development of an artificial cornea, further experiments are warranted to fully understand the limits of human corneal diffusion and its clinical relevance. Copyright © 2012 S. Karger AG, Basel.
Mutual diffusion of sodium hyaluranate in aqueous solutions
International Nuclear Information System (INIS)
Veríssimo, Luís M.P.; Valada, Teresa I.C.; Sobral, Abilio J.F.N.; Azevedo, Eduarda E.F.G.; Azevedo, Maria L.G.; Ribeiro, Ana C.F.
2014-01-01
Highlights: • Binary diffusion coefficients for the systems containing sodium hyaluronate. • Influence of the aggregation on diffusion of the sodium hyaluronate in the aqueous media. • Estimation of the thermodynamic and mobility factors from mutual diffusion. -- Abstract: The Taylor dispersion technique has been used for measuring mutual diffusion coefficients of sodium hyaluronate in aqueous solutions at T = 298.15 K, and concentrations ranging from (0.00 to 0.50) g · dm −3 . The results are interpreted on the basis of Nernst, and Onsager and Fuoss theoretical equations. From the diffusion coefficient at infinitesimal concentration, the limiting ionic conductivity and the tracer diffusion coefficient of hyaluronate ion were estimated. These studies have been complemented by molecular mechanics calculations
International Nuclear Information System (INIS)
Mundy, J.N.; Rothman, S.J.; Lam, N.Q.; Nowicki, L.J.; Hoff, H.A.
1978-01-01
The lack of understanding of self-diffusion in Group VI metals together with the wide scatter in the measured values of tungsten self-diffusion has prompted the present measurements to be made over a wide temperature range (1/2Tsub(m) to Tsub(m)). The diffusion coefficients have been measured in the temperature range 1430-2630 0 C. The present measurements show non-linear Arrhenius behavior but a reliable two-exponential fit of the data should await further measurements. (Auth.)
Collective diffusion in carbon nanotubes: Crossover between one dimension and three dimensions
International Nuclear Information System (INIS)
Chen Pei-Rong; Xu Zhi-Cheng; Gu Yu; Zhong Wei-Rong
2016-01-01
Using non-equilibrium molecular dynamics and Monte Carlo methods, we study the collective diffusion of helium in carbon nanotubes. The results show that the collective diffusion coefficient (CDC) increases with the dimension of the channel. The collective diffusion coefficient has a linear relationship with the temperature and the concentration. There exist a ballistic transport in short carbon nanotubes and a diffusive transport in long carbon nanotubes. Fick’s law has an invalid region in the nanoscale channel. (paper)
Diffusion of hydrous species in model basaltic melt
Zhang, Li; Guo, Xuan; Wang, Qinxia; Ding, Jiale; Ni, Huaiwei
2017-10-01
Water diffusion in Fe-free model basaltic melt with up to 2 wt% H2O was investigated at 1658-1846 K and 1 GPa in piston-cylinder apparatus using both hydration and diffusion couple techniques. Diffusion profiles measured by FTIR are consistent with a model in which both molecular H2O (H2Om) and hydroxyl (OH) contribute to water diffusion. OH diffusivity is roughly 13% of H2Om diffusivity, showing little dependence on temperature or water concentration. Water diffusion is dominated by the motion of OH until total H2O (H2Ot) concentration reaches 1 wt%. The dependence of apparent H2Ot diffusivity on H2Ot concentration appears to be overestimated by a previous study on MORB melt, but H2Ot diffusivity at 1 wt% H2Ot in basaltic melt is still greater than those in rhyolitic to andesitic melts. The appreciable contribution of OH to water diffusion in basaltic melt can be explained by enhanced mobility of OH, probably associated with the development of free hydroxyl bonded with network-modifying cations, as well as higher OH concentration. Calculation based on the Nernst-Einstein equation demonstrates that OH may serve as an effective charge carrier in hydrous basaltic melt, which could partly account for the previously observed strong influence of water on electrical conductivity of basaltic melt.
International Nuclear Information System (INIS)
Brzoska, A.M.; Lenz, F.; Thies, M.; Negele, J.W.
2005-01-01
A phenomenological analysis of the distribution of Wilson loops in SU(2) Yang-Mills theory is presented in which Wilson loop distributions are described as the result of a diffusion process on the group manifold. It is shown that, in the absence of forces, diffusion implies Casimir scaling and, conversely, exact Casimir scaling implies free diffusion. Screening processes occur if diffusion takes place in a potential. The crucial distinction between screening of fundamental and adjoint loops is formulated as a symmetry property related to the center symmetry of the underlying gauge theory. The results are expressed in terms of an effective Wilson loop action and compared with various limits of SU(2) Yang-Mills theory
Diffusion between evolving interfaces
International Nuclear Information System (INIS)
Juntunen, Janne; Merikoski, Juha
2010-01-01
Diffusion in an evolving environment is studied by continuous-time Monte Carlo simulations. Diffusion is modeled by continuous-time random walkers on a lattice, in a dynamic environment provided by bubbles between two one-dimensional interfaces driven symmetrically towards each other. For one-dimensional random walkers constrained by the interfaces, the bubble size distribution dominates diffusion. For two-dimensional random walkers, it is also controlled by the topography and dynamics of the interfaces. The results of the one-dimensional case are recovered in the limit where the interfaces are strongly driven. Even with simple hard-core repulsion between the interfaces and the particles, diffusion is found to depend strongly on the details of the dynamical rules of particles close to the interfaces.
Peppin, Stephen S. L.
2009-01-01
concentrations they form a nearly rigid porous glass through which the fluid permeates. The theoretically determined pressure drop is nonlinear in the diffusion regime and linear in the permeation regime, in quantitative agreement with experimental measurements
DEFF Research Database (Denmark)
Pries-Heje, Jan; Baskerville, Richard
2014-01-01
approach. The study context is a design case in which an organization desires to diffuse its best practices across different groups. The design goal is embodied in organizational mechanisms to achieve this diffusion. The study used Theory of Planned Behavior (TPB) as a kernel theory. The artifacts...... resulting from the design were two-day training workshops conceptually anchored to TBP. The design theory was evaluated through execution of eight diffusion workshops involving three different groups in the same company. The findings indicate that the match between the practice and the context materialized...... that the behavior will be effective). These two factors were especially critical if the source context of the best practice is qualitatively different from the target context into which the organization is seeking to diffuse the best practice....
Detection of diffusible substances
Energy Technology Data Exchange (ETDEWEB)
Warembourg, M [Lille-1 Univ., 59 - Villeneuve-d' Ascq (France)
1976-12-01
The different steps of a radioautographic technique for the detection of diffusible substances are described. Using this radioautographic method, the topographic distribution of estradiol-concentrating neurons was studied in the nervous system and pituitary of the ovariectomized mouse and guinea-pig. A relatively good morphological preservation of structures can be ascertained on sections from unfixed, unembedded tissues prepared at low temperatures and kept-under relatively low humidity. The translocation or extraction of diffusible substances is avoided by directly mounting of frozen sections on dried photographic emulsion. Since no solvent is used, this technique excludes the major sources of diffusion artifacts and permits to be in favourable conditions for the localization of diffusible substances.
Peppin, Stephen S. L.
2009-01-01
Diffusion and permeation are discussed within the context of irreversible thermodynamics. A new expression for the generalized Stokes-Einstein equation is obtained which links the permeability to the diffusivity of a two-component solution and contains the poroelastic Biot-Willis coefficient. The theory is illustrated by predicting the concentration and pressure profiles during the filtration of a protein solution. At low concentrations the proteins diffuse independently while at higher concentrations they form a nearly rigid porous glass through which the fluid permeates. The theoretically determined pressure drop is nonlinear in the diffusion regime and linear in the permeation regime, in quantitative agreement with experimental measurements. © 2009 Walter de Gruyter, Berlin, New York.
Molecular machines open cell membranes.
García-López, Víctor; Chen, Fang; Nilewski, Lizanne G; Duret, Guillaume; Aliyan, Amir; Kolomeisky, Anatoly B; Robinson, Jacob T; Wang, Gufeng; Pal, Robert; Tour, James M
2017-08-30
Beyond the more common chemical delivery strategies, several physical techniques are used to open the lipid bilayers of cellular membranes. These include using electric and magnetic fields, temperature, ultrasound or light to introduce compounds into cells, to release molecular species from cells or to selectively induce programmed cell death (apoptosis) or uncontrolled cell death (necrosis). More recently, molecular motors and switches that can change their conformation in a controlled manner in response to external stimuli have been used to produce mechanical actions on tissue for biomedical applications. Here we show that molecular machines can drill through cellular bilayers using their molecular-scale actuation, specifically nanomechanical action. Upon physical adsorption of the molecular motors onto lipid bilayers and subsequent activation of the motors using ultraviolet light, holes are drilled in the cell membranes. We designed molecular motors and complementary experimental protocols that use nanomechanical action to induce the diffusion of chemical species out of synthetic vesicles, to enhance the diffusion of traceable molecular machines into and within live cells, to induce necrosis and to introduce chemical species into live cells. We also show that, by using molecular machines that bear short peptide addends, nanomechanical action can selectively target specific cell-surface recognition sites. Beyond the in vitro applications demonstrated here, we expect that molecular machines could also be used in vivo, especially as their design progresses to allow two-photon, near-infrared and radio-frequency activation.
Molecular machines open cell membranes
García-López, Víctor; Chen, Fang; Nilewski, Lizanne G.; Duret, Guillaume; Aliyan, Amir; Kolomeisky, Anatoly B.; Robinson, Jacob T.; Wang, Gufeng; Pal, Robert; Tour, James M.
2017-08-01
Beyond the more common chemical delivery strategies, several physical techniques are used to open the lipid bilayers of cellular membranes. These include using electric and magnetic fields, temperature, ultrasound or light to introduce compounds into cells, to release molecular species from cells or to selectively induce programmed cell death (apoptosis) or uncontrolled cell death (necrosis). More recently, molecular motors and switches that can change their conformation in a controlled manner in response to external stimuli have been used to produce mechanical actions on tissue for biomedical applications. Here we show that molecular machines can drill through cellular bilayers using their molecular-scale actuation, specifically nanomechanical action. Upon physical adsorption of the molecular motors onto lipid bilayers and subsequent activation of the motors using ultraviolet light, holes are drilled in the cell membranes. We designed molecular motors and complementary experimental protocols that use nanomechanical action to induce the diffusion of chemical species out of synthetic vesicles, to enhance the diffusion of traceable molecular machines into and within live cells, to induce necrosis and to introduce chemical species into live cells. We also show that, by using molecular machines that bear short peptide addends, nanomechanical action can selectively target specific cell-surface recognition sites. Beyond the in vitro applications demonstrated here, we expect that molecular machines could also be used in vivo, especially as their design progresses to allow two-photon, near-infrared and radio-frequency activation.
Directory of Open Access Journals (Sweden)
K. Banoo
1998-01-01
equation in the discrete momentum space. This is shown to be similar to the conventional drift-diffusion equation except that it is a more rigorous solution to the Boltzmann equation because the current and carrier densities are resolved into M×1 vectors, where M is the number of modes in the discrete momentum space. The mobility and diffusion coefficient become M×M matrices which connect the M momentum space modes. This approach is demonstrated by simulating electron transport in bulk silicon.
Advanced manufacturing: Technology diffusion
Energy Technology Data Exchange (ETDEWEB)
Tesar, A.
1995-12-01
In this paper we examine how manufacturing technology diffuses rom the developers of technology across national borders to those who do not have the capability or resources to develop advanced technology on their own. None of the wide variety of technology diffusion mechanisms discussed in this paper are new, yet the opportunities to apply these mechanisms are growing. A dramatic increase in technology diffusion occurred over the last decade. The two major trends which probably drive this increase are a worldwide inclination towards ``freer`` markets and diminishing isolation. Technology is most rapidly diffusing from the US In fact, the US is supplying technology for the rest of the world. The value of the technology supplied by the US more than doubled from 1985 to 1992 (see the Introduction for details). History shows us that technology diffusion is inevitable. It is the rates at which technologies diffuse to other countries which can vary considerably. Manufacturers in these countries are increasingly able to absorb technology. Their manufacturing efficiency is expected to progress as technology becomes increasingly available and utilized.
International Nuclear Information System (INIS)
Dungey, J.W.
1984-01-01
The authors want to talk about future work, but first he will reply to Stan Cowley's comment on his naivety in believing in the whole story to 99% confidence in '65, when he knew about Fairfield's results. Does it matter whether you make the right judgment about theories? Yes, it does, particularly for experimentalists perhaps, but also for theorists. The work you do later depends on the judgment you've made on previous work. People have wasted a lot of time developing on insecure or even wrong foundations. Now for future work. One mild surprise the authors have had is that they haven't heard more about diffusion, in two contexts. Gordon Rostoker is yet to come and he may talk about particles getting into the magnetosphere by diffusion. Lots of noise is observed and so diffusion must happen. If time had not been short, the authors were planning to discuss in a handwaving way what sort of diffusion mechanisms one might consider. The other aspect of diffusion he was going to talk about is at the other end of things and is velocity diffusion, which is involved in anomalous resistivity
Determination of Matrix Diffusion Properties of Granite
International Nuclear Information System (INIS)
Holtta, Pirkko; Siitari-Kauppi, Marja; Huittinen, Nina; Poteri, Antti
2007-01-01
Rock-core column experiments were introduced to estimate the diffusion and sorption properties of Kuru Grey granite used in block-scale experiments. The objective was to examine the processes causing retention in solute transport through rock fractures, especially matrix diffusion. The objective was also to estimate the importance of retention processes during transport in different scales and flow conditions. Rock-core columns were constructed from cores drilled into the fracture and were placed inside tubes to form flow channels in the 0.5 mm gap between the cores and the tube walls. Tracer experiments were performed using uranin, HTO, 36 Cl, 131 I, 22 Na and 85 Sr at flow rates of 1-50 μL.min -1 . Rock matrix was characterized using 14 C-PMMA method, scanning electron microscopy (SEM), energy dispersive X-ray micro analysis (EDX) and the B.E.T. method. Solute mass flux through a column was modelled by applying the assumption of a linear velocity profile and molecular diffusion. Coupling of the advection and diffusion processes was based on the model of generalised Taylor dispersion in the linear velocity profile. Experiments could be modelled applying a consistent parameterization and transport processes. The results provide evidence that it is possible to investigate matrix diffusion at the laboratory scale. The effects of matrix diffusion were demonstrated on the slightly-sorbing tracer breakthrough curves. Based on scoping calculations matrix diffusion begins to be clearly observable for non-sorbing tracer when the flow rate is 0.1 μL.min -1 . The experimental results presented here cannot be transferred directly to the spatial and temporal scales that prevail in an underground repository. However, the knowledge and understanding of transport and retention processes gained from this study is transferable to different scales from laboratory to in-situ conditions. (authors)
Advectional enhancement of eddy diffusivity under parametric disorder
International Nuclear Information System (INIS)
Goldobin, Denis S
2010-01-01
Frozen parametric disorder can lead to the appearance of sets of localized convective currents in an otherwise stable (quiescent) fluid layer heated from below. These currents significantly influence the transport of an admixture (or any other passive scalar) along the layer. When the molecular diffusivity of the admixture is small in comparison to the thermal one, which is quite typical in nature, disorder can enhance the effective (eddy) diffusivity by several orders of magnitude in comparison to the molecular diffusivity. In this paper, we study the effect of an imposed longitudinal advection on the delocalization of convective currents, both numerically and analytically, and report a subsequent drastic boost of the effective diffusivity for weak advection.
International Nuclear Information System (INIS)
Gardes, E.
2006-06-01
Proper knowledge of the diffusion rates of lead in monazite is necessary to understand the U-Th-Pb age anomalies of this mineral, which is one of the most used in geochronology after zircon. Diffusion experiments were performed in NdPO 4 monocrystals and in Nd 0.66 Ca 0.17 Th 0.17 PO 4 polycrystals from Nd 0.66 Pb 0.17 Th 0.17 PO 4 thin films to investigate Pb 2+ + Th 4+ ↔ 2 Nd 3+ and Pb 2+ ↔ Ca 2+ exchanges. Diffusion annealings were run between 1200 and 1500 Celsius degrees, at room pressure, for durations ranging from one hour to one month. The diffusion profiles were analysed using TEM (transmission electronic microscopy) and RBS (Rutherford backscattering spectroscopy). The diffusivities extracted for Pb 2+ + Th 4+ ↔ 2 Nd 3+ exchange follow an Arrhenius law with parameters E equals 509 ± 24 kJ mol -1 and log(D 0 (m 2 s -1 )) equals -3.41 ± 0.77. Preliminary data for Pb 2+ ↔ Ca 2+ exchange are in agreement with this result. The extrapolation of our data to crustal temperatures yields very slow diffusivities. For instance, the time necessary for a 50 μm grain to lose all of its lead at 800 Celsius degrees is greater than the age of the Earth. From these results and other evidence from the literature, we conclude that most of the perturbations in U-Th-Pb ages of monazite cannot be attributed to lead diffusion, but rather to interactions with fluids. (author)
Wetting and Diffusion of Water on Pristine and Strained Phosphorene
Zhang, Wei; Ye, Chao; Bi, Lin; Yang, Zaixing; Zhou, Ruhong
2015-01-01
Phosphorene, a newly fabricated two-dimensional (2D) nanomaterial, have exhibited promising application prospect in biology. Nonetheless, the wetting and diffusive properties of bio-fluids on phosphorene are still elusive. In this study, using molecular dynamics (MD) simulations, we investigated the structural and dynamic properties of water on pristine and strained phosphorene. The MD simulations illustrated that the diffusion of water molecules on the phosphorene surface is anisotropic, whi...
Bicarbonate diffusion through mucus.
Livingston, E H; Miller, J; Engel, E
1995-09-01
The mucus layer overlying duodenal epithelium maintains a pH gradient against high luminal acid concentrations. Despite these adverse conditions, epithelial surface pH remains close to neutrality. The exact nature of the gradient-forming barrier remains unknown. The barrier consists of mucus into which HCO3- is secreted. Quantification of the ability of HCO3- to establish and maintain the gradient depends on accurate measurement of this ion's diffusion coefficient through mucus. We describe new experimental and mathematical methods for diffusion measurement and report diffusion coefficients for HCO3- diffusion through saline, 5% mucin solutions, and rat duodenal mucus. The diffusion coefficients were 20.2 +/- 0.10, 3.02 +/- 0.31, and 1.81 +/- 0.12 x 10(-6) cm2/s, respectively. Modeling of the mucobicarbonate layer with this latter value suggests that for conditions of high luminal acid strength the neutralization of acid by HCO3- occurs just above the epithelial surface. Under these conditions the model predicts that fluid convection toward the lumen could be important in maintaining the pH gradient. In support of this hypothesis we were able to demonstrate a net luminal fluid flux of 5 microliters.min-1.cm-2 after perfusion of 0.15 N HCl in the rat duodenum.
Hydrogen diffusion along grain boundaries in erbium oxide coatings
International Nuclear Information System (INIS)
Mao, Wei; Chikada, Takumi; Suzuki, Akihiro; Terai, Takayuki
2014-01-01
Diffusion of interstitial atomic hydrogen in erbium oxide (Er 2 O 3 ) was investigated using density functional theory (DFT) and molecular dynamics (MD) methods. Hydrogen diffusivity in bulk, on (0 0 1) surface, and along Σ13 (4–3–1)/[1 1 1] symmetric tilt grain boundaries (GBs) were evaluated in a temperature range of 673–1073 K, as well as hydrogen diffusion barriers. It was found that H diffusion shows the faster on (0 0 1) surface than along GBs and in bulk. Also, energy barrier of H diffusion in bulk estimated by DFT and MD methods is somewhat higher than that along GBs evaluated in the experiments. This suggests that H diffusion in Er 2 O 3 coatings depends on GBs rather than bulk. In addition, with a correction of GB density, the simulated diffusivity along GBs in MD simulations is in good agreement with the experimental data within one order of magnitude. The discrepancy of H diffusivity between the experiments and the simulations should be reduced by considering H concentration, H diffusion direction, deviations of the initial configuration, vacancy defects, etc
International Nuclear Information System (INIS)
Evans, R.B. III; Davis, W. Jr.; Sutton, A.L. Jr.
1980-05-01
Experiments on diffusion of 137 Cs in five types of graphite were performed. The document provides a completion of the report that was started and includes a presentation of all of the diffusion data, previously unpublished. Except for data on mass transfer of 137 Cs in the Hawker-Siddeley graphite, analyses of experimental results were initiated but not completed. The mass transfer process of cesium in HS-1-1 graphite at 600 to 1000 0 C in a helium atmosphere is essentially pure diffusion wherein values of (E/epsilon) and ΔE of the equation D/epsilon = (D/epsilon) 0 exp [-ΔE/RT] are about 4 x 10 -2 cm 2 /s and 30 kcal/mole, respectively
Apparatus for diffusion separation
International Nuclear Information System (INIS)
Nierenberg, W.A.; Pontius, R.B.
1976-01-01
The method of testing the separation efficiency of porous permeable membranes is described which comprises causing a stream of a gaseous mixture to flow into contact with one face of a finely porous permeable membrane under such conditions that a major fraction of the mixture diffuses through the membrane, maintaining a rectangular cross section of the gaseous stream so flowing past said membrane, continuously recirculating the gas that diffuses through said membrane and continuously withdrawing the gas that does not diffuse through said membrane and maintaining the volume of said recirculating gas constant by continuously introducing into said continuously recirculating gas stream a mass of gas equivalent to that which is continuously withdrawn from said gas stream and comparing the concentrations of the light component in the entering gas, the withdrawn gas and the recirculated gas in order to determine the efficiency of said membrane
Energy Technology Data Exchange (ETDEWEB)
Brogaard Kristensen, S.
2000-06-01
This report describes the work done on modelling and simulation of the complex diffusion of gas through the wall of a flexible pipe. The diffusion and thus the pressure in annulus depends strongly on the diffusion and solubility parameters of the gas-polymer system and on the degree of blocking of the outer surface of the inner liner due to pressure reinforcements. The report evaluates the basis modelling required to describe the complex geometries and flow patterns. Qualitatively results of temperature and concentration profiles are shown in the report. For the program to serve any modelling purpose in 'real life' the results need to be validated and possibly the model needs corrections. Hopefully, a full-scale test of a flexible pipe will provide the required temperatures and pressures in annulus to validate the models. (EHS)
DEFF Research Database (Denmark)
Schultz, Ulrik Pagh
2007-01-01
. Programming a modular, self-reconfigurable robot is however a complicated task: the robot is essentially a real-time, distributed embedded system, where control and communication paths often are tightly coupled to the current physical configuration of the robot. To facilitate the task of programming modular....... This approach allows the programmer to dynamically distribute behaviors throughout a robot and moreover provides a partial abstraction over the concrete physical shape of the robot. We have implemented a prototype of a distributed control diffusion system for the ATRON modular, self-reconfigurable robot......, self-reconfigurable robots, we present the concept of distributed control diffusion: distributed queries are used to identify modules that play a specific role in the robot, and behaviors that implement specific control strategies are diffused throughout the robot based on these role assignments...
DEFF Research Database (Denmark)
Zhang, Chen; Yu, Tao; Heiselberg, Per Kvols
cooling capacity, energy saving, low investment cost and low noise level; while the limitations include condensation risk and the limit on the room geometry. Furthermore, the crucial design parameters are summarized and their effects on the system performance are discussed. In addition to the stand...... is not well structured with this system. These become the motivations in developing the design guide. This design guide aims to establish a systematic understanding of diffuse ceiling ventilation and provide assistance in designing of such a system. The guide is targeted at design engineers, architects...... and manufacturers and the users of diffuse ceiling technology. The design guide introduces the principle and key characteristics of room air distribution with diffuse ceiling ventilation. It provides an overview of potential benefit and limitations of this technology. The benefits include high thermal comfort, high...
Vrentas, James S
2013-01-01
The book first covers the five elements necessary to formulate and solve mass transfer problems, that is, conservation laws and field equations, boundary conditions, constitutive equations, parameters in constitutive equations, and mathematical methods that can be used to solve the partial differential equations commonly encountered in mass transfer problems. Jump balances, Green’s function solution methods, and the free-volume theory for the prediction of self-diffusion coefficients for polymer–solvent systems are among the topics covered. The authors then use those elements to analyze a wide variety of mass transfer problems, including bubble dissolution, polymer sorption and desorption, dispersion, impurity migration in plastic containers, and utilization of polymers in drug delivery. The text offers detailed solutions, along with some theoretical aspects, for numerous processes including viscoelastic diffusion, moving boundary problems, diffusion and reaction, membrane transport, wave behavior, sedime...
Energy Technology Data Exchange (ETDEWEB)
Brogaard Kristensen, S
2000-06-01
This report describes the work done on modelling and simulation of the complex diffusion of gas through the wall of a flexible pipe. The diffusion and thus the pressure in annulus depends strongly on the diffusion and solubility parameters of the gas-polymer system and on the degree of blocking of the outer surface of the inner liner due to pressure reinforcements. The report evaluates the basis modelling required to describe the complex geometries and flow patterns. Qualitatively results of temperature and concentration profiles are shown in the report. For the program to serve any modelling purpose in 'real life' the results need to be validated and possibly the model needs corrections. Hopefully, a full-scale test of a flexible pipe will provide the required temperatures and pressures in annulus to validate the models. (EHS)
Experimental Investigation of Radio-Turbulence Induced Diffusion -- Final Report
Energy Technology Data Exchange (ETDEWEB)
Spitz, H. B.; Usman, S.
2005-07-07
The outcome of this research project suggests that the transport of radon in water is significantly greater than that predicted solely by molecular diffusion. The original study was related to the long term storage of {sup 226}Ra-bearing sand at the DOE Fernald site and determining whether a barrier of water covering the sand would be effective in reducing the emanation of {sup 222}Rn from the sand. Initial observations before this study found the transport of radon in water to be greater than that predicted solely by molecular diffusion. Fick's law on diffusion was used to model the transport of radon in water including the impact associated with radioactive decay. Initial measurements suggested that the deposition of energy in water associated with the radioactive decay process influences diffusion and enhances transport of radon. A multi-region, one-dimensional, steady-state transport model was used to analyze the movement of radon through a sequential column of air, water and air. An effective diffusion coefficient was determined by varying the thickness of the water column and measuring the time for transport of {sup 222}Rn through of the water barrier. A one-region, one-dimensional transient diffusion equation was developed to investigate the build up of radon at the end of the water column to the time when a steady-state, equilibrium condition was achieved. This build up with time is characteristic of the transport rate of radon in water and established the basis for estimating the effective diffusion coefficient for {sup 222}Rn in water. Several experiments were conducted using different types and physical arrangements of water barriers to examine how radon transport is influenced by the water barrier. Results of our measurements confirm our theoretical analyses which suggest that convective forces other than pure molecular diffusion impact the transport of {sup 222}Rn through the water barrier. An effective diffusion coefficient is defined that
Time-delayed feedback control of diffusion in random walkers
Ando, Hiroyasu; Takehara, Kohta; Kobayashi, Miki U.
2017-07-01
Time delay in general leads to instability in some systems, while specific feedback with delay can control fluctuated motion in nonlinear deterministic systems to a stable state. In this paper, we consider a stochastic process, i.e., a random walk, and observe its diffusion phenomenon with time-delayed feedback. As a result, the diffusion coefficient decreases with increasing delay time. We analytically illustrate this suppression of diffusion by using stochastic delay differential equations and justify the feasibility of this suppression by applying time-delayed feedback to a molecular dynamics model.
Directory of Open Access Journals (Sweden)
R.T. DeHoff
2002-09-01
Full Text Available The phenomenological formalism, which yields Fick's Laws for diffusion in single phase multicomponent systems, is widely accepted as the basis for the mathematical description of diffusion. This paper focuses on problems associated with this formalism. This mode of description of the process is cumbersome, defining as it does matrices of interdiffusion coefficients (the central material properties that require a large experimental investment for their evaluation in three component systems, and, indeed cannot be evaluated for systems with more than three components. It is also argued that the physical meaning of the numerical values of these properties with respect to the atom motions in the system remains unknown. The attempt to understand the physical content of the diffusion coefficients in the phenomenological formalism has been the central fundamental problem in the theory of diffusion in crystalline alloys. The observation by Kirkendall that the crystal lattice moves during diffusion led Darken to develop the concept of intrinsic diffusion, i.e., atom motion relative to the crystal lattice. Darken and his successors sought to relate the diffusion coefficients computed for intrinsic fluxes to those obtained from the motion of radioactive tracers in chemically homogeneous samples which directly report the jump frequencies of the atoms as a function of composition and temperature. This theoretical connection between tracer, intrinsic and interdiffusion behavior would provide the basis for understanding the physical content of interdiffusion coefficients. Definitive tests of the resulting theoretical connection have been carried out for a number of binary systems for which all three kinds of observations are available. In a number of systems predictions of intrinsic coefficients from tracer data do not agree with measured values although predictions of interdiffusion coefficients appear to give reasonable agreement. Thus, the complete
Wu Zhuo Qun; Li Hui Lai; Zhao Jun Ning
2001-01-01
Nonlinear diffusion equations, an important class of parabolic equations, come from a variety of diffusion phenomena which appear widely in nature. They are suggested as mathematical models of physical problems in many fields, such as filtration, phase transition, biochemistry and dynamics of biological groups. In many cases, the equations possess degeneracy or singularity. The appearance of degeneracy or singularity makes the study more involved and challenging. Many new ideas and methods have been developed to overcome the special difficulties caused by the degeneracy and singularity, which
Phase transformation and diffusion
Kale, G B; Dey, G K
2008-01-01
Given that the basic purpose of all research in materials science and technology is to tailor the properties of materials to suit specific applications, phase transformations are the natural key to the fine-tuning of the structural, mechanical and corrosion properties. A basic understanding of the kinetics and mechanisms of phase transformation is therefore of vital importance. Apart from a few cases involving crystallographic martensitic transformations, all phase transformations are mediated by diffusion. Thus, proper control and understanding of the process of diffusion during nucleation, g
International Nuclear Information System (INIS)
Silva, T.L. da.
1987-01-01
Is this thesis, a numerical method for the solution of the linear diffusion equation for a plasma containing two types of ions, with the possibility of charge exchange, has been developed. It has been shown that the decay time of the electron and ion densities is much smaller than that in a plasma containing only a single type of ion. A non-linear diffusion equation, which includes the effects of an external electric field varying linearly in time, to describe a slightly ionized plasma has also been developed. It has been verified that the decay of the electron density in the presence of such an electric field is very slow. (author)
Axial dispersion via shear-enhanced diffusion in colloidal suspensions
Griffiths, I. M.
2012-03-01
The familiar example of Taylor dispersion of molecular solutes is extended to describe colloidal suspensions, where the fluctuations that contribute to dispersion arise from hydrodynamic interactions. The generic scheme is illustrated for a suspension of particles in a pressure-driven pipe flow, with a concentration-dependent diffusivity that captures both the shear-induced and Brownian contributions. The effect of the cross-stream migration via shear-induced diffusion is shown to dramatically reduce the axial dispersion predicted by classical Taylor dispersion for a molecular solute. Analytic and numerical solutions are presented that illustrate the effect of the concentration dependence of this nonlinear hydrodynamic mechanism. Copyright © EPLA, 2012.
International Nuclear Information System (INIS)
Chan, J.H.M.; Tsui, E.Y.K.; Yuen, M.K.; Peh, W.C.G.; Fong, D.; Fok, K.F.; Leung, K.M.; Fung, K.K.L.
2003-01-01
Myelinated axons of white matter demonstrate prominent directional differences in water diffusion. We performed diffusion-weighted imaging on ten patients with head injury to explore the feasibility of using water diffusion anisotropy for quantitating diffuse axonal injury. We showed significant decrease in diffusion anisotropy indices in areas with or without signal abnormality on T2 and T2*-weighted images. We conclude that the water diffusion anisotropy index a potentially useful, sensitive and quantitative way of diagnosing and assessing patients with diffuse axonal injury. (orig.)
Energy Technology Data Exchange (ETDEWEB)
Baig, Mohammad Saad, E-mail: saad110baig@gmail.com; Chakraborty, Brahmananda; Ramaniah, Lavanya M. [High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-85 (India)
2016-05-23
NaF-ZrF{sub 4} is used as a waste incinerator and as a coolant in Generation IV reactors.Structural and dynamical properties of molten NaF-ZrF{sub 4} system were studied along with Onsagercoefficients and Maxwell–Stefan (MS) Diffusivities applying Green–Kubo formalism and molecular dynamics (MD) simulations. The zirconium ions are found to be 8 fold coordinated with fluoride ions for all temperatures and concentrations. All the diffusive flux correlations show back-scattering. Even though the MS diffusivities are expected to depend very lightly on the composition because of decoupling of thermodynamic factor, the diffusivity Đ{sub Na-F} shows interesting behavior with the increase in concentration of ZrF{sub 4}. This is because of network formation in NaF-ZrF{sub 4}. Positive entropy constraints have been plotted to authenticate negative diffusivities observed.
Diffusive retention of atmospheric gases in chert
Pettitt, E.; Cherniak, D. J.; Watson, E. B.; Schaller, M. F.
2016-12-01
Throughout Earth's history, the volatile contents (N2, CO2, Ar) of both deep and shallow terrestrial reservoirs has been dynamic. Volatiles are important chemical constituents because they play a significant role in regulating Earth's climate, mediating the evolution of complex life, and controlling the properties of minerals and rocks. Estimating levels of atmospheric volatiles in the deep geological past requires interrogation of materials that have acquired and retained a chemical memory from that time. Cherts have the potential to trap atmospheric components during formation and later release those gases for analysis in the laboratory. However, cherts have been underexploited in this regard, partly because their ability to retain a record of volatile components has not been adequately evaluated. Before cherts can be reliably used as indicators of past levels of major atmospheric gases, it is crucial that we understand the diffusive retentiveness of these cryptocrystalline silica phases. As the first step toward quantifying the diffusivity and solubility of carbon dioxide and nitrogen in chert, we have performed 1-atmosphere diffusive-uptake experiments at temperatures up to 450°C. Depth profiles of in-diffusing gases are measured by nuclear reaction analysis (NRA) to help us understand the molecular-scale transport of volatiles and thus the validity of using chert-bound volatiles to record information about Earth history. Data collected to date suggest that at least some cherts are ideal storage containers and can retain volatiles for a geologically long time. In addition to these diffusion experiments, preliminary online-crush fast-scan measurements using a quadrupole mass spectrometer indicate that atmospheric volatiles are released upon crushing various chert samples. By coupling such volatile-release measurements made by mass spectrometry with diffusion experiments, we are uniquely able to address the storage and fidelity of volatiles bound in crustal
Anisotropy in "isotropic diffusion" measurements due to nongaussian diffusion
DEFF Research Database (Denmark)
Jespersen, Sune Nørhøj; Olesen, Jonas Lynge; Ianuş, Andrada
2017-01-01
Designing novel diffusion-weighted NMR and MRI pulse sequences aiming to probe tissue microstructure with techniques extending beyond the conventional Stejskal-Tanner family is currently of broad interest. One such technique, multidimensional diffusion MRI, has been recently proposed to afford...... model-free decomposition of diffusion signal kurtosis into terms originating from either ensemble variance of isotropic diffusivity or microscopic diffusion anisotropy. This ability rests on the assumption that diffusion can be described as a sum of multiple Gaussian compartments, but this is often...
International Nuclear Information System (INIS)
Ramsdell, J.V.
1988-03-01
Straight-line Gaussian models adequately describe atmospheric diffusion for many applications. They have been modified for use in estimating diffusion in building wakes by adding terms that include projected building area and by redefining the diffusion coefficients so that the coefficients have minimum values that are related to building dimensions. In a recent study, Ramsdell reviewed the building-wake dispersion models used by the Nuclear Regulatory Commission (NRC) in its control room habitability assessments. The review included comparison of model estimates of centerline concentrations with concentrations observed in experiments at seven nuclear reactors. In general, the models are conservative in that they tend to predict concentrations that are greater than those actually observed. However, the models show little skill in accounting for variations in the observed concentrations. Subsequently, the experimental data and multiples linear regression techniques have been used to develop a new building wake diffusion model. This paper describes the new building wake model and compares it with other models. 8 refs., 2 figs
Sack, Jeff
2005-01-01
OsmoBeaker is a CD-ROM designed to enhance the learning of diffusion and osmosis by presenting interactive experimentation to the student. The software provides several computer simulations that take the student through different scenarios with cells, having different concentrations of solutes in them.
Diffusion Based Photon Mapping
DEFF Research Database (Denmark)
Schjøth, Lars; Sporring, Jon; Fogh Olsen, Ole
2008-01-01
. To address this problem, we introduce a photon mapping algorithm based on nonlinear anisotropic diffusion. Our algorithm adapts according to the structure of the photon map such that smoothing occurs along edges and structures and not across. In this way, we preserve important illumination features, while...
Bronnen van diffuse bodembelasting
Lijzen JPA; Ekelenkamp A; LBG; DGM/BO
1995-01-01
The aim of this study was to support the policy on preventive soil protection with information on the diffuse (non-local) emissions to soil and the influence on future soil quality. This study is related to inventories on (potential) sources of local soil pollution (e.g. industrial areas,
Energy Technology Data Exchange (ETDEWEB)
Mubarak, A S
1991-12-31
Rutherford backscattering spectromertry technique (RBS) was used to characterize and investigate the depth distribution profiles of Ca-impurities of Ca-doped soda-time glass. The purposely added Ca-impurities were introduced inti the glass matrix by a normal ion exchange diffusion process. The measurements and analysis were performed using 2 MeV {sup 2}He{sup +} ions supplied from the University of Jordan Van de Graff acceierator (JOVAG). The normalized concetration versus depth profile distributions for the Ca-imourities were determined, both theoretically and experimentally. The theoretical treatment was carried out by setting up and soiving the diffusion equation under the conditions of the experiment. The resulting profiles are characterized by a compiementary error function. the theoretical treeatment was extended to include the various methods of enhancing the diffusion process, e.g. using an electric field. The diffusion coefficient, assumed constant, of the Ca-impurities exchanged in the soda-lime glass was determined to be 1.23 x 10{sup 13} cm{sup 2}/s. A comparison between theoretically and experimentally determined profiles is made and commented at, where several conclusions are drawn and suggestions for future work are mentioned. (author). 38 refs., 21 figs., 10 Tabs.
DEFF Research Database (Denmark)
Schulz, Alexander
2015-01-01
is currently matter of discussion, called passive symplasmic loading. Based on the limited material available, this review compares the different loading modes and suggests that diffusion is the driving force in apoplasmic loaders, while bulk flow plays an increasing role in plants having a continuous...
Multienergy anomalous diffuse scattering
Czech Academy of Sciences Publication Activity Database
Kopecký, Miloš; Fábry, Jan; Kub, Jiří; Lausi, A.; Busetto, E.
2008-01-01
Roč. 100, č. 19 (2008), 195504/1-195504/4 ISSN 0031-9007 R&D Projects: GA AV ČR IAA100100529 Institutional research plan: CEZ:AV0Z10100523 Keywords : diffuse scattering * x-rays * structure determination Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 7.180, year: 2008
DEFF Research Database (Denmark)
Zhang, Chen; Yu, Tao; Heiselberg, Per Kvols
with conventional ventilation systems (mixing or displacement ventilation), diffuse ceiling ventilation can significantly reduce or even eliminate draught risk in the occupied zone. Moreover, this ventilation system presents a promising opportunity for energy saving, because of the low pressure loss, extended free...
DEFF Research Database (Denmark)
Zhang, Chen; Heiselberg, Per; Nielsen, Peter V.
2014-01-01
As a novel air distribution system, diffuse ceiling ventilation combines the suspended acoustic ceiling with ventilation supply. Due to the low-impulse supply from the large ceiling area, the system does not generate draught when supplying cold air. However, heat sources play an important role...
Pelleg, Joshua
2016-01-01
This textbook provides an introduction to changes that occur in solids such as ceramics, mainly at high temperatures, which are diffusion controlled, as well as presenting research data. Such changes are related to the kinetics of various reactions such as precipitation, oxidation and phase transformations, but are also related to some mechanical changes, such as creep. The book is composed of two parts, beginning with a look at the basics of diffusion according to Fick's Laws. Solutions of Fick’s second law for constant D, diffusion in grain boundaries and dislocations are presented along with a look at the atomistic approach for the random motion of atoms. In the second part, the author discusses diffusion in several technologically important ceramics. The ceramics selected are monolithic single phase ones, including: A12O3, SiC, MgO, ZrO2 and Si3N4. Of these, three refer to oxide ceramics (alumina, magnesia and zirconia). Carbide based ceramics are represented by the technologically very important Si-ca...
Magnetismo Molecular (Molecular Magentism)
Energy Technology Data Exchange (ETDEWEB)
Reis, Mario S [Universidade Federal Fluminense, Brasil; Moreira Dos Santos, Antonio F [ORNL
2010-07-01
The new synthesis processes in chemistry open a new world of research, new and surprising materials never before found in nature can now be synthesized and, as a wonderful result, observed a series of physical phenomena never before imagined. Among these are many new materials the molecular magnets, the subject of this book and magnetic properties that are often reflections of the quantum behavior of these materials. Aside from the wonderful experience of exploring something new, the theoretical models that describe the behavior these magnetic materials are, in most cases, soluble analytically, which allows us to know in detail the physical mechanisms governing these materials. Still, the academic interest in parallel this subject, these materials have a number of properties that are promising to be used in technological devices, such as in computers quantum magnetic recording, magnetocaloric effect, spintronics and many other devices. This volume will journey through the world of molecular magnets, from the structural description of these materials to state of the art research.
Essential Non-Translational Functions of tRNA Synthetases
Guo, Min; Schimmel, Paul
2013-01-01
Nontranslational functions of vertebrate aminoacyl tRNA synthetases (aaRSs), which catalyze the production of aminoacyl-tRNAs for protein synthesis, have recently been discovered. While these new functions were thought to be ‘moonlighting activities’, many are as critical for cellular homeostasis as the activity in translation. New roles have been associated with cytoplasmic forms as well as with nuclear and secreted extracellular forms that impact pathways for cardiovascular development, the immune response, and mTOR, IFN-γ and p53 signaling. The associations of aaRSs with autoimmune disorders, cancers and neurological disorders further highlight nontranslational functions of these proteins. Novel architecture elaborations of the aaRSs accompany their functional expansion in higher organisms and have been associated with the nontranslational functions for several aaRSs. While a general understanding of how these functions developed is limited, the expropriation of aaRSs for essential nontranslational functions may have been initiated by co-opting the amino acid binding site for another purpose. PMID:23416400
Patterns of diagnostic marker assessment in adult diffuse glioma
DEFF Research Database (Denmark)
Woehrer, Adelheid; Kristensen, Bjarne W.; Vital, Anne
2017-01-01
The 2016 update of the WHO classification has introduced an integrated diagnostic approach that incorporates both tumor morphology and molecular information. This conceptual change has far-reaching implications, especially for neuropathologists who are in the forefront of translating molecular...... markers to routine diagnostic use. Adult diffuse glioma is a prototypic example for a group of tumors that underwent substantial regrouping, and it represents a major workload for surgical neuropathologists. Hence, we conducted a survey among members of the European Confederation of Neuropathological...
CN radical in diffuse interstellar clouds
International Nuclear Information System (INIS)
Federman, S.R.; Danks, A.C.; Lambert, D.L.
1984-01-01
A survey of 15 lines of sight for the CN B 2 Σ + --X 2 Σ + interstellar absorption lines shows that the CN column density in diffuse interstellar clouds follows the relation log N(CN)proportionalm log N(H 2 ), where mroughly-equal3. This result is reproduced by a reaction network in which CN is produced primarily from C 2 by the neutral-neutral reaction C 2 +N → CN+C, and photodissociation is the main destruction pathway for the neutral molecules CH, C 2 , and CN. The CN radical is the first molecular species observed in diffuse clouds that requires a neutral-neutral reaction for its formation in the gas phase. The network also reproduces the observed ratio N(CN)/N(H 2 )
Triplet exciton diffusion in organic semiconductors
Energy Technology Data Exchange (ETDEWEB)
Koehler, Anna [Department of Physics, University of Bayreuth (Germany)
2010-07-01
Efficient triplet exciton emission has allowed improved operation of organic light-emitting diodes (LEDs). To enhance the device performance, it is necessary to understand what governs the motion of triplet excitons through the organic semiconductor. We use a series of poly(p-phenylene)-type conjugated polymers and oligomers of variable degree of molecular distortion (i.e. polaron formation) and energetic disorder as model systems to study the Dexter-type triplet exciton diffusion in thin films. We show that triplet diffusion can be quantitatively described in the framework of a Holstein small polaron model (Marcus theory) that is extended to include contributions from energetic disorder. The model predicts a tunnelling process at low temperatures followed by a thermally activated hopping process above a transition temperature. In contrast to charge transfer, the activation energy required for triplet exciton transfer can be deduced from the optical spectra. We discuss the implications for device architecture.
Evidence for Enhanced Matrix Diffusion in Geological Environment
Sato, Kiminori; Fujimoto, Koichiro; Nakata, Masataka; Shikazono, Naotatsu
2013-01-01
Molecular diffusion in rock matrix, called as matrix diffusion, has been appreciated as a static process for elemental migration in geological environment that has been acknowledged in the context of geological disposal of radioactive waste. However, incomprehensible enhancement of matrix diffusion has been reported at a number of field test sites. Here, the matrix diffusion of saline water at Horonobe, Hokkaido, Japan is highlighted directly probing angstrom-scale pores on a field scale up to 1 km by positron--positronium annihilation spectroscopy. The first application of positron--positronium annihilation spectroscopy to field-scale geophysical research reveals the slight variation of angstrom-scale pores influenced by saline water diffusion with complete accuracy. We found widely interconnected 3 Å pores, which offer the pathway of saline water diffusion with the highly enhanced effective matrix diffusion coefficient of 4× 10-6 cm2 s-1. The present findings provide unambiguous evidence that the angstrom-scale pores enhance effective matrix diffusion on a field scale in geological environment.
Study on diffusion behavior of nuclide in buffer material
International Nuclear Information System (INIS)
Suzuki, Satoru
2002-05-01
Bentonite is a promising candidate of buffer material for geological disposal of high-level radioactive waste (HLW). Mass transport in bentonite is mainly controlled by diffusion process because of extremely low-permeability. Geological environments, e.g. salinity of ground water and temperature can strongly influence on migration behavior in bentonite, and therefore diffusivity and diffusion mechanism have been investigated experimentally and theoretically. In chapter 1, the author summarizes how the diffusivity in the buffer material has been treated in the safety assessment. In chapter 2, results of diffusion experiments as a function of salinity and temperature have been shown. In chapter 3, relationship between diffusivity and pore structure of bentonite has been investigated theoretically. In chapter 4, sorption structure of strontium on smectite has been studied by using molecular dynamics simulation. In chapter 5, vibrational property of pore water has been investigated. Diffusivity in bentonite has been discussed based on rock capacity factor, microstructure and interaction between diffusant and bentonite. (author)
Watson, E. B.; Cherniak, D. J.
1997-05-01
Oxygen diffusion in natural, non-metamict zircon was characterized under both dry and water-present conditions at temperatures ranging from 765°C to 1500°C. Dry experiments were performed at atmospheric pressure by encapsulating polished zircon samples with a fine powder of 18O-enriched quartz and annealing the sealed capsules in air. Hydrothermal runs were conducted in cold-seal pressure vessels (7-70 MPa) or a piston cylinder apparatus (400-1000 MPa) on zircon samples encapsulated with both 18O-enriched quartz and 18O water. Diffusive-uptake profiles of 18O were measured in all samples with a particle accelerator, using the 18O(p, α) 15N reaction. For dry experimental conditions at 1100-1500°C, the resulting oxygen diffusivities (24 in all) are well described by: D dry (m 2/s) = 1.33 × 10 -4exp(-53920/T) There is no suggestion of diffusive anisotropy. Under wet conditions at 925°C, oxygen diffusion shows little or no dependence upon P H 2O in the range 7-1000 MPa, and is insensitive to total pressure as well. The results of 27 wet experiments at 767-1160°C and 7-1000 MPa can be described a single Arrhenius relationship: D wet (m 2/s) = 5.5 × 10 -12exp(-25280/T) The insensitivity of oxygen diffusion to P H 2O means that applications to geologic problems can be pursued knowing only whether the system of interest was 'wet' (i.e., P H 2O > 7MPa ) or 'dry'. Under dry conditions (presumably rare in the crust), zircons are extremely retentive of their oxygen isotopic signatures, to the extent that δ 18O would be perturbed at the center of a 200 μm zircon only during an extraordinarily hot and protracted event (e.g., 65 Ma at 900°C). Under wet conditions, δ 18O may or may not be retained in the central regions of individual crystals, cores or overgrowth rims, depending upon the specific thermal history of the system.
The Pearson diffusions: A class of statistically tractable diffusion processes
DEFF Research Database (Denmark)
Forman, Julie Lyng; Sørensen, Michael
The Pearson diffusions is a flexible class of diffusions defined by having linear drift and quadratic squared diffusion coefficient. It is demonstrated that for this class explicit statistical inference is feasible. Explicit optimal martingale estimating func- tions are found, and the corresponding...
Effects of Defects on Hydrogen Diffusion in NbC
Energy Technology Data Exchange (ETDEWEB)
Salehinia, Iman, E-mail: isalehinia@niu.edu [Department of Mechanical Engineering, Northern Illinois University, DeKalb, IL 60115 (United States); Mastorakos, Ioannis [Department of Mechanical and Aeronautical Engineering, Clarkson University, Potsdam, NY 13699 (United States); Zbib, Hussein M. [School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164 (United States)
2017-04-15
Highlights: • MD simulations are used to study the effects of defects on the H diffusion in NbC. • Buckingham potential is more accurate for diffusion of H atoms than LJ potential. • H diffusion coefficient (D) increases with carbon vacancy concentration. • H diffusion coefficient for 6 Å pore (radius = 6 Å) is as high as that for 20 Å pore. • For small pores, H diffusion coefficient drops notably at elevated temperatures. - Abstract: Exceptional mechanical and physical properties of transition metal carbides and nitrides make them good coating-material candidates for extreme corrosive environments such as oil and natural gas wells. However, existence of small pores, pinholes and columnar structures of these ceramics significantly affect their resistance to corrosion, as pore sites would accelerate the diffusion of corrosive media into the substrate. In this research, molecular dynamics atomistic simulations are employed to investigate the effects of the isolated vacancies and the columnar structure on the diffusion rate of H atoms in NbC single crystal at various temperatures. Diffusion coefficient (D) of H atoms in NbC increased with C vacancy concentration. At elevated temperatures, the trapping effect of Nb vacancies is less effective when C vacancies are also present, as H atoms gain enough energy to jump back and forth between the C vacancies. Atomistic simulations also showed a jump in diffusion coefficient for cylindrical pore size of larger than 3 Å radius. Furthermore, D increased monotonically with temperature up to 1000 K in the presence of cylindrical pores. Further increase in temperature resulted in a drop in the diffusion coefficient for small pores while the large pores only showed a lower increasing trend in diffusion coefficient with the temperature.
National Research Council Canada - National Science Library
Provan, Drew; Gribben, John
2010-01-01
... The molecular basis of hemophilia, 219 Paul LF Giangrande 4 The genetics of acute myeloid leukemias, 42 Carolyn J Owen & Jude Fitzgibbon 19 The molecular basis of von Willebrand disease, 233 Luciano Baronc...
Energy Technology Data Exchange (ETDEWEB)
Sathiyanarayanan, Rajesh, E-mail: rajessat@in.ibm.com, E-mail: rajesh.sathiyanarayanan@gmail.com; Pandey, R. K.; Murali, K. V. R. M. [IBM Semiconductor Research and Development Center, Bangalore 560045 (India)
2015-01-21
Using first-principles simulations, we have computed incorporation energies and diffusion barriers of ammonia, the nitrogen molecule and atomic nitrogen in monoclinic hafnia (m-HfO{sub 2}). Our calculations show that ammonia is likely to dissociate into an NH{sub 2} molecular unit, whereas the nitrogen molecule remains as a molecule either in the interstitial space or at an oxygen lattice site. The lowest energy pathway for the diffusion of atomic nitrogen interstitials consists of the hopping of the nitrogen interstitial between neighboring three-coordinated lattice oxygen atoms that share a single Hf atom, and the barrier for such hops is determined by a switching mechanism. The substitutional nitrogen atom shows a preference for diffusion through the doubly positive oxygen vacancy-mediated mechanism. Furthermore, we have investigated the impact of nitrogen atoms on the diffusion barriers of oxygen and hydrogen interstitials in m-HfO{sub 2}. Our results show that nitrogen incorporation has a significant impact on the barriers for oxygen and hydrogen diffusion: nitrogen atoms attract oxygen and hydrogen interstitials diffusing in the vicinity, thereby slowing down (reducing) their diffusion (diffusion length)
Beam formation in molecular flow
International Nuclear Information System (INIS)
Gottwald, B.A.
1974-01-01
Comparison of experimental angular distribution data with theoretical models has show a considerable disagreement with the Clausing model (free molecular flow with diffuse reflexion). For a real system this idealized model has to be modified by taking into consideration possible perturbations of the Clausing flow chemical reactions, surface diffusion and deviations from diffuse reflexion. By comparison with the diffusion differential equation and Monte Carlo stimulations, it has been shown that the iteration of a system of appropriately modified Clausing integral equations is especially suited for solving this complex problem. Suitable characterized parameters for angular distribution data are the beam half-width upsilon 1/2 and the peaking factor chi defined according to Olander and Jones. The computer program in a first step calculates the real steady state of molecular flow. In a second step the computer program calculates the dependence of upsilon 1/2 and chi upon the parameters L/2R (orifice geometry) and m' (order of the surface reaction preceding the desorption from the inner wall of the cylindrical orifice). For the real steady state of molecular flow
International Nuclear Information System (INIS)
Hanna, S.R.
1976-01-01
It is hoped that urban diffusion models of air pollutants can eventually confidently be used to make major decisions, such as in planning the layout of a new industrial park, determining the effects of a new highway on air quality, or estimating the results of a new automobile emissions exhaust system. The urban diffusion model itself should be able to account for point, line, and area sources, and the local aerodynamic effects of street canyons and building wakes. Removal or transformations due to dry or wet deposition and chemical reactions are often important. It would be best if the model included meteorological parameters such as wind speed and temperature as dependent variables, since these parameters vary significantly when air passes from rural surfaces over urban surfaces
Directory of Open Access Journals (Sweden)
Roberto Cipriani
2011-06-01
Full Text Available It is quite likely that the origins of prayer are to be found in ancient mourning and bereavement rites. Primeval ritual prayer was codified and handed down socially to become a deep-rooted feature of people’s cultural behavior, so much so, that it may surface again several years later, in the face of death, danger, need, even in the case of relapse from faith and religious practice. Modes of prayer depend on religious experience, on relations between personal prayer and political action, between prayer and forgiveness, and between prayer and approaches to religions. Various forms of prayer exist, from the covert-hidden to the overt-manifest kind. How can they be investigated? How can one, for instance, explore mental prayer? These issues regard the canon of diffused religion and, therefore, of diffused prayer.
International Nuclear Information System (INIS)
Cable, J.W.
1987-01-01
The diffuse scattering of neutrons from magnetic materials provides unique and important information regarding the spatial correlations of the atoms and the spins. Such measurements have been extensively applied to magnetically ordered systems, such as the ferromagnetic binary alloys, for which the observed correlations describe the magnetic moment fluctuations associated with local environment effects. With the advent of polarization analysis, these techniques are increasingly being applied to study disordered paramagnetic systems such as the spin-glasses and the diluted magnetic semiconductors. The spin-pair correlations obtained are essential in understanding the exchange interactions of such systems. In this paper, we describe recent neutron diffuse scattering results on the atom-pair and spin-pair correlations in some of these disordered magnetic systems. 56 refs
Diffusion in heterogeneous lattices
Czech Academy of Sciences Publication Activity Database
Tarasenko, Alexander; Jastrabík, Lubomír
2010-01-01
Roč. 256, č. 17 (2010), s. 5137-5144 ISSN 0169-4332 R&D Projects: GA AV ČR KAN301370701; GA MŠk(CZ) 1M06002 Institutional research plan: CEZ:AV0Z10100522 Keywords : lattice- gas systems * diffusion * Monte Carlo simulations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.795, year: 2010
International Nuclear Information System (INIS)
Peters, R.D.
1978-01-01
The applications of diffusion bonding at the General Electric Neutron Devices Department are briefly discussed, with particular emphasis on the gold/gold or gold/indium joints made between metallized alumina ceramic parts in the vacuum switch tube and the crystal resonator programs. Fixtures which use the differential expansion of dissimilar metals are described and compared to one that uses hydraulic pressure to apply the necessary bonding force
International Nuclear Information System (INIS)
Mezin, M.
1976-01-01
The report presents an introduction to general basic principles of the gaseous diffusion process for the separation of uranium isotopes. Dealt with are: a) theoretical background and basic considerations of separation work and production costs, b) construction of a single separation stage and a multistage plant, c) the components of a plant and the optimization factors, d) cost factors. The text is illustrated by instructive diagrammes and flow charts. (RB) [de
Surface diffusion of sorbed radionuclides
International Nuclear Information System (INIS)
Berry, J.A.; Bond, K.A.
1991-01-01
Surface diffusion has in the past been invoked to explain rates of radionuclide migration which were greater than those predicted. Results were generally open to interpretation but the possible existence of surface diffusion, whereby sorbed radionuclides could potentially migrate at much enhanced rates, necessitated investigation. In this work through-diffusion experiments have shown that although surface diffusion does exist for some nuclides, the magnitude of the phenomenon is not sufficient to affect repository safety assessment modelling. (author)
Diffusion in cladding materials
International Nuclear Information System (INIS)
Anand, M.S.; Pande, B.M.; Agarwala, R.P.
1992-01-01
Aluminium has been used as a cladding material in most research reactors because its low neutron absorption cross section and ease of fabrication. However, it is not suitable for cladding in power reactors and as such zircaloy-2 is normally used as a clad because it can withstand high temperature. It has low neutron absorption cross section, good oxidation, corrosion, creep properties and possesses good mechanical strength. With the passage of time, further development in this branch of science took place and designers started looking for better neutron economy and less hydrogen pickup in PHW reactors. The motion of fission products in the cladding material could pose a problem after long operation. In order to understand their behaviour under reactor environment, it is essential to study first the diffusion under normal conditions. These studies will throw light on the interaction of defects with impurities which would in turn help in understanding the mechanism of diffusion. In this article, it is intended to discuss the diffusion behaviour of impurities in cladding materials.(i.e. aluminium, zircaloy-2, zirconium-niobium alloy etc.). (author). 94 refs., 4 figs., 3 tabs
Surface self-diffusion of adatom on Pt cluster with truncated octahedron structure
International Nuclear Information System (INIS)
Yang Jianyu; Hu Wangyu; Chen Shuguang
2010-01-01
Surface diffusion of single Pt adatom on Pt cluster with truncated octahedron structure is investigated through a combination of molecular dynamics and nudged elastic band method. Using an embedded atom method to describe the atomic interactions, the minimum energy paths are determined and the energy barriers for adatom diffusion across and along step are evaluated. The diffusion of adatom crossing step edge between {111} and {100} facets has a surprisingly low barrier of 0.03 eV, which is 0.12 eV lower than the barrier for adatom diffusion from {111} to neighboring {111} facet. Owing to the small barrier of adatom diffusion across the step edge between {111} and {100} facets, the diffusion of adatom along the step edge cannot occur. The molecular dynamics simulations at low temperatures also support these results. Our results show that mass transport will prefer step with {100} microfacet and the Pt clusters can have only {111} facets in epitaxial growth.
Solute diffusivity in undisturbed soil
DEFF Research Database (Denmark)
Lægdsmand, Mette; Møldrup, Per; Schjønning, Per
2012-01-01
Solute diffusivity in soil plays a major role in many important processes with relation to plant growth and environmental issues. Soil solute diffusivity is affected by the volumetric water content as well as the morphological characteristics of water-filled pores. The solute diffusivity in intact...
Profiling of diffuse large B-cell lymphoma by immunohistochemistry
DEFF Research Database (Denmark)
Sjö, Lene Dissing; Poulsen, Christian Bjørn; Hansen, Mads
2007-01-01
Diffuse large B-cell lymphoma (DLBCL) is a frequent lymphoma subtype with a heterogeneous behavior and a variable response to conventional chemotherapy. This clinical diversity is believed to reflect differences in the molecular pathways leading to lymphomagenesis. In this study, we have analyzed...
Mitosis, diffusible crosslinkers, and the ideal gas law.
Odde, David J
2015-03-12
During mitosis, molecular motors hydrolyze ATP to generate sliding forces between adjacent microtubules and form the bipolar mitotic spindle. Lansky et al. now show that the diffusible microtubule crosslinker Ase1p can generate sliding forces between adjacent microtubules, and it does so without ATP hydrolysis. Copyright © 2015 Elsevier Inc. All rights reserved.
Diffusion of Zonal Variables Using Node-Centered Diffusion Solver
Energy Technology Data Exchange (ETDEWEB)
Yang, T B
2007-08-06
Tom Kaiser [1] has done some preliminary work to use the node-centered diffusion solver (originally developed by T. Palmer [2]) in Kull for diffusion of zonal variables such as electron temperature. To avoid numerical diffusion, Tom used a scheme developed by Shestakov et al. [3] and found their scheme could, in the vicinity of steep gradients, decouple nearest-neighbor zonal sub-meshes leading to 'alternating-zone' (red-black mode) errors. Tom extended their scheme to couple the sub-meshes with appropriate chosen artificial diffusion and thereby solved the 'alternating-zone' problem. Because the choice of the artificial diffusion coefficient could be very delicate, it is desirable to use a scheme that does not require the artificial diffusion but still able to avoid both numerical diffusion and the 'alternating-zone' problem. In this document we present such a scheme.
Influence of adsorption thermodynamics on guest diffusivities in nanoporous crystalline materials
Krishna, R.; van Baten, J.M.
2013-01-01
Published experimental data, underpinned by molecular simulations, are used to highlight the strong influence of adsorption thermodynamics on diffusivities of guest molecules inside ordered nanoporous crystalline materials such as zeolites, metal-organic frameworks (MOFs), and zeolitic imidazolate
Kinetic Monte Carlo Simulation of Oxygen and Cation Diffusion in Yttria-Stabilized Zirconia
Good, Brian
2011-01-01
Yttria-stabilized zirconia (YSZ) is of interest to the aerospace community, notably for its application as a thermal barrier coating for turbine engine components. In such an application, diffusion of both oxygen ions and cations is of concern. Oxygen diffusion can lead to deterioration of a coated part, and often necessitates an environmental barrier coating. Cation diffusion in YSZ is much slower than oxygen diffusion. However, such diffusion is a mechanism by which creep takes place, potentially affecting the mechanical integrity and phase stability of the coating. In other applications, the high oxygen diffusivity of YSZ is useful, and makes the material of interest for use as a solid-state electrolyte in fuel cells. The kinetic Monte Carlo (kMC) method offers a number of advantages compared with the more widely known molecular dynamics simulation method. In particular, kMC is much more efficient for the study of processes, such as diffusion, that involve infrequent events. We describe the results of kinetic Monte Carlo computer simulations of oxygen and cation diffusion in YSZ. Using diffusive energy barriers from ab initio calculations and from the literature, we present results on the temperature dependence of oxygen and cation diffusivity, and on the dependence of the diffusivities on yttria concentration and oxygen sublattice vacancy concentration. We also present results of the effect on diffusivity of oxygen vacancies in the vicinity of the barrier cations that determine the oxygen diffusion energy barriers.
Molecular clouds without detectable CO
International Nuclear Information System (INIS)
Blitz, L.; Bazell, D.; Desert, F.X.
1990-01-01
The clouds identified by Desert, Bazell, and Boulanger (DBB clouds) in their search for high-latitude molecular clouds were observed in the CO (J = 1-0) line, but only 13 percent of the sample was detected. The remaining 87 percent are diffuse molecular clouds with CO abundances of about 10 to the -6th, a typical value for diffuse clouds. This hypothesis is shown to be consistent with Copernicus data. The DBB clouds are shown to be an essentially complete catalog of diffuse molecular clouds in the solar vicinity. The total molecular surface density in the vicinity of the sun is then only about 20 percent greater than the 1.3 solar masses/sq pc determined by Dame et al. (1987). Analysis of the CO detections indicates that there is a sharp threshold in extinction of 0.25 mag before CO is detectable and is derived from the IRAS I(100) micron threshold of 4 MJy/sr. This threshold is presumably where the CO abundance exhibits a sharp increase 18 refs
Particle diffusion in a spheromak
International Nuclear Information System (INIS)
Meyerhofer, D.D.; Levinton, F.M.; Yamada, M.
1988-01-01
The local carbon particle diffusion coefficient was measured in the Proto S-1/C spheromak using a test particle injection scheme. When the plasma was not in a force-free Taylor state, and when there were pressure gradients in the plasma, the particle diffusion was five times that predicted by Bohm and was consistent with collisional drift wave diffusion. The diffusion appears to be driven by correlations of the fluctuating electric field and density. During the decay phase of the discharge when the plasma was in the Taylor state, the diffusion coefficient of the carbon was classical. 23 refs., 4 figs
Advanced diffusion processes and phenomena
Öchsner, Andreas; Belova, Irina
2014-01-01
This topical volume on Advanced Diffusion Processes and Phenomena addresses diffusion in a wider sense of not only mass diffusion but also heat diffusion in fluids and solids. Both diffusion phenomena play an important role in the characterization of engineering materials and corresponding structures. Understanding these different transport phenomena at many levels, from atomistic to macro, has therefore long attracted the attention of many researchers in materials science and engineering and related disciplines. The present topical volume captures a representative cross-section of some of the
Measuring methods of matrix diffusion
International Nuclear Information System (INIS)
Muurinen, A.; Valkiainen, M.
1988-03-01
In Finland the spent nuclear fuel is planned to be disposed of at large depths in crystalline bedrock. The radionuclides which are dissolved in the groundwater may be able to diffuse into the micropores of the porous rock matrix and thus be withdrawn from the flowing water in the fractures. This phenomenon is called matrix diffusion. A review over matrix diffusion is presented in the study. The main interest is directed to the diffusion of non-sorbing species. The review covers diffusion experiments and measurements of porosity, pore size, specific surface area and water permeability
A Simple Educational Method for the Measurement of Liquid Binary Diffusivities
Rice, Nicholas P.; de Beer, Martin P.; Williamson, Mark E.
2014-01-01
A simple low-cost experiment has been developed for the measurement of the binary diffusion coefficients of liquid substances. The experiment is suitable for demonstrating molecular diffusion to small or large undergraduate classes in chemistry or chemical engineering. Students use a cell phone camera in conjunction with open-source image…
Modelling of monovacancy diffusion in W over wide temperature range
International Nuclear Information System (INIS)
Bukonte, L.; Ahlgren, T.; Heinola, K.
2014-01-01
The diffusion of monovacancies in tungsten is studied computationally over a wide temperature range from 1300 K until the melting point of the material. Our modelling is based on Molecular Dynamics technique and Density Functional Theory. The monovacancy migration barriers are calculated using nudged elastic band method for nearest and next-nearest neighbour monovacancy jumps. The diffusion pre-exponential factor for monovacancy diffusion is found to be two to three orders of magnitude higher than commonly used in computational studies, resulting in attempt frequency of the order 10 15 Hz. Multiple nearest neighbour jumps of monovacancy are found to play an important role in the contribution to the total diffusion coefficient, especially at temperatures above 2/3 of T m , resulting in an upward curvature of the Arrhenius diagram. The probabilities for different nearest neighbour jumps for monovacancy in W are calculated at different temperatures
Diffusion of Sites versus Polymers in Polyelectrolyte Complexes and Multilayers.
Fares, Hadi M; Schlenoff, Joseph B
2017-10-18
It has long been assumed that the spontaneous formation of materials such as complexes and multilayers from charged polymers depends on (inter)diffusion of these polyelectrolytes. Here, we separately examine the mass transport of polymer molecules and extrinsic sites-charged polyelectrolyte repeat units balanced by counterions-within thin films of polyelectrolyte complex, PEC, using sensitive isotopic labeling techniques. The apparent diffusion coefficients of these sites within PEC films of poly(diallyldimethylammonium), PDADMA, and poly(styrenesulfonate), PSS, are at least 2 orders of magnitude faster than the diffusion of polyelectrolytes themselves. This is because site diffusion requires only local rearrangements of polyelectrolyte repeat units, placing far fewer kinetic limitations on the assembly of polyelectrolyte complexes in all of their forms. Site diffusion strongly depends on the salt concentration (ionic strength) of the environment, and diffusion of PDADMA sites is faster than that of PSS sites, accounting for the asymmetric nature of multilayer growth. Site diffusion is responsible for multilayer growth in the linear and into the exponential regimes, which explains how PDADMA can mysteriously "pass through" layers of PSS. Using quantitative relationships between site diffusion coefficient and salt concentration, conditions were identified that allowed the diffusion length to always exceed the film thickness, leading to full exponential growth over 3 orders of magnitude thickness. Both site and polymer diffusion were independent of molecular weight, suggesting that ion pairing density is a limiting factor. Polyelectrolyte complexes are examples of a broader class of dynamic bulk polymeric materials that (self-) assemble via the transport of cross-links or defects rather than actual molecules.
International Nuclear Information System (INIS)
Kwiotek, A.; Grzywna, Z.J.
2005-01-01
Diffusion in a bounded region (or diffusive mass transport) can be seen from at least three platforms: - chemistry of he Fick's equation; - chemical engineering. To pose a particular problem we have to provide some additional conditions (initial conditions, boundary conditions and further). As we understood it in all cases diffusion is considered in an open region (in other words in one phase). Chemical engineering however brings an idea of 'diffusion' between phases. We claim that there isn't diffusion between phases. One can only consider mass transport between phases. Mass transport (or transfer in chemical engineering jargon) from one phase to another composes of: diffusion in first phase partition at an interface diffusion in second phase. (author)
Anion and cation diffusion in barium titanate and strontium titanate
International Nuclear Information System (INIS)
Kessel, Markus Franz
2012-01-01
Perovskite oxides show various interesting properties providing several technical applications. In many cases the defect chemistry is the key to understand and influence the material's properties. In this work the defect chemistry of barium titanate and strontium titanate is analysed by anion and cation diffusion experiments and subsequent time-of-flight secondary ion mass spectrometry (ToF-SIMS). The reoxidation equation for barium titanate used in multi-layer ceramic capacitors (MLCCs) is found out by a combination of different isotope exchange experiments and the analysis of the resulting tracer diffusion profiles. It is shown that the incorporation of oxygen from water vapour is faster by orders of magnitude than from molecular oxygen. Chemical analysis shows the samples contain various dopants leading to a complex defect chemistry. Dysprosium is the most important dopant, acting partially as a donor and partially as an acceptor in this effectively acceptor-doped material. TEM and EELS analysis show the inhomogeneous distribution of Dy in a core-shell microstructure. The oxygen partial pressure and temperature dependence of the oxygen tracer diffusion coefficients is analysed and explained by the complex defect chemistry of Dy-doped barium titanate. Additional fast diffusion profiles are attributed to fast diffusion along grain boundaries. In addition to the barium titanate ceramics from an important technical application, oxygen diffusion in cubic, nominally undoped BaTiO 3 single crystals has been studied by means of 18 O 2 / 16 O 2 isotope exchange annealing and subsequent determination of the isotope profiles in the solid by ToF-SIMS. It is shown that a correct description of the diffusion profiles requires the analysis of the diffusion through the surface space-charge into the material's bulk. Surface exchange coefficients, space-charge potentials and bulk diffusion coefficients are analysed as a function of oxygen partial pressure and temperature. The
Diffusion in silicon isotope heterostructures
Energy Technology Data Exchange (ETDEWEB)
Silvestri, Hughes Howland [Univ. of California, Berkeley, CA (United States)
2004-01-01
The simultaneous diffusion of Si and the dopants B, P, and As has been studied by the use of a multilayer structure of isotopically enriched Si. This structure, consisting of 5 pairs of 120 nm thick natural Si and ^{28}Si enriched layers, enables the observation of ^{30}Si self-diffusion from the natural layers into the ^{28}Si enriched layers, as well as dopant diffusion from an implanted source in an amorphous Si cap layer, via Secondary Ion Mass Spectrometry (SIMS). The dopant diffusion created regions of the multilayer structure that were extrinsic at the diffusion temperatures. In these regions, the Fermi level shift due to the extrinsic condition altered the concentration and charge state of the native defects involved in the diffusion process, which affected the dopant and self-diffusion. The simultaneously recorded diffusion profiles enabled the modeling of the coupled dopant and self-diffusion. From the modeling of the simultaneous diffusion, the dopant diffusion mechanisms, the native defect charge states, and the self- and dopant diffusion coefficients can be determined. This information is necessary to enhance the physical modeling of dopant diffusion in Si. It is of particular interest to the modeling of future electronic Si devices, where the nanometer-scale features have created the need for precise physical models of atomic diffusion in Si. The modeling of the experimental profiles of simultaneous diffusion of B and Si under p-type extrinsic conditions revealed that both species are mediated by neutral and singly, positively charged Si self-interstitials. The diffusion of As and Si under extrinsic n-type conditions yielded a model consisting of the interstitialcy and vacancy mechanisms of diffusion via singly negatively charged self-interstitials and neutral vacancies. The simultaneous diffusion of P and Si has been modeled on the basis of neutral and singly negatively charged self-interstitials and neutral and singly
Diffusion of aqueous solutions of ionic, zwitterionic, and polar solutes
Teng, Xiaojing; Huang, Qi; Dharmawardhana, Chamila Chathuranga; Ichiye, Toshiko
2018-06-01
The properties of aqueous solutions of ionic, zwitterionic, and polar solutes are of interest to many fields. For instance, one of the many anomalous properties of aqueous solutions is the behavior of water diffusion in different monovalent salt solutions. In addition, solutes can affect the stabilities of macromolecules such as proteins in aqueous solution. Here, the diffusivities of aqueous solutions of sodium chloride, potassium chloride, tri-methylamine oxide (TMAO), urea, and TMAO-urea are examined in molecular dynamics simulations. The decrease in the diffusivity of water with the concentration of simple ions and urea can be described by a simple model in which the water molecules hydrogen bonded to the solutes are considered to diffuse at the same rate as the solutes, while the remainder of the water molecules are considered to be bulk and diffuse at almost the same rate as pure water. On the other hand, the decrease in the diffusivity of water with the concentration of TMAO is apparently affected by a decrease in the diffusion rate of the bulk water molecules in addition to the decrease due to the water molecules hydrogen bonded to TMAO. In other words, TMAO enhances the viscosity of water, while urea barely affects it. Overall, this separation of water molecules into those that are hydrogen bonded to solute and those that are bulk can provide a useful means of understanding the short- and long-range effects of solutes on water.
Numerical modelling of random walk one-dimensional diffusion
International Nuclear Information System (INIS)
Vamos, C.; Suciu, N.; Peculea, M.
1996-01-01
The evolution of a particle which moves on a discrete one-dimensional lattice, according to a random walk low, approximates better the diffusion process smaller the steps of the spatial lattice and time are. For a sufficiently large assembly of particles one can assume that their relative frequency at lattice knots approximates the distribution function of the diffusion process. This assumption has been tested by simulating on computer two analytical solutions of the diffusion equation: the Brownian motion and the steady state linear distribution. To evaluate quantitatively the similarity between the numerical and analytical solutions we have used a norm given by the absolute value of the difference of the two solutions. Also, a diffusion coefficient at any lattice knots and moment of time has been calculated, by using the numerical solution both from the diffusion equation and the particle flux given by Fick's low. The difference between diffusion coefficient of analytical solution and the spatial lattice mean coefficient of numerical solution constitutes another quantitative indication of the similarity of the two solutions. The results obtained show that the approximation depends first on the number of particles at each knot of the spatial lattice. In conclusion, the random walk is a microscopic process of the molecular dynamics type which permits simulations precision of the diffusion processes with given precision. The numerical method presented in this work may be useful both in the analysis of real experiments and for theoretical studies
International Nuclear Information System (INIS)
Leo, Stefano de; Rotelli, Pietro
2009-01-01
We present the results of the planar diffusion of a Dirac particle by step and barrier potentials, when the incoming wave impinges at an arbitrary angle with the potential. Except for right-angle incidence this process is characterized by the appearance of spin flip terms. For the step potential, spin flip occurs for both transmitted and reflected waves. However, we find no spin flip in the transmitted barrier result. This is surprising because the barrier result may be derived directly from a two-step calculation. We demonstrate that the spin flip cancellation indeed occurs for each ''particle'' (wave packet) contribution. (orig.)
International Nuclear Information System (INIS)
Pretzsch, G.; Boerner, E.; Lehmann, R.; Sarenio, O.
1986-01-01
The invention relates to the detection of radioactive gases emitting alpha particles like radon, thoron and their alpha-decaying daughters by means of a diffusion chamber with a passive detector, preferably with a solid state track detector. In the chamber above and towards the detector there is a single metallized electret with negative polarity. The distance between electret and detector corresponds to the range of the alpha particles of radon daughters in air at the most. The electret collects the positively charged daughters and functions as surface source. The electret increases the sensitivity by the factor 4
International Nuclear Information System (INIS)
Ott, D.J.; Chen, Y.M.; Hewson, E.G.; Richter, J.E.; Wu, W.C.; Gelfand, D.W.; Castell, D.O.
1988-01-01
Radiologic and manometric findings were correlated in 17 patients with diffuse esophageal spasm (DES). All patients initially had chest pain and/or dysphagia and had a manometric diagnosis of DES. Mean percentage of normal peristalsis manometrically was 46% (range, 20%-80%). Based on radiologic examination, an esophageal motor disorder consistent with DES was diagnosed in 12 of 17 patients, and there was one misinterpretation of achalasia. Radiologic detection was not related significantly to the percentage of peristalsis seen on manometric examination. Mean esophageal wall thickness as measured radiographically in patients with DES was 2.6 mm, compared with 2.5 mm in 17 individuals with normal results of manometry
International Nuclear Information System (INIS)
Michaud, Georges; Montmerle, Thierry
1977-01-01
This paper is dealing with the origin of the elements in the universe. The scheme of nucleosynthesis is kept to explain the stellar generation of helium, carbon, etc... from the initial hydrogen; but a nonlinear theory is then elaborated to account for the anomalous abundances which were observed. The chemical elements would diffuse throughout the outer layers of a star under the action of the opposite forces of gravitation and radiation. This theory, with completing the nucleosynthesis, would contribute to give a consistent scheme of the elemental origin and abundances [fr
International Nuclear Information System (INIS)
Yeh, C.H.
2011-09-01
Diffusion magnetic resonance imaging (dMRI) has made a significant breakthrough in neurological disorders and brain research thanks to its exquisite sensitivity to tissue cyto-architecture. However, as the water diffusion process in neuronal tissues is a complex biophysical phenomena at molecular scale, it is difficult to infer tissue microscopic characteristics on a voxel scale from dMRI data. The major methodological contribution of this thesis is the development of an integrated and generic Monte Carlo simulation framework, 'Diffusion Microscopist Simulator' (DMS), which has the capacity to create 3D biological tissue models of various shapes and properties, as well as to synthesize dMRI data for a large variety of MRI methods, pulse sequence design and parameters. DMS aims at bridging the gap between the elementary diffusion processes occurring at a micrometric scale and the resulting diffusion signal measured at millimetric scale, providing better insights into the features observed in dMRI, as well as offering ground-truth information for optimization and validation of dMRI acquisition protocols for different applications. We have verified the performance and validity of DMS through various benchmark experiments, and applied to address particular research topics in dMRI. Based on DMS, there are two major application contributions in this thesis. First, we use DMS to investigate the impact of finite diffusion gradient pulse duration (delta) on fibre orientation estimation in dMRI. We propose that current practice of using long delta, which is enforced by the hardware limitation of clinical MRI scanners, is actually beneficial for mapping fibre orientations, even though it violates the underlying assumption made in q-space theory. Second, we employ DMS to investigate the feasibility of estimating axon radius using a clinical MRI system. The results suggest that the algorithm for mapping the direct microstructures is applicable to dMRI data acquired from
Influence of the pore network on hydrogen diffusion through blended cement pastes
International Nuclear Information System (INIS)
Boher, Cedric; Frizon, Fabien; Bart, Florence; Lorente, Sylvie
2013-01-01
This article presents a study on the influence of the pore size distribution on gas diffusion through CEM V cement pastes, for different water saturation degrees. The numerical results are compared to the experimental hydrogen diffusion coefficients obtained with water saturation levels ranging from 20% to 95%. The model developed in our research group accounts for the various types of transfer through the pore network: Knudsen diffusion or molecular diffusion depending on the pore size, together with hydrogen diffusion through water. The virtual pore network is created from mercury porosimetry data as a result of the combination of different sizes pore families. By testing different combinations, we could propose pore arrangements leading to diffusion coefficients corresponding to the experimental ones, and show how the combinations of the biggest pore family contribute to control the gas diffusion process. (authors)
Diffusion in Solids Fundamentals, Methods, Materials, Diffusion-Controlled Processes
Mehrer, Helmut
2007-01-01
Diffusion is a vital topic in solid-state physics and chemistry, physical metallurgy and materials science. Diffusion processes are ubiquitous in solids at elevated temperatures. A thorough understanding of diffusion in materials is crucial for materials development and engineering. This book first gives an account of the central aspects of diffusion in solids, for which the necessary background is a course in solid state physics. It then provides easy access to important information about diffuson in metals, alloys, semiconductors, ion-conducting materials, glasses and nanomaterials. Several diffusion-controlled phenomena, including ionic conduction, grain-boundary and dislocation pipe diffusion, are considered as well. Graduate students in solid-state physics, physical metallurgy, materials science, physical and inorganic chemistry or geophysics will benefit from this book as will physicists, chemists, metallurgists, materials engineers in academic and industrial research laboratories.
Diffusion of neon in white dwarf stars.
Hughto, J; Schneider, A S; Horowitz, C J; Berry, D K
2010-12-01
Sedimentation of the neutron rich isotope 22Ne may be an important source of gravitational energy during the cooling of white dwarf stars. This depends on the diffusion constant for 22Ne in strongly coupled plasma mixtures. We calculate self-diffusion constants D(i) from molecular dynamics simulations of carbon, oxygen, and neon mixtures. We find that D(i) in a mixture does not differ greatly from earlier one component plasma results. For strong coupling (coulomb parameter Γ> few), D(i) has a modest dependence on the charge Z(i) of the ion species, D(i)∝Z(i)(-2/3). However, D(i) depends more strongly on Z(i) for weak coupling (smaller Γ). We conclude that the self-diffusion constant D(Ne) for 22Ne in carbon, oxygen, and neon plasma mixtures is accurately known so that uncertainties in D(Ne) should be unimportant for simulations of white dwarf cooling.
Diffusion and perfusion imaging of bone marrow
International Nuclear Information System (INIS)
Biffar, Andreas; Dietrich, Olaf; Sourbron, Steven; Duerr, Hans-Roland; Reiser, Maximilian F.; Baur-Melnyk, Andrea
2010-01-01
In diffusion-weighted magnetic resonance imaging (DWI), the observed MRI signal intensity is attenuated by the self-diffusion of water molecules. DWI provides information about the microscopic structure and organization of a biological tissue, since the extent and orientation of molecular motion is influenced by these tissue properties. The most common method to measure perfusion in the body using MRI is T1-weighted dynamic contrast enhancement (DCE-MRI). The analysis of DCE-MRI data allows determining the perfusion and permeability of a biological tissue. DWI as well as DCE-MRI are established techniques in MRI of the brain, while significantly fewer studies have been published in body imaging. In recent years, both techniques have been applied successfully in healthy bone marrow as well as for the characterization of bone marrow alterations or lesions; e.g., DWI has been used in particular for the differentiation of benign and malignant vertebral compression fractures. In this review article, firstly a short introduction to diffusion-weighted and dynamic contrast-enhanced MRI is given. Non-quantitative and quantitative approaches for the analysis of DWI and semiquantitative and quantitative approaches for the analysis of DCE-MRI are introduced. Afterwards a detailed overview of the results of both techniques in healthy bone marrow and their applications for the diagnosis of various bone-marrow pathologies, like osteoporosis, bone tumors, and vertebral compression fractures are described.
Apparatus for diffusion separation
International Nuclear Information System (INIS)
Nierenberg, W.A.
1976-01-01
A diffuser separator apparatus is described which comprises a plurality of flow channels in a single stage. Each of said channels has an inlet port and an outlet port and a constant cross sectional area between said ports. At least a portion of the defining surface of each of said channels is a diffusion separation membrane, and each of said channels is a different cross sectional area. Means are provided for connecting said channels in series so that each successive channel of said series has a smaller cross sectional area than the previous channel of said series. Also provided are a source of gaseous mixture, individual means for flowing said gaseous mixture to the inlet port of each of said channels, gas receiving and analyzing means, individual means for flowing gas passing from each of said outlet ports and means for flowing gas passing through said membranes to said receiving and analyzing means, and individual means for connecting the outlet port of each channel with the inlet port of the channel having the next smaller cross sectional area
The diffusion of microfinance.
Banerjee, Abhijit; Chandrasekhar, Arun G; Duflo, Esther; Jackson, Matthew O
2013-07-26
To study the impact of the choice of injection points in the diffusion of a new product in a society, we developed a model of word-of-mouth diffusion and then applied it to data on social networks and participation in a newly available microfinance loan program in 43 Indian villages. Our model allows us to distinguish information passing among neighbors from direct influence of neighbors' participation decisions, as well as information passing by participants versus nonparticipants. The model estimates suggest that participants are seven times as likely to pass information compared to informed nonparticipants, but information passed by nonparticipants still accounts for roughly one-third of eventual participation. An informed household is not more likely to participate if its informed friends participate. We then propose two new measures of how effective a given household would be as an injection point. We show that the centrality of the injection points according to these measures constitutes a strong and significant predictor of eventual village-level participation.
Diffuse infiltrative lung disease
International Nuclear Information System (INIS)
Niden, A.H.; Mishkin, F.S.
1984-01-01
The authors discuss their approach to the diagnosis and management of patients with DILD. Gallium scans play a central role in this process. Not only do they help them decide whom to biopsy, but also where to biopsy. The scans can be used for the early detection of disease in a high-risk population, for following the progression and regression of disease, for the regulation of medication, and for the evaluation of therapy. Bronchoalveolar lung lavage appears to be equally sensitive. However, patients are less willing to undergo repeated fiberoptic bronchoscopies than lung scans. Both tests may prove useful, one complementing the other. Gallium imaging has also been utilized by the authors in select patients with questionable diffuse lung infiltrates roentgenographically or with a normal chest roentgenogram, chronic respiratory symptoms, and abnormal pulmonary function studies. An abnormal gallium lung scan in these clinical situations helps them select which patients have a diffuse active pulmonary process meriting transbronchial biopsies. This has proven to be of particular value in the management of older patients
Reaction and diffusion in turbulent combustion
Energy Technology Data Exchange (ETDEWEB)
Pope, S.B. [Mechanical and Aerospace Engineering, Ithaca, NY (United States)
1993-12-01
The motivation for this project is the need to obtain a better quantitative understanding of the technologically-important phenomenon of turbulent combustion. In nearly all applications in which fuel is burned-for example, fossil-fuel power plants, furnaces, gas-turbines and internal-combustion engines-the combustion takes place in a turbulent flow. Designers continually demand more quantitative information about this phenomenon-in the form of turbulent combustion models-so that they can design equipment with increased efficiency and decreased environmental impact. For some time the PI has been developing a class of turbulent combustion models known as PDF methods. These methods have the important virtue that both convection and reaction can be treated without turbulence-modelling assumptions. However, a mixing model is required to account for the effects of molecular diffusion. Currently, the available mixing models are known to have some significant defects. The major motivation of the project is to seek a better understanding of molecular diffusion in turbulent reactive flows, and hence to develop a better mixing model.
Molecular communications and nanonetworks from nature to practical systems
Atakan, Barış
2014-01-01
In this book, the concepts of molecular communications and nanonetworks are introduced. Throughout the book, the existing molecular communication paradigms are categorized into two main groups. The first group includes the Passive Molecular Communication (PMC) paradigms in which molecules freely diffuse to transfer information from a transmitter to a receiver. The second group includes the Active Molecular Communication (AMC) paradigms in which molecules are carried or guided by some mediators such as molecular motors, gap junction channels and bacteria. In the book, after briefly discussing why molecular communication is needed for the sophisticated nano and biotechnology applications, the existing molecular communication systems are first presented. Then, the principles of diffusion phenomena and molecular reception with absorbers and the ligand-receptor binding mechanism are introduced. Based on these principles, the communication theories and techniques are given for the PMC. Then, the physical dynamics o...
Choe, Hyonmin; Deirmengian, Carl A.; Hickok, Noreen J.; Morrison, Tiffany N.; Tuan, Rocky S.
2015-01-01
Orthopaedic infections are complex conditions that require immediate diagnosis and accurate identification of the causative organisms to facilitate appropriate management. Conventional methodologies for diagnosis of these infections sometimes lack accuracy or sufficient rapidity. Current molecular diagnostics are an emerging area of bench-to-bedside research in orthopaedic infections. Examples of promising molecular diagnostics include measurement of a specific biomarker in the synovial fluid...
International Nuclear Information System (INIS)
Parkinson, D.R.; Krontiris, T.G.
1986-01-01
In this chapter the authors review new findings concerning the molecular genetics of malignant melanoma in the context of other information obtained from clinical, epidemiologic, and cytogenetic studies in this malignancy. These new molecular approaches promise to provide a more complete understanding of the mechanisms involved in the development of melanoma, thereby suggesting new methods for its treatment and prevention
Indian Academy of Sciences (India)
Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 5. Molecular Modeling: A Powerful Tool for Drug Design and Molecular Docking. Rama Rao Nadendla. General Article Volume 9 Issue 5 May 2004 pp 51-60. Fulltext. Click here to view fulltext PDF. Permanent link:
Confinement and diffusion in tokamaks
International Nuclear Information System (INIS)
McWilliams, R.
1988-01-01
The effect of electric field fluctuations on confinement and diffusion in tokamak is discussed. Based on the experimentally determined cross-field turbolent diffusion coefficient, D∼3.7*cT e /eB(δn i /n i ) rms which is also derived by a simple theory, the cross-field diffusion time, tp=a 2 /D, is calculated and compared to experimental results from 51 tokamak for standard Ohmic operation
Diffuse scattering of neutrons
International Nuclear Information System (INIS)
Novion, C.H. de.
1981-02-01
The use of neutron scattering to study atomic disorder in metals and alloys is described. The diffuse elastic scattering of neutrons by a perfect crystal lattice leads to a diffraction spectrum with only Bragg spreads. the existence of disorder in the crystal results in intensity and position modifications to these spreads, and above all, to the appearance of a low intensity scatter between Bragg peaks. The elastic scattering of neutrons is treated in this text, i.e. by measuring the number of scattered neutrons having the same energy as the incident neutrons. Such measurements yield information on the static disorder in the crystal and time average fluctuations in composition and atomic displacements [fr
Diffuse lung disease: Pneumoconioses
International Nuclear Information System (INIS)
McLoud, T.C.
1987-01-01
This paper begins with a discussion of the 1980 International Labour Organization classification of the pneumoconioses. Emphasis is on the common pneumoconioses, that is, silicosis, coalworker's pneumoconiosis, and asbestos-related pleural and parenchymal disease. Examples of the five radiographic forms of silicosis-simple and complicated silicosis, Caplan syndrome, silicotuberculosis, and acute silicosis- are presented, and the differential diagnoses are discussed. Discussion of asbestos-related disease included pleural manifestations such as plaques, diffuse pleural thickening, and asbestos pleural effusion as well as asbestosis and malignancies associated with asbestos exposure, such as bronchogenic carcinoma and malignant mesothelioma. Although the standard radiographic findings are stressed, the use of CT in the diagnosis of pneumoconiosis and the staging of dust-related malignancies is also discussed
On Diffusive Climatological Models.
Griffel, D. H.; Drazin, P. G.
1981-11-01
A simple, zonally and annually averaged, energy-balance climatological model with diffusive heat transport and nonlinear albedo feedback is solved numerically. Some parameters of the model are varied, one by one, to find the resultant effects on the steady solution representing the climate. In particular, the outward radiation flux, the insulation distribution and the albedo parameterization are varied. We have found an accurate yet simple analytic expression for the mean annual insolation as a function of latitude and the obliquity of the Earth's rotation axis; this has enabled us to consider the effects of the oscillation of the obliquity. We have used a continuous albedo function which fits the observed values; it considerably reduces the sensitivity of the model. Climatic cycles, calculated by solving the time-dependent equation when parameters change slowly and periodically, are compared qualitatively with paleoclimatic records.
Diffuse parenchymal lung disease
Directory of Open Access Journals (Sweden)
Sara Tomassetti
2017-04-01
Full Text Available Between September 2015 and August 2016 there were >1500 publications in the field of diffuse parenchymal lung diseases (DPLDs. For the Clinical Year in Review session at the European Respiratory Society Congress that was held in London, UK, in September 2016, we selected only five articles. This selection, made from the enormous number of published papers, does not include all the relevant studies that will significantly impact our knowledge in the field of DPLDs in the near future. This review article provides our personal view on the following topics: early diagnosis of idiopathic pulmonary fibrosis, current knowledge on the multidisciplinary team diagnosis of DPLDs and the diagnostic role of transbronchial cryobiopsy in this diagnostic setting, insights on the new entity of interstitial pneumonia with autoimmune features, and new therapeutic approaches for scleroderma-related interstitial lung disease.
Convergence of Nelson diffusions
International Nuclear Information System (INIS)
Dell'Antonio, G.; Posilicano, A.
1991-01-01
Let ψ t , ψ t n , n≥1, be solutions of Schroedinger equations with potentials form-bounded by -1/2 Δ and initial data in H 1 (R d ). Let P, P n , n≥1, be the probability measures on the path space Ω=C(R + , R d ) given by the corresponding Nelson diffusions. We show that if {ψ t n } n≥1 converges to ψ t in H 2 (R d ), uniformly in t over compact intervals, then {P n } n≥1 converges to P in total variation. Moreover, if the potentials are in the Kato class K d , we show that the above result follows from H 1 -convergence of initial data, and K d -convergence of potentials. (orig.)
Hereditary diffuse gastric cancer
DEFF Research Database (Denmark)
van der Post, Rachel S; Vogelaar, Ingrid P; Carneiro, Fátima
2015-01-01
Germline CDH1 mutations confer a high lifetime risk of developing diffuse gastric (DGC) and lobular breast cancer (LBC). A multidisciplinary workshop was organised to discuss genetic testing, surgery, surveillance strategies, pathology reporting and the patient's perspective on multiple aspects......, including diet post gastrectomy. The updated guidelines include revised CDH1 testing criteria (taking into account first-degree and second-degree relatives): (1) families with two or more patients with gastric cancer at any age, one confirmed DGC; (2) individuals with DGC before the age of 40 and (3...... the high mortality associated with invasive disease, prophylactic total gastrectomy at a centre of expertise is advised for individuals with pathogenic CDH1 mutations. Breast cancer surveillance with annual breast MRI starting at age 30 for women with a CDH1 mutation is recommended. Standardised endoscopic...
The diffuse interstellar medium
Cox, Donald P.
1990-01-01
The last 20 years of the efforts to understand the diffuse ISM are reviewed, with recent changes of fundamental aspects being highlighted. Attention is given to the interstellar pressure and its components, the weight of the ISM, the midplane pressure contributions, and pressure contributions at 1 kpc. What velocity dispersions, cosmic ray pressure, and magnetic field pressure that can be expected for a gas in a high magnetic field environment is addressed. The intercloud medium is described, with reference to the work of Cox and Slavin (1989). Various caveats are discussed and a number of areas for future investigation are identified. Steps that could be taken toward a successful phase segregation model are discussed.
Nonlocal diffusion and applications
Bucur, Claudia
2016-01-01
Working in the fractional Laplace framework, this book provides models and theorems related to nonlocal diffusion phenomena. In addition to a simple probabilistic interpretation, some applications to water waves, crystal dislocations, nonlocal phase transitions, nonlocal minimal surfaces and Schrödinger equations are given. Furthermore, an example of an s-harmonic function, its harmonic extension and some insight into a fractional version of a classical conjecture due to De Giorgi are presented. Although the aim is primarily to gather some introductory material concerning applications of the fractional Laplacian, some of the proofs and results are new. The work is entirely self-contained, and readers who wish to pursue related subjects of interest are invited to consult the rich bibliography for guidance.
MHD diffuser model test program
Energy Technology Data Exchange (ETDEWEB)
Idzorek, J J
1976-07-01
Experimental results of the aerodynamic performance of seven candidate diffusers are presented to assist in determining their suitability for joining an MHD channel to a steam generator at minimum spacing. The three dimensional diffusers varied in area ratio from 2 to 3.8 and wall half angle from 2 to 5 degrees. The program consisted of five phases: (1) tailoring a diffuser inlet nozzle to a 15 percent blockage; (2) comparison of isolated diffusers at enthalpy ratios 0.5 to 1.0 with respect to separation characteristics and pressure recovery coefficients; (3) recording the optimum diffuser exit flow distribution; (4) recording the internal flow distribution within the steam generator when attached to the diffuser; and (5) observing isolated diffuser exhaust dynamic characteristics. The 2 and 2-1/3 degree half angle rectangular diffusers showed recovery coefficients equal to 0.48 with no evidence of flow separation or instability. Diffusion at angles greater than these produced flow instabilities and with angles greater than 3 degrees random flow separation and reattachment.
MHD diffuser model test program
International Nuclear Information System (INIS)
Idzorek, J.J.
1976-07-01
Experimental results of the aerodynamic performance of seven candidate diffusers are presented to assist in determining their suitability for joining an MHD channel to a steam generator at minimum spacing. The three dimensional diffusers varied in area ratio from 2 to 3.8 and wall half angle from 2 to 5 degrees. The program consisted of five phases: (1) tailoring a diffuser inlet nozzle to a 15 percent blockage; (2) comparison of isolated diffusers at enthalpy ratios 0.5 to 1.0 with respect to separation characteristics and pressure recovery coefficients; (3) recording the optimum diffuser exit flow distribution; (4) recording the internal flow distribution within the steam generator when attached to the diffuser; and (5) observing isolated diffuser exhaust dynamic characteristics. The 2 and 2-1/3 degree half angle rectangular diffusers showed recovery coefficients equal to 0.48 with no evidence of flow separation or instability. Diffusion at angles greater than these produced flow instabilities and with angles greater than 3 degrees random flow separation and reattachment
Diffusion rates for elevated releases
International Nuclear Information System (INIS)
Ramsdell, J.V.
1983-11-01
A search of the literature related to diffusion from elevated sources has determined that an adequate data base exists for use in developing parameterizations for estimating diffusion rates for material released from free standing stacks at nuclear power plants. A review of published data analyses indicates that a new parameterization of horizontal diffusion rates specifically for elevated releases is not likely to significantly change the magnitudes of horizontal diffusion coefficients on the average. However, the uncertainties associated with horizontal diffusion coefficient estimates under any given set of atmospheric conditions could be reduced by a new parameterization. Similarly, a new parameterization of vertical diffusion rates would be unlikely to significantly alter the magnitudes of diffusion coefficients for unstable atmospheric conditons. However, for neutral and stable atmospheric conditions, a new parameterization of vertical diffusion rates might increase vertical diffusion coefficients significantly. The increase would move ground-level time-integrated concentration maxima closer to the plant and would increase the maxima. 55 references, 2 figures, 4 tables
International Nuclear Information System (INIS)
Wehinger, Björn; Krisch, Michael; Bosak, Alexeï; Chernyshov, Dmitry; Bulat, Sergey; Ezhov, Victor
2014-01-01
Single crystals of ice Ih, extracted from the subglacial Lake Vostok accretion ice layer (3621 m depth) were investigated by means of diffuse x-ray scattering and inelastic x-ray scattering. The diffuse scattering was identified as mainly inelastic and rationalized in the frame of ab initio calculations for the ordered ice XI approximant. Together with Monte-Carlo modelling, our data allowed reconsidering previously available neutron diffuse scattering data of heavy ice as the sum of thermal diffuse scattering and static disorder contribution. (paper)
Diffusion of condenser water discharge
International Nuclear Information System (INIS)
Iwakiri, Toshio
1977-01-01
Thermal and nuclear power stations in Japan are mostly located in coastal area, and the cooling water is discharged into sea as warm water. Recently, large interest is taken in this matter, and it is desirable to predict the diffusion of warm discharge accurately and to take effective measures for lowering the temperature. As for the methods of predicting the diffusion of warm discharge, simplified estimation, mathematical analysis and hydrographical model experiment are used corresponding to objects and conditions. As for the measures to lower temperature, the method of discharging warm water into deep sea bottom was confirmed to be very effective. In this paper, the phenomena of diffusion of warm discharge in sea, the methods of predicting the diffusion of warm discharge, and the deep sea discharge as the measure for lowering temperature are outlined. The factors concerning the diffusion of warm discharge in sea are the conditions of discharge, topography and sea state, and the diffusion is roughly divided into mixing diffusion in the vicinity of warm water outlet and eddy diffusion in distant region. It is difficult to change artificially the conditions of diffusion in distant region, and the measures of raising the rate of dilution in near region are effective, therefore the deep sea discharge is adopted. (Kako, I.)
Diffusion effects in undulator radiation
Directory of Open Access Journals (Sweden)
Ilya Agapov
2014-11-01
Full Text Available Quantum diffusion effects in undulator radiation in semiclassical approximation are considered. Short-term effects on the electron beam motion are discussed and it is shown that approaches based on diffusion approximation with drift-diffusion coefficients derived from undulator or bending magnet radiation spectrum, and on Poisson statistics with radiation spectrum defined by the local beding field, all lead to similar results in terms of electron energy spread for cases of practical interest. An analytical estimate of the influence of quantum diffusion on the undulator radiation spectrum is derived.
Sodium diffusion in boroaluminosilicate glasses
DEFF Research Database (Denmark)
Smedskjaer, Morten M.; Zheng, Qiuju; Mauro, John C.
2011-01-01
of isothermal sodium diffusion in BAS glasses by ion exchange, inward diffusion, and tracer diffusion experiments. By varying the [SiO2]/[Al2O3] ratio of the glasses, different structural regimes of sodium behavior are accessed. We show that the mobility of the sodium ions decreases with increasing [SiO2]/[Al2O......Understanding the fundamentals of alkali diffusion in boroaluminosilicate (BAS) glasses is of critical importance for advanced glass applications, e.g., the production of chemically strengthened glass covers for personal electronic devices. Here, we investigate the composition dependence...
Zhang, Guangwen; Wang, Shuangshuang; Wen, Didi; Zhang, Jing; Wei, Xiaocheng; Ma, Wanling; Zhao, Weiwei; Wang, Mian; Wu, Guosheng; Zhang, Jinsong
2016-12-09
Water molecular diffusion in vivo tissue is much more complicated. We aimed to compare non-Gaussian diffusion models of diffusion-weighted imaging (DWI) including intra-voxel incoherent motion (IVIM), stretched-exponential model (SEM) and Gaussian diffusion model at 3.0 T MRI in patients with rectal cancer, and to determine the optimal model for investigating the water diffusion properties and characterization of rectal carcinoma. Fifty-nine consecutive patients with pathologically confirmed rectal adenocarcinoma underwent DWI with 16 b-values at a 3.0 T MRI system. DWI signals were fitted to the mono-exponential and non-Gaussian diffusion models (IVIM-mono, IVIM-bi and SEM) on primary tumor and adjacent normal rectal tissue. Parameters of standard apparent diffusion coefficient (ADC), slow- and fast-ADC, fraction of fast ADC (f), α value and distributed diffusion coefficient (DDC) were generated and compared between the tumor and normal tissues. The SEM exhibited the best fitting results of actual DWI signal in rectal cancer and the normal rectal wall (R 2 = 0.998, 0.999 respectively). The DDC achieved relatively high area under the curve (AUC = 0.980) in differentiating tumor from normal rectal wall. Non-Gaussian diffusion models could assess tissue properties more accurately than the ADC derived Gaussian diffusion model. SEM may be used as a potential optimal model for characterization of rectal cancer.
Turing instability in reaction-diffusion systems with nonlinear diffusion
Energy Technology Data Exchange (ETDEWEB)
Zemskov, E. P., E-mail: zemskov@ccas.ru [Russian Academy of Sciences, Dorodnicyn Computing Center (Russian Federation)
2013-10-15
The Turing instability is studied in two-component reaction-diffusion systems with nonlinear diffusion terms, and the regions in parametric space where Turing patterns can form are determined. The boundaries between super- and subcritical bifurcations are found. Calculations are performed for one-dimensional brusselator and oregonator models.
Direct measurement of time dependent diffusion for Ag and Au under ambient conditions
Energy Technology Data Exchange (ETDEWEB)
Yoo, Pil Sun; Jo, Han Yeol; Kim, Tae Kyeong [Hankuk University of Foreign Studies, Yongin (Korea, Republic of)
2014-12-15
Time-dependent diffusion for Ag and Au metal atoms was measured using the scanning tunneling microscope break-junction technique in ambient conditions. We observed that Ag contacts do not form long single-atomic chains compared to Au contacts during the elongation of each metal electrode, and Ag atoms diffuse more quickly than Au atoms after metal contact rupture. This is consistent with previous results of molecular dynamic simulations. Further, we found a correlation between diffusion length and the evolution time on an atomic scale to reveal the time-dependent diffusion for Ag and Au metal atoms.
Chaotic advection, diffusion, and reactions in open flows
International Nuclear Information System (INIS)
Tel, Tamas; Karolyi, Gyoergy; Pentek, Aron; Scheuring, Istvan; Toroczkai, Zoltan; Grebogi, Celso; Kadtke, James
2000-01-01
We review and generalize recent results on advection of particles in open time-periodic hydrodynamical flows. First, the problem of passive advection is considered, and its fractal and chaotic nature is pointed out. Next, we study the effect of weak molecular diffusion or randomness of the flow. Finally, we investigate the influence of passive advection on chemical or biological activity superimposed on open flows. The nondiffusive approach is shown to carry some features of a weak diffusion, due to the finiteness of the reaction range or reaction velocity. (c) 2000 American Institute of Physics
Diffusion of radionuclide chains through an adsorbing medium
International Nuclear Information System (INIS)
Burkholder, H.C.; DeFigh-Price, C.
1977-01-01
The diffusion of radionuclide chains from an underground nuclear waste disposal site through the surrounding geologic medium to the surface is investigated for impulse and band releases. Numerical calculation of the analytical solutions shows that differences in adsorption characteristics among chain members and radioactive decay during transit reduce radionuclide discharges to the biosphere. Results suggest that molecular diffusion is unlikely to be an important transfer mechanism from geologic isolation, and that disposal of radionuclides in deep geologic formations and in the seabed under conditions of very low or nonexistent water flow is likely to be very effective in preventing radioactivity releases to the biosphere
Modelling and simulation of diffusive processes methods and applications
Basu, SK
2014-01-01
This book addresses the key issues in the modeling and simulation of diffusive processes from a wide spectrum of different applications across a broad range of disciplines. Features: discusses diffusion and molecular transport in living cells and suspended sediment in open channels; examines the modeling of peristaltic transport of nanofluids, and isotachophoretic separation of ionic samples in microfluidics; reviews thermal characterization of non-homogeneous media and scale-dependent porous dispersion resulting from velocity fluctuations; describes the modeling of nitrogen fate and transport
Serag, Maged F.
2014-10-06
Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields.
Serag, Maged F.; Abadi, Maram; Habuchi, Satoshi
2014-01-01
Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields.
Variation of diffusivity with the cation radii in molten salts of ...
Indian Academy of Sciences (India)
Abstract. A molecular dynamics study of the dependence of diffusivity of the cation on ionic radii in molten. AgI is reported. ... potential) to carry out molecular dynamics simulations on α-AgI. ..... There is no clustering of these ions. The anionic.
Diffusion of gases in metal containing carbon aerogels
Energy Technology Data Exchange (ETDEWEB)
Marques, L.M.; Conceicao, F.L.; Carrott, M.M.L. Ribeiro; Carrott, P.J.M. [Evora Univ. (Portugal). Centro de Quimica de Evora
2011-02-15
Carbon aerogels containing Fe, Ni, Cu or no metal were prepared by carbonisation of polymer aerogels synthesised from 2,4-dihydroxybenzoic acid and formaldehyde and modified by CVD of benzene. Uptakes and diffusion coefficients of CO{sub 2}, CH{sub 4}, N{sub 2} and O{sub 2} were measured and the results compared with those obtained using a commercial carbon molecular sieve. The results indicated that the diffusion of light gas molecules in carbon aerogels cannot be interpreted solely on the basis of micropore diffusion, but that the very high mesopore volumes of the aerogel monoliths exert a strong influence on the kinetics of diffusion in these materials. The mesoporosity is decreased when the % solids used during synthesis of the polymer precursor increases and this resulted in kinetic behaviour which was more similar to that predicted by Fickian or LDF models. Increasing % solids was also accompanied by generally slower diffusion rates and generally lower uptakes. The single gas uptakes and diffusion coefficients could be altered by varying the % solids used during synthesis of the polymer precursor, by introducing different metals into the polymer hydrogel by ion exchange, or by CVD of benzene on the carbon aerogel. (author)
Diffuse scattering as an indicator for martensitic variant selection
International Nuclear Information System (INIS)
Gao, Lei; Ding, Xiangdong; Zong, Hongxiang; Lookman, Turab; Sun, Jun; Ren, Xiaobing; Saxena, Avadh
2014-01-01
Diffuse scattering is an important precursor phenomenon prior to the martensitic transformation (MT). It is related to the correlated atomic position fluctuations prior to the MT and can provide important hints of the transformation mechanism. However, the role of this precursor phenomenon in the MT is not clear so far. Here we study the evolution of diffraction patterns prior to temperature- and stress-induced MTs and consider the evolution of atomic configurations during the whole MT process, using molecular dynamics simulations on a generic body-centered cubic–hexagonal close-packed transformation as an example. Our results show that, although the diffuse scattering changes with external fields, there exists a general relationship between the transformation pathways, the diffuse scattering streaks and the martensitic products. Two preferred transformation pathways with opposite shuffle directions lead to a single specific diffuse scattering streak prior to the MT and form one pair of anti-variants after the MT. Thus the distribution of diffuse scattering acts as an indicator of the selection of martensitic variants. In addition, we find that the applied stress can change the shear order parameter of the phase transformation, and subsequently determines the preferred transformation pathways and the distribution of diffuse scattering streaks. This work establishes a relationship between the transformation mechanism, the precursor phenomenon and the products after the MT under the influence of external fields
Diffusion of gases in metal containing carbon aerogels
International Nuclear Information System (INIS)
Marques, L.M.; Conceicao, F.L.; Carrott, M.M.L. Ribeiro; Carrott, P.J.M.
2011-01-01
Carbon aerogels containing Fe, Ni, Cu or no metal were prepared by carbonisation of polymer aerogels synthesised from 2,4-dihydroxybenzoic acid and formaldehyde and modified by CVD of benzene. Uptakes and diffusion coefficients of CO 2 , CH 4 , N 2 and O 2 were measured and the results compared with those obtained using a commercial carbon molecular sieve. The results indicated that the diffusion of light gas molecules in carbon aerogels cannot be interpreted solely on the basis of micropore diffusion, but that the very high mesopore volumes of the aerogel monoliths exert a strong influence on the kinetics of diffusion in these materials. The mesoporosity is decreased when the % solids used during synthesis of the polymer precursor increases and this resulted in kinetic behaviour which was more similar to that predicted by Fickian or LDF models. Increasing % solids was also accompanied by generally slower diffusion rates and generally lower uptakes. The single gas uptakes and diffusion coefficients could be altered by varying the % solids used during synthesis of the polymer precursor, by introducing different metals into the polymer hydrogel by ion exchange, or by CVD of benzene on the carbon aerogel. (author)
Rodger, Alison
1995-01-01
Molecular Geometry discusses topics relevant to the arrangement of atoms. The book is comprised of seven chapters that tackle several areas of molecular geometry. Chapter 1 reviews the definition and determination of molecular geometry, while Chapter 2 discusses the unified view of stereochemistry and stereochemical changes. Chapter 3 covers the geometry of molecules of second row atoms, and Chapter 4 deals with the main group elements beyond the second row. The book also talks about the complexes of transition metals and f-block elements, and then covers the organometallic compounds and trans
Spatially Different Tissue-Scale Diffusivity Shapes ANGUSTIFOLIA3 Gradient in Growing Leaves.
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
Plessis, S.; McDougall, D.; Mandt, K.; Greathouse, T.; Luspay-Kuti, A.
2015-11-01
Bimolecular diffusion coefficients are important parameters used by atmospheric models to calculate altitude profiles of minor constituents in an atmosphere. Unfortunately, laboratory measurements of these coefficients were never conducted at temperature conditions relevant to the atmosphere of Titan. Here we conduct a detailed uncertainty analysis of the bimolecular diffusion coefficient parameters as applied to Titan's upper atmosphere to provide a better understanding of the impact of uncertainty for this parameter on models. Because temperature and pressure conditions are much lower than the laboratory conditions in which bimolecular diffusion parameters were measured, we apply a Bayesian framework, a problem-agnostic framework, to determine parameter estimates and associated uncertainties. We solve the Bayesian calibration problem using the open-source QUESO library which also performs a propagation of uncertainties in the calibrated parameters to temperature and pressure conditions observed in Titan's upper atmosphere. Our results show that, after propagating uncertainty through the Massman model, the uncertainty in molecular diffusion is highly correlated to temperature and we observe no noticeable correlation with pressure. We propagate the calibrated molecular diffusion estimate and associated uncertainty to obtain an estimate with uncertainty due to bimolecular diffusion for the methane molar fraction as a function of altitude. Results show that the uncertainty in methane abundance due to molecular diffusion is in general small compared to eddy diffusion and the chemical kinetics description. However, methane abundance is most sensitive to uncertainty in molecular diffusion above 1200 km where the errors are nontrivial and could have important implications for scientific research based on diffusion models in this altitude range.
Models of diffuse solar radiation
Energy Technology Data Exchange (ETDEWEB)
Boland, John; Ridley, Barbara [Centre for Industrial and Applied Mathematics, University of South Australia, Mawson Lakes Boulevard, Mawson Lakes, SA 5095 (Australia); Brown, Bruce [Department of Statistics and Applied Probability, National University of Singapore, Singapore 117546 (Singapore)
2008-04-15
For some locations both global and diffuse solar radiation are measured. However, for many locations, only global is measured, or inferred from satellite data. For modelling solar energy applications, the amount of radiation on a tilted surface is needed. Since only the direct component on a tilted surface can be calculated from trigonometry, we need to have diffuse on the horizontal available. There are regression relationships for estimating the diffuse on a tilted surface from diffuse on the horizontal. Models for estimating the diffuse radiation on the horizontal from horizontal global that have been developed in Europe or North America have proved to be inadequate for Australia [Spencer JW. A comparison of methods for estimating hourly diffuse solar radiation from global solar radiation. Sol Energy 1982; 29(1): 19-32]. Boland et al. [Modelling the diffuse fraction of global solar radiation on a horizontal surface. Environmetrics 2001; 12: 103-16] developed a validated model for Australian conditions. We detail our recent advances in developing the theoretical framework for the approach reported therein, particularly the use of the logistic function instead of piecewise linear or simple nonlinear functions. Additionally, we have also constructed a method, using quadratic programming, for identifying values that are likely to be erroneous. This allows us to eliminate outliers in diffuse radiation values, the data most prone to errors in measurement. (author)
Osmosis and Diffusion Conceptual Assessment
Fisher, Kathleen M.; Williams, Kathy S.; Lineback, Jennifer Evarts
2011-01-01
Biology student mastery regarding the mechanisms of diffusion and osmosis is difficult to achieve. To monitor comprehension of these processes among students at a large public university, we developed and validated an 18-item Osmosis and Diffusion Conceptual Assessment (ODCA). This assessment includes two-tiered items, some adopted or modified…
The diffusion of constitutional rights
Goderis, B.V.G.; Versteeg, M.
Constitutions are commonly regarded as uniquely national products, shaped by domestic ideals and politics. This paper develops and empirically investigates a novel hypothesis, which is that constitutions are also shaped by transnational influence, or “diffusion.” Constitutional rights can diffuse
Diffusion measurements by Raman spectroscopy
DEFF Research Database (Denmark)
Hansen, Susanne Brunsgaard; Shapiro, Alexander; Berg, Rolf W.
Poster "Diffusion measurements by Raman spectroscopy", See poster at http://www.kemi.dtu.dk/~ajo/rolf/petroday2004.ppt......Poster "Diffusion measurements by Raman spectroscopy", See poster at http://www.kemi.dtu.dk/~ajo/rolf/petroday2004.ppt...
Consequences of Diffusion of Innovations.
Goss, Kevin F.
1979-01-01
The article traces evolution of diffusion theory; illustrates undesirable consequences in a cross-cultural setting, reviews criticisms of several scholars; considers distributional effects and unanticipated consequences for potential ameliorative impact on diffusion theory; and codifies these factors into a framework for research into consequences…
Enhancement of diffusers BRDF accuracy
Otter, Gerard; Bazalgette Courrèges-Lacoste, Gregory; van Brug, Hedser; Schaarsberg, Jos Groote; Delwart, Steven; del Bello, Umberto
2017-11-01
This paper reports the result of an ESA study conducted at TNO to investigate properties of various diffusers. Diffusers are widely used in space instruments as part of the on-board absolute calibration. Knowledge of the behaviour of the diffuser is therefore most important. From measurements of launched instruments in-orbit it has been discovered that when a diffuser is used in the vacuum of space the BRDF can change with respect to the one in ambient conditions. This is called the air/vacuum effect and has been simulated in this study by measuring the BRDF in a laboratory in ambient as well as vacuum conditions. Another studied effect is related to the design parameters of the optical system and the scattering properties of the diffuser. The effect is called Spectral Features and is a noise like structure superimposed on the diffuser BRDF. Modern space spectrometers, which have high spectral resolution and/or a small field of view (high spatial resolution) are suffering from this effect. The choice of diffuser can be very critical with respect to the required absolute radiometric calibration of an instrument. Even if the Spectral Features are small it can influence the error budget of the retrieval algorithms for the level 2 products. in this presentation diffuser trade-off results are presented and the Spectral Features model applied to the optical configuration of the MERIS instrument is compared to in-flight measurements of MERIS.
Application of polycrystalline diffusion barriers
International Nuclear Information System (INIS)
Tsymbal, V.A.; Kolupaev, I.N.
2010-01-01
Degradation of contacts of the electronic equipment at the raised temperatures is connected with active diffusion redistribution of components contact - metalized systems (CMS) and phase production on interphase borders. One of systems diffusion barriers (DB) are polycrystalline silicide a film, in particular silicides of the titan. Reception disilicide the titan (TiSi 2 ) which on the parameters is demanded for conditions of microelectronics from known silicides of system Ti-Si, is possible as a result of direct reaction of a film of the titan and a substrate of silicon, and at sedimentation of layer Ti-Si demanded stoichiometric structure. Simultaneously there is specific problem polycrystalline diffusion a barrier (PDB): the polycrystalline provides structural balance and metastability film disilicide, but leaves in it borders of grains - easy local ways of diffusion. In clause the analysis diffusion permeability polycrystalline and polyphase DB is made and recommendations for practical methods of increase of blocking properties PDB are made.
DEFF Research Database (Denmark)
Jennum, Karsten Stein
This thesis includes the synthesis and characterisation of organic compounds designed for molecular electronics. The synthesised organic molecules are mainly based on two motifs, the obigo(phenyleneethynylenes) (OPE)s and tetrathiafulvalene (TTF) as shown below. These two scaffolds (OPE and TTF......) are chemically merged together to form cruciform-like structures that are an essential part of the thesis. The cruciform molecules were subjected to molecular conductance measurements to explore their capability towards single-crystal field-effect transistors (Part 1), molecular wires, and single electron......, however, was obtained by a study of a single molecular transistor. The investigated OPE5-TTF compound was captured in a three-terminal experiment, whereby manipulation of the molecule’s electronic spin was possible in different charge states. Thus, we demonstrated how the cruciform molecules could...
International Nuclear Information System (INIS)
Anon.
1975-01-01
The research in molecular sciences summarized includes photochemistry, radiation chemistry, geophysics, electromechanics, heavy-element oxidizers , heavy element chemistry collisions, atoms, organic solids. A list of publications is included
Energy Technology Data Exchange (ETDEWEB)
Chakraborty, Brahmananda, E-mail: brahma@barc.gov.in; Ramaniah, Lavanya M. [High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085 (India)
2015-06-24
Applying Green–Kubo formalism and equilibrium molecular dynamics (MD) simulations, we have studied the dynamic correlation, Onsager coeeficients and Maxwell–Stefan (MS) Diffusivities of molten salt LiF-BeF{sub 2}, which is used as coolant in high temperature reactor. All the diffusive flux correlations show back-scattering or cage dynamics which becomes pronouced at higher temperature. Although the MS diffusivities are expected to depend very lightly on the composition due to decoupling of thermodynamic factor, the diffusivity Đ{sub Li-F} and Đ{sub Be-F} decreases sharply for higher concentration of LiF and BeF{sub 2} respectively. Interestingly, all three MS diffusivities have highest magnitude for eutectic mixture at 1000K (except Đ{sub Be-F} at lower LiF mole fraction) which is desirable from coolant point of view. Although the diffusivity for positive-positive ion pair is negative it is not in violation of the second law of thermodynamics as it satisfies the non-negative entropic constraints.
The magnetic diffusion of neutrons; La diffusion magnetique des neutrons
Energy Technology Data Exchange (ETDEWEB)
Koehler, W C [Commissariat a l' Energie Atomique, Saclay (France).Centre d' Etudes Nucleaires
1959-07-01
The purpose of this report is to examine briefly the diffusion of neutrons by substances, particularly by crystals containing permanent atomic or ionic magnetic moments. In other words we shall deal with ferromagnetic, antiferromagnetic, ferrimagnetic or paramagnetic crystals, but first it is necessary to touch on nuclear diffusion of neutrons. We shall start with the interaction of the neutron with a single diffusion centre; the results will then be applied to the magnetic interactions of the neutron with the satellite electrons of the atom; finally we shall discuss the diffusion of neutrons by crystals. (author) [French] Le but de ce rapport est d'examiner, brievement, la diffusion des neutrons par les substances, et surtout, par des cristaux qui contiennent des moments magnetiques atomiques ou ioniques permanents. C'est-a-dire que nous nous interesserons aux cristaux ferromagnetiques, antiferromagnetiques, ferrimagnetiques ou paramagnetiques; il nous faut cependant rappeler d'abord la diffusion nucleaire des neutrons. Nous commencerons par l'interaction du neutron avec un seul centre diffuseur; puis les resultats seront appliques aux interactions magnetiques du neutron avec les electrons satellites de l'atome; enfin nous discuterons la diffusion des neutrons par les cristaux. (auteur)
Multidimensional diffusion processes
Stroock, Daniel W
1997-01-01
From the reviews: "… Both the Markov-process approach and the Itô approach … have been immensely successful in diffusion theory. The Stroock-Varadhan book, developed from the historic 1969 papers by its authors, presents the martingale-problem approach as a more powerful - and, in certain regards, more intrinsic-means of studying the foundations of the subject. […] … the authors make the uncompromising decision not "to proselytise by intimidating the reader with myriad examples demonstrating the full scope of the techniques", but rather to persuade the reader "with a careful treatment of just one problem to which they apply". […] Most of the main tools of stochastic-processes theory are used, ..but it is the formidable combination of probability theory with analysis … which is the core of the work. […] I have emphasized the great importance of the Stroock-Varadhan book. It contains a lot more than I have indicated; in particular, its many exercises conain much interesting material. For immediat...
Diffusive instabilities in hyperbolic reaction-diffusion equations
Zemskov, Evgeny P.; Horsthemke, Werner
2016-03-01
We investigate two-variable reaction-diffusion systems of the hyperbolic type. A linear stability analysis is performed, and the conditions for diffusion-driven instabilities are derived. Two basic types of eigenvalues, real and complex, are described. Dispersion curves for both types of eigenvalues are plotted and their behavior is analyzed. The real case is related to the Turing instability, and the complex one corresponds to the wave instability. We emphasize the interesting feature that the wave instability in the hyperbolic equations occurs in two-variable systems, whereas in the parabolic case one needs three reaction-diffusion equations.
Classically exact surface diffusion constants at arbitrary temperature
International Nuclear Information System (INIS)
Voter, A.F.; Cohen, J.M.
1989-01-01
An expression is presented for computing the classical diffusion constant of a point defect (e.g., an adatom) in an infinite lattice of binding sites at arbitrary temperature. The transition state theory diffusion constant is simply multiplied by a dynamical correction factor that is computed from short-time classical trajectories initiated at the site boundaries. The time scale limitations of direct molecular dynamics are thus avoided in the low- and middle-temperature regimes. The expression results from taking the time derivative of the particle mean-square displacement in the lattice-discretized coordinate system. Applications are presented for surface diffusion on fcc(100) and fcc(111) Lennard-Jones crystal faces
Diffusing passive tracers in random incompressible flows: Statistical topography aspects
International Nuclear Information System (INIS)
Klyatskin, V.I.; Woyczynski, W.A.; Gurarie, D.
1996-01-01
The paper studies statistical characteristics of the passive tracer concentrations and of its spatial gradient, in random incompressible velocity fields from the viewpoint of statistical topography. The statistics of interest include mean values, probability distributions, as well as various functionals characterizing topographic features of tracers. The functional approach is used. We consider the influence of the mean flow (the linear shear flow) and the molecular diffusion coefficient on the statistics of the tracer. Most of our analysis is carried out in the framework of the delta-correlated (in time) approximation and conditions for its applicability are established. But we also consider the diffusion approximation scheme for finite correlation radius. The latter is applied to a diffusing passive tracer that undergoes sedimentation in a random velocity field
Internal Diffusion-Controlled Enzyme Reaction: The Acetylcholinesterase Kinetics.
Lee, Sangyun; Kim, Ji-Hyun; Lee, Sangyoub
2012-02-14
Acetylcholinesterase is an enzyme with a very high turnover rate; it quenches the neurotransmitter, acetylcholine, at the synapse. We have investigated the kinetics of the enzyme reaction by calculating the diffusion rate of the substrate molecule along an active site channel inside the enzyme from atomic-level molecular dynamics simulations. In contrast to the previous works, we have found that the internal substrate diffusion is the determinant of the acetylcholinesterase kinetics in the low substrate concentration limit. Our estimate of the overall bimolecular reaction rate constant for the enzyme is in good agreement with the experimental data. In addition, the present calculation provides a reasonable explanation for the effects of the ionic strength of solution and the mutation of surface residues of the enzyme. The study suggests that internal diffusion of the substrate could be a key factor in understanding the kinetics of enzymes of similar characteristics.
Energy Technology Data Exchange (ETDEWEB)
Strecker, Kevin E.; Chandler, David W.
2009-09-01
A molecular fountain directs slowly moving molecules against gravity to further slow them to translational energies that they can be trapped and studied. If the molecules are initially slow enough they will return some time later to the position from which they were launched. Because this round trip time can be on the order of a second a single molecule can be observed for times sufficient to perform Hz level spectroscopy. The goal of this LDRD proposal was to construct a novel Molecular Fountain apparatus capable of producing dilute samples of molecules at near zero temperatures in well-defined user-selectable, quantum states. The slowly moving molecules used in this research are produced by the previously developed Kinematic Cooling technique, which uses a crossed atomic and molecular beam apparatus to generate single rotational level molecular samples moving slowly in the laboratory reference frame. The Kinematic Cooling technique produces cold molecules from a supersonic molecular beam via single collisions with a supersonic atomic beam. A single collision of an atom with a molecule occurring at the correct energy and relative velocity can cause a small fraction of the molecules to move very slowly vertically against gravity in the laboratory. These slowly moving molecules are captured by an electrostatic hexapole guiding field that both orients and focuses the molecules. The molecules are focused into the ionization region of a time-of-flight mass spectrometer and are ionized by laser radiation. The new molecular fountain apparatus was built utilizing a new design for molecular beam apparatus that has allowed us to miniaturize the apparatus. This new design minimizes the volumes and surface area of the machine allowing smaller pumps to maintain the necessary background pressures needed for these experiments.
Diffusion tensor optical coherence tomography
Marks, Daniel L.; Blackmon, Richard L.; Oldenburg, Amy L.
2018-01-01
In situ measurements of diffusive particle transport provide insight into tissue architecture, drug delivery, and cellular function. Analogous to diffusion-tensor magnetic resonance imaging (DT-MRI), where the anisotropic diffusion of water molecules is mapped on the millimeter scale to elucidate the fibrous structure of tissue, here we propose diffusion-tensor optical coherence tomography (DT-OCT) for measuring directional diffusivity and flow of optically scattering particles within tissue. Because DT-OCT is sensitive to the sub-resolution motion of Brownian particles as they are constrained by tissue macromolecules, it has the potential to quantify nanoporous anisotropic tissue structure at micrometer resolution as relevant to extracellular matrices, neurons, and capillaries. Here we derive the principles of DT-OCT, relating the detected optical signal from a minimum of six probe beams with the six unique diffusion tensor and three flow vector components. The optimal geometry of the probe beams is determined given a finite numerical aperture, and a high-speed hardware implementation is proposed. Finally, Monte Carlo simulations are employed to assess the ability of the proposed DT-OCT system to quantify anisotropic diffusion of nanoparticles in a collagen matrix, an extracellular constituent that is known to become highly aligned during tumor development.
Molecular mechanisms in gliomagenesis
DEFF Research Database (Denmark)
Hulleman, Esther; Helin, Kristian
2005-01-01
Glioma, and in particular high-grade astrocytoma termed glioblastoma multiforme (GBM), is the most common primary tumor of the brain. Primarily because of its diffuse nature, there is no effective treatment for GBM, and relatively little is known about the processes by which it develops. Therefore......, in order to design novel therapies and treatments for GBM, research has recently intensified to identify the cellular and molecular mechanisms leading to GBM formation. Modeling of astrocytomas by genetic manipulation of mice suggests that deregulation of the pathways that control gliogenesis during normal...... brain development, such as the differentiation of neural stem cells (NSCs) into astrocytes, might contribute to GBM formation. These pathways include growth factor-induced signal transduction routes and processes that control cell cycle progression, such as the p16-CDK4-RB and the ARF-MDM2-p53 pathways...
Molecular dynamics simulations
International Nuclear Information System (INIS)
Alder, B.J.
1985-07-01
The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs
Shi, Wei; Sorescu, Dan C; Luebke, David R; Keller, Murphy J; Wickramanayake, Shan
2010-05-20
Classical molecular dynamics and Monte Carlo simulations are used to calculate the self-diffusivity and solubility of pure and mixed CO(2), H(2), and Ar gases absorbed in the ionic liquid 1-n-hexyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide ([hmim][Tf(2)N]). Overall, the computed absorption isotherms, Henry's law constants, and partial molar enthalpies for pure H(2) agree well with the experimental data obtained by Maurer et al. [J. Chem. Eng. Data 2006, 51, 1364] and the experimental values determined in this work. However, the agreement is poor between the simulations and the experimental data by Noble et al. [Ind. Eng. Chem. Res. 2008, 47, 3453] and Costa Gomes [J. Chem. Eng. Data 2007, 52, 472] at high temperatures. The computed H(2) permeability values are in good agreement with the experimental data at 313 K obtained by Luebke et al. [J. Membr. Sci. 2007, 298, 41; ibid, 2008, 322, 28], but about three times larger than the experimental value at 573 K from the same group. Our computed H(2) solubilities using different H(2) potential models have similar values and solute polarizations were found to have a negligible effect on the predicted gas solubilities for both the H(2) and Ar. The interaction between H(2) and the ionic liquid is weak, about three times smaller than between the ionic liquid and Ar and six times smaller than that of CO(2) with the ionic liquid, results that are consistent with a decreasing solubility from CO(2) to Ar and to H(2). The molar volume of the ionic liquid was found to be the determining factor for the H(2) solubility. For mixed H(2) and Ar gases, the solubilities for both solutes decrease compared to the respective pure gas solubilities. For mixed gases of CO(2) and H(2), the solubility selectivity of CO(2) over H(2) decreases from about 30 at 313 K to about 3 at 573 K. For the permeability, the simulated values for CO(2) in [hmim][Tf(2)N] are about 20-60% different than the experimental data by Luebke et al. [J. Membr
Macrolides for diffuse panbronchiolitis.
Lin, Xiufang; Lu, Jing; Yang, Ming; Dong, Bi Rong; Wu, Hong Mei
2015-01-25
Diffuse panbronchiolitis (DPB) is a chronic airways disease predominantly affecting East Asians. Macrolides, a class of antibiotics, have been used as the main treatment for DPB, based on evidence from retrospective and non-randomised studies. To assess the efficacy and safety of macrolides for DPB. We searched CENTRAL (2014, Issue 6), MEDLINE (1966 to July week 1, 2014), EMBASE (1974 to July 2014), Chinese Biomedical Literature Database (CBM) (1978 to July 2014), China National Knowledge Infrastructure (CNKI) (1974 to July 2014), KoreaMed (1997 to July 2014) and Database of Japana Centra Revuo Medicina (1983 to July 2014). Randomised controlled trials (RCTs) or quasi-RCTs assessing the effect of macrolides for DPB. Two review authors independently assessed study quality and subsequent risk of bias according to The Cochrane Collaboration's tool for assessing risk of bias. The primary outcomes were five-year survival rate, lung function and clinical response. We used risk ratios (RR) for individual trial results in the data analysis and measured all outcomes with 95% confidence intervals (CI). Only one RCT (19 participants) with significant methodological limitations was included in this review. It found that the computerised tomography images of all participants treated with a long-term, low-dose macrolide (erythromycin) improved from baseline, while the images of 71.4% of participants in the control group (with no treatment) worsened and 28.6% remained unchanged. Adverse effects were not reported. This review was previously published in 2010 and 2013. For this 2014 update, we identified no new trials for inclusion or exclusion. There is little evidence for macrolides in the treatment of DPB. We are therefore unable to make any new recommendations. It may be reasonable to use low-dose macrolides soon after diagnosis is made and to continue this treatment for at least six months, according to current guidelines.
In-vitro transdentinal diffusion of monomers from adhesives.
Putzeys, Eveline; Duca, Radu Corneliu; Coppens, Lieve; Vanoirbeek, Jeroen; Godderis, Lode; Van Meerbeek, Bart; Van Landuyt, Kirsten L
2018-06-01
Biocompatibility of adhesives is important since adhesives may be applied on dentin near the pulp. Accurate knowledge of the quantity of monomers reaching the pulp is important to determine potential side effects. The aim of this study was to assess the transdentinal diffusion of residual monomers from dental adhesive systems using an in-vitro pulp chamber model. Dentin disks with a thickness of 300 µm were produced from human third molars. These disks were fixed between two open-ended glass tubes, representing an in-vitro pulp chamber. The etch-and-rinse adhesive OptiBond FL and the self-etch adhesive Clearfil SE Bond were applied to the dentin side of the disks, while on in the pulpal side, the glass tube was filled with 600 µL water. The transdentinal diffusion of different monomers was quantified using ultra-performance liquid chromatography-tandem mass spectrometry. The monomers HEMA, CQ, BisGMA, GPDM, 10-MDP and UDMA eluted from the dental materials and were able to diffuse through the dentin disks to a certain extent. Compounds with a lower molecular weight (uncured group: HEMA 7850 nmol and CQ 78.2 nmol) were more likely to elute and diffuse compared to monomers with a higher molecular weight (uncured group: BisGMA 0.42 nmol). When the adhesives were left uncured, diffusion was up to 10 times higher compared to the cured conditions. This in-vitro research resulted in the quantification of various monomers able to diffuse through dentin and therefore contributes to a more detailed understanding about the potential exposure of the dental pulp to monomers from dental adhesives. Biocompatibility of adhesives is important since adhesives may be applied on dentin near the pulp, where tubular density and diameter are greatest. Copyright © 2018. Published by Elsevier Ltd.
How well do different tracers constrain the firn diffusivity profile?
Directory of Open Access Journals (Sweden)
C. M. Trudinger
2013-02-01
Full Text Available Firn air transport models are used to interpret measurements of the composition of air in firn and bubbles trapped in ice in order to reconstruct past atmospheric composition. The diffusivity profile in the firn is usually calibrated by comparing modelled and measured concentrations for tracers with known atmospheric history. However, in most cases this is an under-determined inverse problem, often with multiple solutions giving an adequate fit to the data (this is known as equifinality. Here we describe a method to estimate the firn diffusivity profile that allows multiple solutions to be identified, in order to quantify the uncertainty in diffusivity due to equifinality. We then look at how well different combinations of tracers constrain the firn diffusivity profile. Tracers with rapid atmospheric variations like CH_{3}CCl_{3}, HFCs and ^{14}CO_{2} are most useful for constraining molecular diffusivity, while &delta:^{15}N_{2} is useful for constraining parameters related to convective mixing near the surface. When errors in the observations are small and Gaussian, three carefully selected tracers are able to constrain the molecular diffusivity profile well with minimal equifinality. However, with realistic data errors or additional processes to constrain, there is benefit to including as many tracers as possible to reduce the uncertainties. We calculate CO_{2} age distributions and their spectral widths with uncertainties for five firn sites (NEEM, DE08-2, DSSW20K, South Pole 1995 and South Pole 2001 with quite different characteristics and tracers available for calibration. We recommend moving away from the use of a firn model with one calibrated parameter set to infer atmospheric histories, and instead suggest using multiple parameter sets, preferably with multiple representations of uncertain processes, to assist in quantification of the uncertainties.
Moessbauer effect and vacancy diffusion
International Nuclear Information System (INIS)
Gunther, L.
1976-01-01
A dynamical theory of vacancy diffusion which was motivated by the need to explain recent experimental results for the Moessbauer spectra of Fe in Cu, Fe in Au and Fe in Al is presented. Diffusion in these systems is dominated by the vacancy mechanism, which involves strong correlations between successive jumps. The theory developed by Singwi and Sjoelander for the Moessbauer spectrum of a diffusing nucleus is therefore not applicable. The inverse of the normalized Moessbauer spectrum evaluated at zero frequency is introduced as a useful means of comparing experimental with theoretical spectral widths
Simulation of multivariate diffusion bridges
DEFF Research Database (Denmark)
Bladt, Mogens; Finch, Samuel; Sørensen, Michael
We propose simple methods for multivariate diffusion bridge simulation, which plays a fundamental role in simulation-based likelihood and Bayesian inference for stochastic differential equations. By a novel application of classical coupling methods, the new approach generalizes a previously...... proposed simulation method for one-dimensional bridges to the mulit-variate setting. First a method of simulating approzimate, but often very accurate, diffusion bridges is proposed. These approximate bridges are used as proposal for easily implementable MCMC algorithms that produce exact diffusion bridges...
Self diffusion in isotopic fluid
International Nuclear Information System (INIS)
Tankeshwar, K.
1991-01-01
Expressions for the second and fourth frequency sum rules of the velocity auto-correlation function have been obtained for an isotopic fluid. These expressions and Mori memory function formalism have been used to study the influence of the particle mass and mole fraction on the self diffusion coefficient. Our results confirm the weak mass dependence of the self diffusion. The influence of the mole fraction of the light particles on the self diffusion constant has been found to increase for the larger particle mass. (author). 17 refs, 1 fig., 2 tabs
Muon diffusion in noble metals
International Nuclear Information System (INIS)
Schillaci, M.E.; Bokema, C.; Heffner, R.H.; Hutson, R.L.; Leon, M.; Olsen, C.E.; Dodds, S.A.; MacLaughlin, D.E.; Richards, P.M.
1983-01-01
Diffusion-induced muon depolarization in dilute AgGd and AgEr were measured in the temperature range 200-700 K and have thereby determined the muon diffusion parameters in Ag. The diffusion parameters for μ + in Cu, Ag, and Au are compared with those of hydrogen. For Ag and Au, the μ + parameters are similar to those of hydrogen, whereas for Cu, the μ + parameters are much smaller. Lattice-activated tunneling and over-barrier hopping are investigated with computational models. 15 references, 1 figure, 2 tables
Muon diffusion in noble metals
International Nuclear Information System (INIS)
Schillaci, M.E.; Boekema, C.; Heffner, R.H.; Hutson, R.L.; Leon, M.; Olsen, C.E.; Dodds, S.A.; MacLaughlin, D.E.; Richards, P.M.
1982-01-01
Diffusion-induced muon depolarization was measured in dilute AgGd and AgEr in the temperature range 200 to 700 0 K and have thereby determined the muon diffusion parameters in Ag. The diffusion parameters for μ + in Cu, Ag, and Au are compared with those of hydrogen. For Ag and Au, the μ + parameters are similar to those of hydrogen, whereas for Cu, the μ + parameters are much smaller. Lattice-activated tunneling and over-barrier hopping are investigated with computational models
O'Neill, Kelly C; Lee, Young Jin
2018-05-01
The ability to determine the age of fingerprints would be immeasurably beneficial in criminal investigations. We explore the possibility of determining the age of fingerprints by analyzing various compounds as they diffuse from the ridges to the valleys of fingerprints using matrix-assisted laser desorption/ionization mass spectrometry imaging. The diffusion of two classes of endogenous fingerprint compounds, fatty acids and triacylglycerols (TGs), was studied in fresh and aged fingerprints on four surfaces. We expected higher molecular weight TGs would diffuse slower than fatty acids and allow us to determine the age of older fingerprints. However, we found interactions between endogenous compounds and the surface have a much stronger impact on diffusion than molecular weight. For example, diffusion of TGs is faster on hydrophilic plain glass or partially hydrophilic stainless steel surfaces, than on a hydrophobic Rain-x treated surface. This result further complicates utilizing a diffusion model to age fingerprints. © 2017 American Academy of Forensic Sciences.
Tuning the thermal diffusivity of silver based nanofluids by controlling nanoparticle aggregation
International Nuclear Information System (INIS)
Agresti, Filippo; Barison, Simona; Battiston, Simone; Pagura, Cesare; Fabrizio, Monica; Colla, Laura; Fedele, Laura
2013-01-01
With the aim of preparing stable nanofluids for heat exchange applications and to study the effect of surfactant on the aggregation of nanoparticles and thermal diffusivity, stable silver colloids were synthesized in water by a green method, reducing AgNO 3 with fructose in the presence of poly-vinylpyrollidone (PVP) of various molecular weights. A silver nanopowder was precipitated from the colloids and re-dispersed at 4 vol% in deionized water. The Ag colloids were characterized by UV–visible spectroscopy, combined dynamic light scattering and ζ-potential measurements, and laser flash thermal diffusivity. The Ag nanopowders were characterized by scanning electron microscopy and thermal gravimetric analysis. It was found that the molecular weight of PVP strongly affects the ζ-potential and the aggregation of nanoparticles, thereby affecting the thermal diffusivity of the obtained colloids. In particular, it was observed that on increasing the molecular weight of PVP the absolute value of the ζ-potential is reduced, leading to increased aggregation of nanoparticles. A clear relation was identified between thermal diffusivity and aggregation, showing higher thermal diffusivity for nanofluids having higher aggregation. A maximum improvement of thermal diffusivity by about 12% was found for nanofluids prepared with PVP having higher molecular weight. (paper)
Study of Li atom diffusion in amorphous Li3PO4 with neural network potential
Li, Wenwen; Ando, Yasunobu; Minamitani, Emi; Watanabe, Satoshi
2017-12-01
To clarify atomic diffusion in amorphous materials, which is important in novel information and energy devices, theoretical methods having both reliability and computational speed are eagerly anticipated. In the present study, we applied neural network (NN) potentials, a recently developed machine learning technique, to the study of atom diffusion in amorphous materials, using Li3PO4 as a benchmark material. The NN potential was used together with the nudged elastic band, kinetic Monte Carlo, and molecular dynamics methods to characterize Li vacancy diffusion behavior in the amorphous Li3PO4 model. By comparing these results with corresponding DFT calculations, we found that the average error of the NN potential is 0.048 eV in calculating energy barriers of diffusion paths, and 0.041 eV in diffusion activation energy. Moreover, the diffusion coefficients obtained from molecular dynamics are always consistent with those from ab initio molecular dynamics simulation, while the computation speed of the NN potential is 3-4 orders of magnitude faster than DFT. Lastly, the structure of amorphous Li3PO4 and the ion transport properties in it were studied with the NN potential using a large supercell model containing more than 1000 atoms. The formation of P2O7 units was observed, which is consistent with the experimental characterization. The Li diffusion activation energy was estimated to be 0.55 eV, which agrees well with the experimental measurements.
International Nuclear Information System (INIS)
Correia, Teresa; Arridge, Simon
2016-01-01
Fluorescence diffuse optical tomography (fDOT) provides 3D images of fluorescence distributions in biological tissue, which represent molecular and cellular processes. The image reconstruction problem is highly ill-posed and requires regularisation techniques to stabilise and find meaningful solutions. Quadratic regularisation tends to either oversmooth or generate very noisy reconstructions, depending on the regularisation strength. Edge preserving methods, such as anisotropic diffusion regularisation (AD), can preserve important features in the fluorescence image and smooth out noise. However, AD has limited ability to distinguish an edge from noise. In this two-part paper, we propose a patch-based anisotropic diffusion regularisation (PAD), where regularisation strength is determined by a weighted average according to the similarity between patches around voxels within a search window, instead of a simple local neighbourhood strategy. However, this method has higher computational complexity and, hence, we wavelet compress the patches (PAD-WT) to speed it up, while simultaneously taking advantage of the denoising properties of wavelet thresholding. The proposed method combines the nonlocal means (NLM), AD and wavelet shrinkage methods, which are image processing methods. Therefore, in this first paper, we used a denoising test problem to analyse the performance of the new method. Our results show that the proposed PAD-WT method provides better results than the AD or NLM methods alone. The efficacy of the method for fDOT image reconstruction problem is evaluated in part 2. (paper)
Translational and Rotational Diffusion in Water in the Gigapascal Range
Bove, L. E.; Klotz, S.; Strässle, Th.; Koza, M.; Teixeira, J.; Saitta, A. M.
2013-11-01
First measurements of the self-dynamics of liquid water in the GPa range are reported. The GPa range has here become accessible through a new setup for the Paris-Edinburgh press specially conceived for quasielastic neutron scattering studies. A direct measurement of both the translational and rotational diffusion coefficients of water along the 400 K isotherm up to 3 GPa, corresponding to the melting point of ice VII, is provided and compared with molecular dynamics simulations. The translational diffusion is observed to strongly decrease with pressure, though its variation slows down for pressures higher than 1 GPa and decouples from that of the shear viscosity. The rotational diffusion turns out to be insensitive to pressure. Through comparison with structural data and molecular dynamics simulations, we show that this is a consequence of the rigidity of the first neighbors shell and of the invariance of the number of hydrogen bonds of a water molecule under high pressure. These results show the inadequacy of the Stokes-Einstein-Debye equations to predict the self-diffusive behavior of water at high temperature and high pressure, and challenge the usual description of hot dense water behaving as a simple liquid.
Transient diffusion from a waste solid into fractured porous rock
International Nuclear Information System (INIS)
Ahn, J.; Chambre, P.L.; Pigford, T.H.
1988-01-01
Previous analytical studies of the advective transport of dissolved contaminants through fractured rock have emphasized the effect of molecular diffusion in the rock matrix in affecting the space-time-dependent concentration of the contaminant as it moves along the fracture. Matrix diffusion only in the direction normal to the fracture surface was assumed. Contaminant sources were constant-concentration surfaces of width equal to the fracture aperture and of finite or infinite extent in the transverse direction. Such studies illustrate the far-field transport features of fractured media. To predict the time-dependent mass transfer from a long waste cylinder surrounded by porous rock and intersected by a fracture, the present study includes diffusion from the waste surface directly into porous rock, as well as the more realistic geometry. Here the authors present numerical results from Chambre's analytical solution for the time-dependent mass transfer from the cylinder for the low-flow conditions wherein near-field mass transfer is expected to be controlled by molecular diffusion
Genetics Home Reference: hereditary diffuse gastric cancer
... Health Conditions Hereditary diffuse gastric cancer Hereditary diffuse gastric cancer Printable PDF Open All Close All Enable Javascript ... Diffuse Gastric Cancer MedlinePlus Encyclopedia: Gastric Cancer National Cancer ... Option Overview General Information from MedlinePlus ( ...
Improved diffuser for augmenting a wind turbine
Foreman, K.M.; Gilbert, B.L.
A diffuser for augmenting a wind turbine having means for energizing the boundary layer at several locations along the diffuser walls is improved by the addition of a short collar extending radially outward from the outlet of the diffuser.
Diffusion tensor analysis with nuclear magnetic resonance in human central nervous system
International Nuclear Information System (INIS)
Nakayama, Naoki
1998-01-01
Nuclear magnetic resonance has been used to measure the diffusivity of water molecules. In central nervous system, anisotropic diffusion, which is characterized by apparent diffusion tensor D app ξ , is thought to be related to neuronal fiber tract orientation. For precise observation of anisotropic diffusion, it is needed to determine the diagonal and off-diagonal elements of D app ξ . Once D app ξ is estimated from a series of diffusion weighted images, a tissue's orthotropic principal axes and diffusivity of each direction are determined from eigenvalues and eigenvectors of D app ξ . There are several methods to represent anisotropic diffusion with D app ξ . Examples are diffusion ellipsoids constructed in each voxel depicting both these principal axes and the mean diffusion length in these directions, trace invariant values and its mapping image, largest eigenvalue, and ratio of largest eigenvalue to the other eigenvalue. In this study, the author investigated practical procedure to analyze diffusion tensor D app ξ using both of spin-echo end echo-planer diffusion weighted imagings with 3-tesla magnetic resonance machine in human brain. The ellipsoid representation provided particularly useful information about microanatomy including neuronal fiber tract orientation and molecular mobility reflective of microstructure. Furthermore, in the lesion of Wallerian degeneration, the loss of anisotropy of local apparent diffusion was observed. It is suggested that the function of axons can be observed via degree of anisotropy of apparent diffusion. Consequently, diffusion tensor analysis is expected to be a powerful, noninvasive method capable of quantitative and functional evaluation of the central nervous system. (author)
Diffusion in crowded biological environments: applications of Brownian dynamics
Długosz, Maciej; Trylska, Joanna
2011-01-01
Biochemical reactions in living systems occur in complex, heterogeneous media with total concentrations of macromolecules in the range of 50 - 400 mg/ml. Molecular species occupy a significant fraction of the immersing medium, up to 40% of volume. Such complex and volume-occupied environments are generally termed 'crowded' and/or 'confined'. In crowded conditions non-specific interactions between macromolecules may hinder diffusion - a major process determining metabolism, transport, and sign...
Ionic diffusion in superionic-conductor melts
International Nuclear Information System (INIS)
Tankeshwar, K.; Tosi, M.P.
1991-03-01
The self-diffusion coefficients D + and D - of the two ionic species in molten AgI, CuCl, CuBr and CuI are evaluated and contrasted with those calculated for molten NaCl. The evaluation adopts a simple model for liquid state dynamics, earlier proposed by Zwanzig to justify the Stokes-Einstein formula for monatomic fluids, and by suitable approximations relates the self-diffusion coefficients to pair potentials and to the pair structure of the melt. The results offer an interpretation for molecular dynamics data showing that, whereas for a ''normal'' system such as NaCl the ratio D + /D - in the melt is of the order unity, a sizable difference between D + and D - persists in salts melting from a fast-cation conducting solid. This difference is explicitly related to liquid structure through differences in the structural backscattering of cations by cations and of halogens by halogens. The calculated magnitudes of D + /D - are quite satisfactory, while the absolute magnitudes of D + and D - are in good agreement with the data only for those salts (AgI, CuBr and NaCl) in which the masses of the two ionic species are not greatly different. (author). 21 refs, 2 tabs
Morris, Garrett M; Lim-Wilby, Marguerita
2008-01-01
Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand-protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Docking can be used to perform virtual screening on large libraries of compounds, rank the results, and propose structural hypotheses of how the ligands inhibit the target, which is invaluable in lead optimization. The setting up of the input structures for the docking is just as important as the docking itself, and analyzing the results of stochastic search methods can sometimes be unclear. This chapter discusses the background and theory of molecular docking software, and covers the usage of some of the most-cited docking software.
Directory of Open Access Journals (Sweden)
Aarti Sharma
2009-01-01
Full Text Available The use of computational chemistry in the development of novel pharmaceuticals is becoming an increasingly important tool. In the past, drugs were simply screened for effectiveness. The recent advances in computing power and the exponential growth of the knowledge of protein structures have made it possible for organic compounds to be tailored to decrease the harmful side effects and increase the potency. This article provides a detailed description of the techniques employed in molecular modeling. Molecular modeling is a rapidly developing discipline, and has been supported by the dramatic improvements in computer hardware and software in recent years.
Combinatorial chemistry approach to development of molecular plastic solar cells
Godovsky, Dmitri; Inganäs, Olle; Brabec, Christoph J.; Sariciftci, N. Serdar; Hummelen, Jan C.; Janssen, Rene A.J.; Prato, M.; Maggini, M.; Segura, Jose; Martin, Nazario
1999-01-01
We used a combinatorial chemistry approach to develop the molecular plastic solar cells based on soluble fullerene derivatives or solubilized TCNQ molecules in combination with conjugated polymers. Profiles, formed by the diffusion of low molecular weight component in the spin-cast polymer host were
Atmospheric turbulence and diffusion research
International Nuclear Information System (INIS)
Hosker, R.P. Jr.
1993-01-01
The Atmospheric Turbulence and Diffusion Division (well known in the atmospheric dispersion community as the Atmospheric Turbulence and Diffusion Laboratory, ATDL) is one of several field facilities of NOAAs Air Resources Laboratory, headquartered in Silver Spring, Maryland. The laboratory conducts research on matters of atmospheric diffusion and turbulent exchange, concerning air quality. ATDD focuses attention on the physics of the lower atmosphere, with special emphasis on the processes contributing to atmospheric transport, dispersion, deposition, and air-surface exchange, and on the development of predictive capabilities using the results of this research. Research is directed toward issues of national and global importance related to the missions of DOE, to DOE's Oak Ridge Field Office, and to NOAA. The program is divided into four major projects: plume transport and diffusion in the planetary boundary layer, complex topography, canopy micrometeorology, and air-surface exchange
Diffusion mechanisms in intermetallic compounds
Energy Technology Data Exchange (ETDEWEB)
Larikov, L N [ANU, Inst. Metallofiziki, Kiev (Ukraine)
1992-08-01
Recent research aimed at the identification of the principal mechanisms of diffusion in intermetallics is reviewed. In particular, attention is given to the effect of the type of interatomic bond on the contribution of different mechanisms to diffusion in ordered metallic compounds. Results of an analysis of experimental determinations of diffusion coefficients D(A) and D(B) in binary intermetallics (CuZn, Cu3Sn, AuCd, AgZn, AgMg, InSb, GaSb, AlSb, Fe3Al, FeAl, FeAl3, Ni3Al, Ni3Nb, FeSn, FeSn2, Ni3Sn2, Ni3Sn4, Co3Sn2, CoSn, CoSn2, and CoGa) are presented, and it is shown that the D(A)/D(B) ratio differs substantially for different diffusion mechanisms. 60 refs.
Diffusion of single oxidation pond
Directory of Open Access Journals (Sweden)
Song Ruo-Yuan
2016-01-01
Full Text Available The hydraulic characteristic of an oxidation pond was studied by the tracer experiment, and an empirical formula of Peclet number was obtained, which can be well applied to the model of plug flow reactor with longitudinal diffusion.
Computational Diffusion MRI : MICCAI Workshop
Grussu, Francesco; Ning, Lipeng; Tax, Chantal; Veraart, Jelle
2018-01-01
This volume presents the latest developments in the highly active and rapidly growing field of diffusion MRI. The reader will find numerous contributions covering a broad range of topics, from the mathematical foundations of the diffusion process and signal generation, to new computational methods and estimation techniques for the in-vivo recovery of microstructural and connectivity features, as well as frontline applications in neuroscience research and clinical practice. These proceedings contain the papers presented at the 2017 MICCAI Workshop on Computational Diffusion MRI (CDMRI’17) held in Québec, Canada on September 10, 2017, sharing new perspectives on the most recent research challenges for those currently working in the field, but also offering a valuable starting point for anyone interested in learning computational techniques in diffusion MRI. This book includes rigorous mathematical derivations, a large number of rich, full-colour visualisations and clinically relevant results. As such, it wil...
Diffusion from cylindrical waste forms
International Nuclear Information System (INIS)
Thomas, G.F.
1985-05-01
The diffusion of a single component material from a finite cylindrical waste form, initially containing a uniform concentration of the material, is investigated. Under the condition that the cylinder is maintained in a well-stirred bath, expressions for the fractional inventory leached and the leach rate are derived with allowance for the possible permanent immobilization of the diffusant through its decay to a stable product and/or its irreversible reaction with the waste form matrix. The usefulness of the reported results in nuclear waste disposal applications is emphasized. The results reported herein are related to those previously derived at Oak Ridge National Laboratory by Bell and Nestor. A numerical scheme involving the partial decoupling of nested infinite summations and the use of rapidly converging rational approximants is recommended for the efficient implementation of the expressions derived to obtain reliable estimates of the bulk diffusion constant and the rate constant describing the diffusant-waste form interaction from laboratory data
Diffusion coefficient for anomalous transport
International Nuclear Information System (INIS)
1986-01-01
A report on the progress towards the goal of estimating the diffusion coefficient for anomalous transport is given. The gyrokinetic theory is used to identify different time and length scale inherent to the characteristics of plasmas which exhibit anomalous transport
Diffusion formation and psychiatric diseases
International Nuclear Information System (INIS)
Reith, W.; Kulikovski, J.
2015-01-01
The basic principle behind diffusion is Brownian motion. The diffusion parameters obtained in a clinical association provide information on the spatial distribution of water molecule mobility and, therefore, evidence of the morphological integrity of the white and grey matters of the brain. In recent years functional magnetic resonance imaging (fMRI) could contribute to obtaining a detailed understanding of the cortical and subcortical cerebral networks. Diffusion tensor imaging (DTI) investigations can demonstrate the extent of anisotropy and the fiber pathways in so-called parametric images. For example, in Alzheimer's disease DTI reveals a reduced structural connectivity between the posterior cingulum and the hippocampus. This article shows examples of the application of diffusion-weighted imaging (DWI) in psychiatric disorders. (orig.) [de
Diffusion processes and memory effects
International Nuclear Information System (INIS)
Mokshin, Anatolii V; Yulmetyev, Renat M; Haenggi, Peter
2005-01-01
We report the results of the numerical estimation of statistical memory effects in diffusion for two various systems: Lennard-Jones fluids and the model of the Brownian particle in a one-dimensional harmonic lattice. We have found the relation between the diffusion coefficient and the non-Markovity parameter, which is linear for the Lennard-Jones systems in liquid state. The relation between the memory measure and the excess entropy is also discussed here
International Nuclear Information System (INIS)
McCollum, M.J.; Plano, M.A.; Haase, M.A.; Robbins, V.M.; Jackson, S.L.; Cheng, K.Y.; Stillman, G.E.
1989-01-01
This paper discusses the use of gas sources in growth by MBE as a result of current interest in growth of InP/InGaAsP/InGaAs lattice matched to InP. For gas flows greater than a few sccm, pumping speed requirements dictate the use of turbomolecular or diffusion pumps. GaAs samples with high p-type mobilities have been grown with diffusion pumped molecular beam epitaxial system. According to the authors, this demonstration of the inherent cleanliness of a properly designed diffusion pumping system indicates that a diffusion pump is an excellent inexpensive and reliable choice for growth by molecular beam epitaxy and gas source molecular beam epitaxy/chemical beam epitaxy
Diffusion through statically compacted clay
International Nuclear Information System (INIS)
Ho, C.L.; Shebl, M.A.A.
1994-01-01
This paper presents experimental work on the effect of compaction on contaminant flow through clay liners. The experimental program included evaluation of soil properties, compaction, permeability and solute diffusion. A permeameter was built of non reactive materials to test samples compacted at different water contents and compactive efforts. The flow of a permeating solute, LiCl, was monitored. Effluent samples were collected for solute concentration measurements. The concentrations were measured by performing atomic adsorption tests. The analyzed results showed different diffusion characteristics when compaction conditions changed. At each compactive effort, permeability decreased as molding water content increased. Consequently, transit time (measured at relative concentration 50%) increased and diffusivity decreased. As compactive effort increased for soils compacted dry of optimum, permeability and diffusion decreased. On the other hand, as compactive effort increased for soils compacted wet of optimum, permeability and diffusivity increased. Tortuosity factor was indirectly measured from the diffusion and retardation rate. Tortuosity factor also decreased as placement water content was increased from dry of optimum to wet of optimum. Then decreases were more pronounced for low compactive effort tests. 27 refs., 7 figs., 5 tabs