Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement

2020 ◽  
Vol 16 (12) ◽  
pp. 7239-7254
Author(s):  
Tetsuro Nagai ◽  
Shuhei Tsurumaki ◽  
Ryo Urano ◽  
Kazushi Fujimoto ◽  
Wataru Shinoda ◽  
...  
Keyword(s):  
Heterogeneous Systems ◽  
Diffusion Constant ◽  
Mean Squared Displacement ◽  
Local Mean

Momentum Removal to Obtain the Position-Dependent Diffusion Constant in Constrained Molecular Dynamics Simulation

2021 ◽  
Author(s):  
Kazushi Fujimoto ◽  
Tetsuro Nagai ◽  
Tsuyoshi Yamaguchi
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Mass Velocity ◽  
Center Of Mass ◽  
Heterogeneous Systems ◽  
Diffusion Constant ◽  
Dynamics Simulation ◽  
Coulombic Interaction ◽  
Ewald Method ◽  
Theoretical Predictions

<div>The position-dependent diffusion coefficient along with free energy profile are important parameters needed to study mass transport in heterogeneous systems such as biological and polymer membranes, and molecular dynamics (MD) calculation is a popular tool to obtain them. Among many methodologies, the Marrink-Berendsen (MB) method is often employed to calculate the position-dependent diffusion coefficient, in which the autocorrelation function of the force on a fixed molecule is related to the friction on the molecule. However, the diffusion coefficient is shown to be affected by the period of the removal of the center-of-mass velocity, which is necessary when performing MD calculations using the Ewald method for Coulombic interaction. We have clarified theoretically in this study how this operation affects the diffusion coefficient calculated by the MB method, and the theoretical predictions are proven by MD calculations. Therefore, we succeeded in providing guidance on how to select an appropriate the period of the removal of the center-of-mass velocity in estimating the position-dependent diffusion coefficient by the MB method. This guideline is applicable also to the Woolf-Roux method.</div>

Momentum Removal to Obtain the Position-Dependent Diffusion Constant in Constrained Molecular Dynamics Simulation

2021 ◽  
Author(s):  
Kazushi Fujimoto ◽  
Tetsuro Nagai ◽  
Tsuyoshi Yamaguchi
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Mass Velocity ◽  
Center Of Mass ◽  
Heterogeneous Systems ◽  
Diffusion Constant ◽  
Dynamics Simulation ◽  
Coulombic Interaction ◽  
Ewald Method ◽  
Theoretical Predictions

<div>The position-dependent diffusion coefficient along with free energy profile are important parameters needed to study mass transport in heterogeneous systems such as biological and polymer membranes, and molecular dynamics (MD) calculation is a popular tool to obtain them. Among many methodologies, the Marrink-Berendsen (MB) method is often employed to calculate the position-dependent diffusion coefficient, in which the autocorrelation function of the force on a fixed molecule is related to the friction on the molecule. However, the diffusion coefficient is shown to be affected by the period of the removal of the center-of-mass velocity, which is necessary when performing MD calculations using the Ewald method for Coulombic interaction. We have clarified theoretically in this study how this operation affects the diffusion coefficient calculated by the MB method, and the theoretical predictions are proven by MD calculations. Therefore, we succeeded in providing guidance on how to select an appropriate the period of the removal of the center-of-mass velocity in estimating the position-dependent diffusion coefficient by the MB method. This guideline is applicable also to the Woolf-Roux method.</div>

Rationale and Design Considerations for a Semantic Mediator in Health Information Systems

1998 ◽  
Vol 37 (04/05) ◽  
pp. 518-526 ◽  
Author(s):  
D. Sauquet ◽  
M.-C. Jaulent ◽  
E. Zapletal ◽  
M. Lavril ◽  
P. Degoulet
Keyword(s):  
Information Systems ◽  
Software Engineering ◽  
Health Information ◽  
Rapid Development ◽  
Heterogeneous Systems ◽  
Health Information Systems ◽  
Semantic Interoperability ◽  
Point Of View ◽  
Current State ◽  
Engineering Environment

AbstractRapid development of community health information networks raises the issue of semantic interoperability between distributed and heterogeneous systems. Indeed, operational health information systems originate from heterogeneous teams of independent developers and have to cooperate in order to exchange data and services. A good cooperation is based on a good understanding of the messages exchanged between the systems. The main issue of semantic interoperability is to ensure that the exchange is not only possible but also meaningful. The main objective of this paper is to analyze semantic interoperability from a software engineering point of view. It describes the principles for the design of a semantic mediator (SM) in the framework of a distributed object manager (DOM). The mediator is itself a component that should allow the exchange of messages independently of languages and platforms. The functional architecture of such a SM is detailed. These principles have been partly applied in the context of the HEllOS object-oriented software engineering environment. The resulting service components are presented with their current state of achievement.

Performance analysis of global local mean square error criterion of stochastic linearization for nonlinear oscillator

2019 ◽  
Author(s):  
Nguyen Cao Thang ◽  
Luu Xuan Hung
Keyword(s):  
Performance Analysis ◽  
Mean Square Error ◽  
Nonlinear Oscillators ◽  
Degree Of Freedom ◽  
Equivalent Linearization ◽  
Mean Square ◽  
Error Criterion ◽  
Stochastic Linearization ◽  
Local Mean ◽  
Mean Square Error Criterion

The paper presents a performance analysis of global-local mean square error criterion of stochastic linearization for some nonlinear oscillators. This criterion of stochastic linearization for nonlinear oscillators bases on dual conception to the local mean square error criterion (LOMSEC). The algorithm is generally built to multi degree of freedom (MDOF) nonlinear oscillators. Then, the performance analysis is carried out for two applications which comprise a rolling ship oscillation and two degree of freedom one. The improvement on accuracy of the proposed criterion has been shown in comparison with the conventional Gaussian equivalent linearization (GEL).

HEAT TRANSFER PECULIARITIES IN HETEROGENEOUS SYSTEMS WITH HIGH UNSTEADY-STATE HEAT TRANSFER RATES

1970 ◽  
Author(s):  
N.V. Antonishin ◽  
S. S. Zabrodsky ◽  
L.E. Simchenko ◽  
V.V. Lushchikov
Keyword(s):  
Heat Transfer ◽  
Heterogeneous Systems ◽  
Unsteady State ◽  
Transfer Rates ◽  
State Heat

Host-Guest Interactions on Electrode Surfaces for Immobilization of Molecular Catalysts

2020 ◽  
Author(s):  
Laurent Sévery ◽  
Jacek Szczerbiński ◽  
Mert Taskin ◽  
Isik Tuncay ◽  
Fernanda Brandalise Nunes ◽  
...  
Keyword(s):  
Aqueous Media ◽  
Heterogeneous Systems ◽  
Catalytic Systems ◽  
New Approach ◽  
Molecular Systems ◽  
Electrode Surfaces ◽  
Catalytic Surfaces ◽  
Oxide Electrodes ◽  
The Stability ◽  
Molecular Catalysts

The strategy of anchoring molecular catalysts on electrode surfaces combines the high selectivity and activity of molecular systems with the practicality of heterogeneous systems. The stability of molecular catalysts is, however, far less than that of traditional heterogeneous electrocatalysts, and therefore a method to easily replace anchored molecular catalysts that have degraded could make such electrosynthetic systems more attractive. Here, we apply a non-covalent “click” chemistry approach to reversibly bind molecular electrocatalysts to electrode surfaces via host-guest complexation with surface-anchored cyclodextrins. The host-guest interaction is remarkably strong and allows the flow of electrons between the electrode and the guest catalyst. Electrosynthesis in both organic and aqueous media was demonstrated on metal oxide electrodes, with stability on the order of hours. The catalytic surfaces can be recycled by controlled release of the guest from the host cavities and readsorption of fresh guest. This strategy represents a new approach to practical molecular-based catalytic systems.

Reaction Mechanisms of Inorganic and Organometallic Systems

2007 ◽  
Author(s):  
Robert B. Jordan
Keyword(s):  
Electron Transfer ◽  
Heterogeneous Systems ◽  
Asymmetric Hydrogenation ◽  
Pressure Effects ◽  
General Level ◽  
Hydrogenation Catalysts ◽  
Methyl Transferase ◽  
Transfer Region ◽  
Previous Edition ◽  
Oxide Synthase

This third edition retains the general level and scope of earlier editions, but has been substantially updated with over 900 new references covering the literature through 2005, and 140 more pages of text than the previous edition. In addition to the general updating of materials, there is new or greatly expanded coverage of topics such as Curtin-Hammett conditions, pressure effects, metal hydrides and asymmetric hydrogenation catalysts, the inverted electron-transfer region, intervalence electron transfer, photochemistry of metal carbonyls, methyl transferase and nitric oxide synthase. The new chapter on heterogeneous systems introduces the basic background to this industrially important area. The emphasis is on inorganic examples of gas/liquid and gas/liquid/solid systems and methods of determining heterogeneity.

Diffusion

2018 ◽  
Author(s):  
Ginestra Bianconi
Keyword(s):  
Random Walks ◽  
Spectral Properties ◽  
Diffusion Constant ◽  
Network Structures ◽  
Multilayer Networks ◽  
Multilayer Network ◽  
Lévy Walk ◽  
Number Of Layers ◽  
Levy Walk ◽  
Speed Up

This chapter addresses diffusion, random walks and congestion in multilayer networks. Here it is revealed that diffusion on a multilayer network can be significantly speed up with respect to diffusion taking place on its single layers taken in isolation, and that sometimes it is possible also to observe super-diffusion. Diffusion is here characterized on multilayer network structures by studying the spectral properties of the supra-Laplacian and the dependence on the diffusion constant among different layers. Random walks and its variations including the Lévy Walk are shown to reflect the improved navigability of multilayer networks with more layers. These results are here compared with the results of traffic on multilayer networks that, on the contrary, point out that increasing the number of layers could be detrimental and could lead to congestion.

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