Literature DB >> 24578582

A multiscale MD-FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure.

M Kojic1, M Milosevic2, N Kojic3, K Kim4, M Ferrari4, A Ziemys4.   

Abstract

Mass transport by diffusion within composite materials may depend not only on internal microstructural geometry, but also on the chemical interactions between the transported substance and the material of the microstructure. Retrospectively, there is a gap in methods and theory to connect material microstructure properties with macroscale continuum diffusion characteristics. Here we present a new hierarchical multiscale model for diffusion within composite materials that couples material microstructural geometry and interactions between diffusing particles and the material matrix. This model, which bridges molecular dynamics (MD) and the finite element (FE) method, is employed to construct a continuum diffusion model based on a novel numerical homogenization procedure. The procedure is general and robust for evaluating constitutive material parameters of the continuum model. These parameters include the traditional bulk diffusion coefficients and, additionally, the distances from the solid surface accounting for surface interaction effects. We implemented our models to glucose diffusion through the following two geometrical/material configurations: tightly packed silica nanospheres, and a complex fibrous structure surrounding nanospheres. Then, rhodamine 6G diffusion analysis through an aga-rose gel network was performed, followed by a model validation using our experimental results. The microstructural model, numerical homogenization and continuum model offer a new platform for modeling and predicting mass diffusion through complex biological environment and within composite materials that are used in a wide range of applications, like drug delivery and nanoporous catalysts.

Entities:  

Keywords:  Composite media; Diffusion; Finite element method; Homogenization; Molecular dynamics; Multiscale

Year:  2014        PMID: 24578582      PMCID: PMC3933172          DOI: 10.1016/j.cma.2013.11.010

Source DB:  PubMed          Journal:  Comput Methods Appl Mech Eng        ISSN: 0045-7825            Impact factor:   6.756


  21 in total

1.  Scalable molecular dynamics with NAMD.

Authors:  James C Phillips; Rosemary Braun; Wei Wang; James Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D Skeel; Laxmikant Kalé; Klaus Schulten
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

2.  Upscaling the diffusion equations in particulate media made of highly conductive particles. II. Application to fibrous materials.

Authors:  J-P Vassal; L Orgéas; D Favier; J-L Auriault; S Le Corre
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2008-01-07

3.  Modelling calcium microdomains using homogenisation.

Authors:  Erin R Higgins; Pranay Goel; Jose L Puglisi; Donald M Bers; Mark Cannell; James Sneyd
Journal:  J Theor Biol       Date:  2007-03-24       Impact factor: 2.691

4.  A mathematical analysis of obstructed diffusion within skeletal muscle.

Authors:  P R Shorten; J Sneyd
Journal:  Biophys J       Date:  2009-06-17       Impact factor: 4.033

5.  Molecular modeling of glucose diffusivity in silica nanochannels.

Authors:  Arturas Ziemys; Mauro Ferrari; Claudio N Cavasotto
Journal:  J Nanosci Nanotechnol       Date:  2009-11

6.  Periodic homogenization and consistent estimates of transport parameters through sphere and polyhedron packings in the whole porosity range.

Authors:  Claude Boutin; Christian Geindreau
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2010-09-16

7.  Water-silica force field for simulating nanodevices.

Authors:  Eduardo R Cruz-Chu; Aleksei Aksimentiev; Klaus Schulten
Journal:  J Phys Chem B       Date:  2006-11-02       Impact factor: 2.991

8.  Second-order modeling of arsenite transport in soils.

Authors:  Hua Zhang; H Magdi Selim
Journal:  J Contam Hydrol       Date:  2011-08-27       Impact factor: 3.188

9.  The relationship of agarose gel structure to the sieving of spheres during agarose gel electrophoresis.

Authors:  G A Griess; K B Guiseley; P Serwer
Journal:  Biophys J       Date:  1993-07       Impact factor: 4.033

10.  Interfacial effects on nanoconfined diffusive mass transport regimes.

Authors:  A Ziemys; M Kojic; M Milosevic; M Ferrari
Journal:  Phys Rev Lett       Date:  2012-06-06       Impact factor: 9.161

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  6 in total

1.  Computational analysis of drug transport in tumor microenvironment as a critical compartment for nanotherapeutic pharmacokinetics.

Authors:  Arturas Ziemys; Steve Klemm; Miljan Milosevic; Kenji Yokoi; Mauro Ferrari; Milos Kojic
Journal:  Drug Deliv       Date:  2015-04-02       Impact factor: 6.419

2.  Capillary-wall collagen as a biophysical marker of nanotherapeutic permeability into the tumor microenvironment.

Authors:  Kenji Yokoi; Milos Kojic; Miljan Milosevic; Tomonori Tanei; Mauro Ferrari; Arturas Ziemys
Journal:  Cancer Res       Date:  2014-05-22       Impact factor: 12.701

3.  A composite smeared finite element for mass transport in capillary systems and biological tissue.

Authors:  M Kojic; M Milosevic; V Simic; E J Koay; J B Fleming; S Nizzero; N Kojic; A Ziemys; M Ferrari
Journal:  Comput Methods Appl Mech Eng       Date:  2017-06-29       Impact factor: 6.756

Review 4.  Predictive Design and Analysis of Drug Transport by Multiscale Computational Models Under Uncertainty.

Authors:  Ali Aykut Akalın; Barış Dedekargınoğlu; Sae Rome Choi; Bumsoo Han; Altug Ozcelikkale
Journal:  Pharm Res       Date:  2022-06-01       Impact factor: 4.580

5.  Liposomal doxorubicin extravasation controlled by phenotype-specific transport properties of tumor microenvironment and vascular barrier.

Authors:  Kenji Yokoi; Diana Chan; Milos Kojic; Miljan Milosevic; David Engler; Rise Matsunami; Tomonori Tanei; Yuki Saito; Mauro Ferrari; Arturas Ziemys
Journal:  J Control Release       Date:  2015-09-25       Impact factor: 9.776

6.  Capillary collagen as the physical transport barrier in drug delivery to tumor microenvironment.

Authors:  Arturas Ziemys; Kenji Yokoi; Milos Kojic
Journal:  Tissue Barriers       Date:  2015-05-06
  6 in total

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