Strategies for multiscale modeling and simulation of organic materials: polymers and biopolymers

Goddard, William A.; Çağın, Tahir; Blanco, Mario; Vaidehi, Nagarajan; Dasgupta, Sanjoy; Floriano, Wely B.; Belmares, M.; Kua, Jeremy; Zamanakos, Georgios; Kashihara, Seichi; Iotov, Mihail; Gao, Guang‐Hua

doi:10.1016/s1089-3156(01)00025-3

Cited by 38 publications

(21 citation statements)

References 62 publications

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“…During recent years, multiscale modelling and simulation has attracted considerable interest in various fields of science (see, e.g., Goddard et al, 2001;E and Engquist, 2003;Deen et al, 2004). The underlying idea is to link processes occurring on different spatial (or temporal) scales -typically in a sequential manner -to obtain a mechanistic description of complex phenomena.…”

Section: Drug Release As a Multiscale Processmentioning

confidence: 99%

Modelling drug release from inert matrix systems: From moving-boundary to continuous-field descriptions

Frenning

2011

International Journal of Pharmaceutics

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The purpose of this review is to provide a comprehensive overview of mathematical procedures that can be used to describe the release of drugs from inert matrix systems. The review focuses on general principles rather than particular applications. The inherent multiscale nature of the drug-release process is pointed out and multiscale modelling is exemplified for inert porous matrices. Although effects of stagnant layers and finite volumes of release media are briefly discussed, the systematic analysis is restricted to systems under sink conditions. When the initial drug loading exceeds the drug solubility in the matrix, Higuchi-type moving-boundary descriptions continue to be highly valuable for obtaining approximate analytical solutions, especially when coupled with integralbalance methods. Continuous-field descriptions have decisive advantages when numerical solutions are sought. This is because the mathematical formulation reduces to a diffusion equation with a nonlinear source term, valid over the entire matrix domain. Solutions can thus be effortlessly determined for arbitrary geometries by using standard numerical packages.

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Section: Drug Release As a Multiscale Processmentioning

confidence: 99%

Modelling drug release from inert matrix systems: From moving-boundary to continuous-field descriptions

Frenning

2011

International Journal of Pharmaceutics

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“…Consequently, this method is limited to the study of small molecules unless large computer clusters are involved and the calculations are done on multiple processors. [4] The next level of modeling is molecular dynamics, wherein individual atoms are modeled using empirical potential functions. This approach provides the capability of simulating small numbers of atoms (of the order of hundreds of atoms) for short physical time intervals (of the order 1-10 ns) on modest-sized Linux clusters in a reasonable time.…”

Section: Overviewmentioning

confidence: 99%

Computational Methods for the Development of Polymeric Biomaterials

Costache¹,

Ghosh²,

Knight³

et al. 2010

Adv Eng Mater

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“…A series of simulation methods are now available to address chemical questions at several time and length scales [1]. The success of these methods in "pure", theoretical chemistry has been matched by their applications in materials science.…”

Section: Overviewmentioning

confidence: 99%

Simulations on many scales: The synapse as an example

Tai

2004

Pure and Applied Chemistry

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Computer simulation methods spanning several temporal and spatial scales are reviewed, focusing on their applications on the neuromuscular synapse. Quantum mechanics treats the enzymatic catalysis of neurotransmitters on the picometer scale. Molecular dynamics reveals conformational changes of the enzyme acetylcholinesterase for nanoseconds. Brownian dynamics follow the substrate molecule in its diffusion on the microsecond level. Methods such as finite elements describe the diffusion of neurotransmitters as a changing concentration continuum in the synapse. Promising directions for future research include integration of methods on several scales, and applying these methods to the acetylcholine receptor. OVERVIEWWith the development of both theory and computer technology, simulation has become a viable way of investigating the behavior of molecules. A series of simulation methods are now available to address chemical questions at several time and length scales [1]. The success of these methods in "pure", theoretical chemistry has been matched by their applications in materials science.Biochemistry, the molecule-based study of life, also requires understanding on several scales, some of which are not readily reached by experiment. Encouragingly, it is possible to apply the simulation methods in biochemistry (Fig. 1, p. 298). Here, some of these endeavors-as applied on an example, the synapse in the nervous system-are discussed, after a short presentation of several simulation methods for different temporal and spatial scales.Quantum mechanics (QM) calculations have been firmly established as a rigorous methodology; their pioneers were awarded a Nobel Prize in chemistry in 1998 [2,3]. Combined with larger-grain methods such as molecular dynamics (see below), treatment of enzymatic catalysis to a degree comparable to that for small-molecule reactions is feasible.First applied to proteins more than 25 years ago by McCammon and coworkers [4], the method of Newtonian molecular dynamics (MD) has now entered the mainstream of biochemistry [5]. MD aptly reveals the macromolecular conformational changes on the nanosecond-level, filling a time-resolution gap (until recently) long left by experimental methods.The methods MD, Brownian dynamics (BD) [6], Monte Carlo (MC) simulation, and the finite elements (FE) [7] together offer a spectrum of tools, describing diffusion either in a discrete fashionmolecule-by-molecule-or as a continuum of concentration. Recently, other mesoscale and multiscale methods have emerged, with the promise of bringing up the scale of simulations to the cellular level. Ambitious projects aim at yet larger scales, but they lie beyond the scope of this review [8,9].

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Strategies for multiscale modeling and simulation of organic materials: polymers and biopolymers

Cited by 38 publications

References 62 publications

Modelling drug release from inert matrix systems: From moving-boundary to continuous-field descriptions

Modelling drug release from inert matrix systems: From moving-boundary to continuous-field descriptions

Computational Methods for the Development of Polymeric Biomaterials

Simulations on many scales: The synapse as an example

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