Browsing by Author "Benke, Matyas"

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    An efficient multi-scale modelling approach for ssDNA motion in fluid flow
    (Elsevier Science B.V., Amsterdam, 2008-12-01T00:00:00Z) Benke, Matyas; Shapiro, Evgeniy; Drikakis, Dimitris
    The paper presents a multi-scale modelling approach for simulating macromolecules in fluid flows. Macromolecule transport at low number densities is frequently encountered in biomedical devices, such as separators, detection and analysis systems. Accurate modelling of this process is challenging due to the wide range of physical scales involved. The continuum approach is not valid for low solute concentrations, but the large timescales of the fluid flow make purely molecular simulations prohibitively expensive. A promising multi-scale modelling strategy is provided by the meta-modelling approach considered in this paper. Meta-models are based on the coupled solution of fluid flow equations and equations of motion for a simplified mechanical model of macromolecules. The approach enables simulation of individual macromolecules at macroscopic time scales. Meta-models often rely on particle-corrector algorithms, which impose length constraints on the mechanical model. Lack of robustness of the particle- corrector algorithm employed can lead to slow convergence and numerical instability. A new FAst Linear COrrector (FALCO) algorithm is introduced in this paper, which significantly improves computational efficiency in comparison with the widely used SHAKE algorithm. Validation of the new particle corrector against a simple analytic solution is performed and improved convergence is demonstrated for ssDNA motion in a lid-driven micro-cavity.
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    Mechanical behaviour of DNA molecules-Elasticity and migration.
    (Elsevier Science B.V., Amsterdam., 2011-09-30T00:00:00Z) Benke, Matyas; Shapiro, Evgeniy; Drikakis, Dimitris
    A novel multi-scale simulation method developed to describe mesoscale phenomena occurring in biofluidic devices is presented. The approach combines the macro-scale modelling of the carrier fluid and the micro-scale description of the transported macromolecules or compounds. Application of the approach is demonstrated through mesoscale simulations of DNA molecules. The investigated phenomena include elastic relaxation of dsDNA molecules and migration of ssDNA molecules in a microchannel flow. The results of the first study demonstrate that the elastic behaviour of the DNA molecules can be captured sucessfully. The second study proves that the migration of ssDNA in pressure-driven microchannel flows can be explained by the hydrodynamic interaction with the carrier liquid.
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    Mesoscale modelling and simulation of macromolecule transport in microfludic channels
    (Cranfield University, 2010-09) Benke, Matyas; Drikakis, Dimitris; Shapiro, Evgeniy
    This thesis concerns the numerical simulation of dilute macromolecular solutions. Present work details the development of a novel mesoscale simulation method. The developed modeling approach is capable to describe both the macroscopic flow field of the carrier liquid and the micromechanical behaviour of the transported large molecules. In this modeling method, the concept of micromechanical structures is introduced in order to represent macromolecules. The motion of the considered mechanical structures is governed by forces arising from the motion of the bulk fluid phase and microscopic forces arising from stochastic Brownian motion of the solvent molecules. This document presents the motivation, the objectives and systematic steps of the model development. The work presents detailed discussion, verification and validation of the developed modeling method.