Density functional theory for inhomogeneous polymer systems. I. Numerical methods

Frischknecht, Amalie L.; Weinhold, Jeffrey D.; Salinger, Andrew G.; Curro, John G.; Frink, Laura J. Douglas; McCoy, John D.

doi:10.1063/1.1518685

Cited by 47 publications

(32 citation statements)

References 66 publications

(59 reference statements)

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“…In particular, in the DFT framework, the fields are customarily obtained within a linear response theory of a bulk uniform fluid to a weak perturbation. For example [ 315,316], the meanmolecular field w α (r) acting on a segment of type α can be approximated by…”

Section: Self-assembled Membrane Modelsmentioning

confidence: 99%

Biological and synthetic membranes: What can be learned from a coarse-grained description?

2006

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We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ simple and soft effective potentials, coarse-grained models can provide rather direct insight into collective phenomena in membranes on large time and length scales. We present a summary of recent progress in this rapidly evolving field, and pay special attention to model development and computational techniques. Applications of coarse-grained models to changes of the membrane topology are illustrated with studies of membrane fusion utilizing simulations and self-consistent field theory.

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Section: Self-assembled Membrane Modelsmentioning

confidence: 99%

Biological and synthetic membranes: What can be learned from a coarse-grained description?

2006

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“…Other large-scale applications that have been analyzed include natural convection flows in 2D enclosures [Salinger et al, 2002a;Burroughs et al, 2004], flows in chemical reactors [Pawlowski et al, 2001], and density functional theory calculations of capillary condensation of confined fluids ] and polymer self-assembly [Frischknecht et al, 2002]. Current work includes the release of a completely new version of LOCA as part of a larger solver framework effort [Heroux et al, 2003], and the development and implementation of alternative algorithms for mitigating or removing the solves of the nearly singular systems in the current algorithms.…”

Section: Introductionmentioning

confidence: 99%

Bifurcation Tracking Algorithms and Software for Large Scale Applications

Salinger

Burroughs

Pawlowski

et al. 2005

Int. J. Bifurcation Chaos

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We present the set of bifurcation tracking algorithms which have been developed in the LOCA software library to work with large scale application codes that use fully coupled Newton's method with iterative linear solvers. Turning point (fold), pitchfork, and Hopf bifurcation tracking algorithms based on Newton's method have been implemented, with particular attention to the scalability to large problem sizes on parallel computers and to the ease of implementation with new application codes. The ease of implementation is accomplished by using block elimination algorithms to solve the Newton iterations of the augmented bifurcation tracking systems. The applicability of such algorithms for large applications is in doubt since the main computational kernel of these routines is the iterative linear solve of the same matrix that is being driven singular by the algorithm. To test the robustness and scalability of these algorithms, the LOCA library has been interfaced with the MPSalsa massively parallel finite element reacting flows code. A bifurcation analysis of an 1.6 Million unknown model of 3D Rayleigh-Bénard convection in a 5 × 5 × 1 box is successfully undertaken, showing that the algorithms can indeed scale to problems of this size while producing solutions of reasonable accuracy.

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“…The numerical methods behind our approach have been detailed elsewhere [19,21,22]. We use a simple collocation finite element strategy combined with specialized Schur-complement based parallel solver algorithms to solve the system of equations [22].…”

mentioning

confidence: 99%

Computational Investigations of Pore Forming Peptide Assemblies in Lipid Bilayers

Frink

Frischknecht

2006

Phys. Rev. Lett.

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This Letter presents the first application of a three-dimensional numerical molecular theory based modeling approach to study the structure and energetics of assemblies of peptides embedded in lipid bilayers. Coarse-grained models were used for both the peptides and lipids. Both barrel-stave and toroidal pore morphologies for the lipids near the peptide assemblies are found, but at different assembly sizes. The free energy of the assembly is found to have a global free energy minimum for a solution with a membrane-spanning toroidal pore. A pairwise approximation to this free energy is found to underpredict the free energy minimum associated with the membrane-spanning pores.

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Density functional theory for inhomogeneous polymer systems. I. Numerical methods

Cited by 47 publications

References 66 publications

Biological and synthetic membranes: What can be learned from a coarse-grained description?

Biological and synthetic membranes: What can be learned from a coarse-grained description?

Bifurcation Tracking Algorithms and Software for Large Scale Applications

Computational Investigations of Pore Forming Peptide Assemblies in Lipid Bilayers

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