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Journal ArticleDOI

Mineral and Protein-Bound Water and Latching Action Control Mechanical Behavior at Protein-Mineral Interfaces in Biological Nanocomposites

14 Sep 2008-Journal of Nanomaterials (Hindawi)-Vol. 2008, Iss: 2008, pp 1-8
TL;DR: The nacre structure consists of laminated interlocked mineral platelets separated by nanoscale organic layers and the role of close proximity of mineral to the proteins on mechanical behavior of the protein is investigated through steered molecular dynamics simulations.
Abstract: The nacre structure consists of laminated interlocked mineral platelets separated by nanoscale organic layers. Here, the role of close proximity of mineral to the proteins on mechanical behavior of the protein is investigated through steered molecular dynamics simulations. Our simulations indicate that energy required for unfolding protein in the proximity of mineral aragonite is several times higher than that for isolated protein in the absence of the mineral. Here, we present details of specific mechanisms which result in higher energy for protein unfolding in the proximity of mineral. At the early stage of pulling, peaks in the load-displacement (LD) plot at mineral proximity are quantitatively correlated to the interaction energy between atoms involved in the latching phenomenon of amino acid side chain to aragonite surface. Water plays an important role during mineral and protein interaction and water molecules closer to the mineral surface are highly oriented and remain rigidly attached as the protein strand is pulled. Also, the high magnitude of load for a given displacement originates from attractive interactions between the protein, protein-bound water, and mineral. This study provides an insight into mineral-protein interactions that are predominant in biological nanocomposites and also provides guidelines towards design of biomimetic nanocomposites.

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Citations
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Journal ArticleDOI
TL;DR: This study has used molecular dynamics and steered molecular dynamics to study directional dependence of deformation response of collagen with respect to the hydroxyapatite surface, and simulations indicate that the mechanics of collagen pulled in different directions with Respect to hydroxyAPatite is significantly different.

58 citations

Journal ArticleDOI
TL;DR: In this article, the authors evaluated the spectrum of a variety of aqueous solutions and found that water may be considered bound even though rapid rotations around the orientation of the electric dipole moment are definitely possible and also a fast exchange of water molecules between the hydration region and the bulk may take place.

41 citations

Journal ArticleDOI
TL;DR: In this article, the influence of the evolving cement paste and the polymer functional group on the interfacial strength at the micro- and molecular-length scales is discussed, and it is found that the free/adsorbed calcium form a metal-complex with the ester functional group of the polymer in addition to the physical interactions.
Abstract: Surface coatings have proved to be one of the most effective methods to protect the concrete structures in aggressive environments. However, coating the structures with polymer after 28 days of curing/hydration to get the best interfacial performance has little scientific backing. The measured surface free energy of the hydrating cement paste showed that the surface energy is high for a 2-day hydrated paste compared to cement paste cured for 7, 28 days. This opens up the possibility for exploration into coating an acrylic based polymer on a concrete surface before it reaches 28 days of hydration, which has been investigated in this study. The practical work of adhesion between the hydrating cement paste and polymer as measured from macro mechanical tests showed to have a dependency on the surface evolution of the cement paste. However, it was also observed that it depends equally on the polymer functional groups. Poly (methyl methacrylate) (PMMA), when coated on a 2-day hydrated cement paste, showed higher interfacial strength than when coated on later days (7, 14, 28 days). In the case of epoxy, irrespective of when the polymer was coated, it had the same interfacial strength. The influence of the evolving cement paste and the polymer functional group (PMMA in particular) on the interfacial strength at the micro- and molecular-length scales are discussed. It is found that the free/adsorbed calcium form a metal-complex with the ester functional group of the polymer in addition to the physical interactions, resulting in higher interfacial strength. The observations shed light on the importance of interfacial science and act as a guideline for the design of effective polymer-cement coatings.

34 citations

Journal ArticleDOI
TL;DR: In this article, the authors studied the swelling behavior of sodium (Na)-montmorillonite clays with increasing amounts of hydration using molecular dynamics and showed the important role of bound water and clay-Na interactions during swelling to stabilize clay structure during hydration.
Abstract: In this work, the swelling behavior of sodium (Na)-montmorillonite clay with increasing amounts of hydration is studied using molecular dynamics. The molecular models of the dry clay and the hydrated clays, consisting of 2, 4, 6, 8, and 10 monolayers of water in the interlayer, are used in this study. This work captures the evolution of interaction energies in the interlayer of Na-montmorillonite swelling clay with increasing hydration and provides insight into swelling mechanisms. This work shows the important role of bound water and clay-Na interactions during swelling to stabilize clay structure during hydration. Changes to water molecule conformations in the interlayer during swelling are also reported. The results and insight provided by this work will help in modeling and predicting exfoliation and resulting particle breakdown in swelling clays, in addition to expounding the key role of interlayer interactions on swelling in smectite clays.

32 citations

Journal ArticleDOI
01 Jul 2017-Fuel
TL;DR: In this article, the complex 3D structure of Green River Type I kerogen was developed from its seven components or fragments using Siskin's two-dimensional (2D) structure.

26 citations

References
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Journal ArticleDOI
TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.

46,130 citations


"Mineral and Protein-Bound Water and..." refers methods in this paper

  • ...Molecular dynamics software NAMD [31] is used for all simulations, and VMD [32] is used for visual analysis....

    [...]

  • ...From the known primary sequence of GS-domain random, structures were generated, minimized, and then solvated by “SOLVATE” module of VMD....

    [...]

Journal ArticleDOI
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
Abstract: CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.

14,725 citations


"Mineral and Protein-Bound Water and..." refers methods in this paper

  • ...The parameters for GS domain are obtained from standard CHARMm protein parameter file [13]....

    [...]

  • ...Molecular dynamics is a useful technique for studying the folding/unfolding behavior of proteins [12, 13]....

    [...]

Journal ArticleDOI
TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

14,558 citations


"Mineral and Protein-Bound Water and..." refers methods in this paper

  • ...Molecular dynamics software NAMD [31] is used for all simulations, and VMD [32] is used for visual analysis....

    [...]

  • ...Hardware support for NAMD at NDSU was provided by Dr. Gregory Wettstein....

    [...]

Journal ArticleDOI
TL;DR: In this article, a replica-exchange method was proposed to overcome the multiple-minima problem by exchanging non-interacting replicas of the system at several temperatures, which allows the calculation of any thermodynamic quantity as a function of temperature in that range.

4,135 citations


"Mineral and Protein-Bound Water and..." refers methods in this paper

  • ...Replica-exchange molecular dynamics method has been successfully used in literature to study the folding unfolding behavior of proteins and peptides [25]....

    [...]