Modeling the response of pyrophyllite interlayer to applied stress using steered molecular dynamics
TL;DR: In this paper, an atomic model of pyrophyllite interlayer was constructed using steered molecular dynamics simulations and external forces were applied to individual atoms to study the response of the model to applied forces.
Abstract: Pyrophyllite is the precursor to other smectite-group minerals which exhibit swelling. The mineral structure of pyrophyllite can lead to other minerals in the smectite group, including montmorillonite, through appropriate isomorphous substitutions. In this work, an atomic model of the pyrophyllite interlayer was constructed. The response of the interlayer was evaluated using steered molecular dynamics simulations. In steered molecular dynamics, external forces were applied to individual atoms to study the response of the model to applied forces. In this work, forces are applied to the surface clay atoms to evaluate the displacement vs. applied stress in the interlayer between clay layers. This paper describes the construction of the model, the simulation procedure, and the results of the simulations which show that under the applied loading, deformation occurs mainly in the interlayer. The clay layers show relatively little deformation. The results show that the relationship between applied stress and displacement of the interlayer is linear. The stress-deformation relationship for the interlayer is presented.
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TL;DR: The design of a novel clay-chitosan-hydroxyapatite composite with improved mechanical properties that has potential applications in bone tissue engineering is represented.
Abstract: Recently, biopolymer-based nanocomposites have been replacing synthetic polymer composites for various biomedical applications. This is often because of the biocompatible and biodegradable behavior of natural polymers. Several studies have been reported pertaining to the synthesis and characterization of chitosan(chi)/montmorillonite(MMT) and chitosan (chi)/hydroxyapatite (HAP) for tissue engineering applications. In the present work, a biopolymer-based novel nanocomposite chitosan/montmorillonite (MMT)/hydroxyapatite (HAP) was developed for biomedical applications. The composite was prepared from chitosan, unmodified MMT and HAP precipitate in aqueous media. The properties of the composites were investigated using x-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), atomic force microscopy (AFM) and thermogravimetric analysis (TGA). Nanomechanical properties were measured using nanoindentation. Cell culture experiments were also conducted in order to ascertain the biocompatibility of the composite. The XRD results indicate that an intercalated structure was formed with an increase in d-spacing of montmorillonite. FTIR studies provide the evidence of molecular interaction among the three different constituents of the composite. AFM images show well-distributed nanoparticles in the chitosan matrix. The composites also exhibit a significant enhancement in nanomechanical property as compared to pure chitosan as well as the chi/HAP and chi/MMT composites. The TGA results indicate that an intercalated nanocomposite was formed with improved thermal properties even compared to chi/MMT composites. The results of cell culture experiments show that the composite is biocompatible and has a better cell proliferation rate compared to chi/HAP composites. This work represents the design of a novel clay-chitosan-hydroxyapatite composite with improved mechanical properties that has potential applications in bone tissue engineering.
220 citations
TL;DR: In this article, the authors used molecular dynamics simulations to evaluate the nature of these interfaces in polyacrylic acid-hydroxyapatite composites and obtained the parameters for monoclinic hydroxyapatites in CVFF from the known potential energy function of apatites.
168 citations
TL;DR: This review addresses the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems and examines the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches.
Abstract: Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.
161 citations
TL;DR: In this article, a combination of experimental (photoacoustic FTIR, XRD) and computational (molecular dynamics (MD)) techniques was used to evaluate molecular interactions in organically modified clay and polymer clay nanocomposite.
151 citations
TL;DR: In this paper, a closed loop approach of microporomechanics modeling, calibration and validation of elastic properties at multiple length scales of shale is presented, showing that the nanogranular nature of this highly heterogeneous material translates into a unique poroelastic signature.
Abstract: Natural composite materials are highly heterogeneous porous materials, with porosities that manifest themselves at scales much below the macroscale of engineering applications. A typical example is shale, the transverse isotropic sealing formation of most hydrocarbon bearing reservoirs. By means of a closed loop approach of microporomechanics modeling, calibration and validation of elastic properties at multiple length scales of shale, we show that the nanogranular nature of this highly heterogeneous material translates into a unique poroelastic signature. The self-consistent scaling of the porous clay stiffness with the clay packing density minimizes the anisotropy of the Biot pore pressure coefficients; whereas the intrinsic anisotropy of the elementary particle translates into a pronounced anisotropy of the Skempton coefficients. This new microporoelasticity model depends only on two shale-specific material parameters which neatly summarize clay mineralogy and bulk density, and which makes the model most appealing for quantitative geomechanics, geophysics and exploitation engineering applications.
132 citations
Cites background from "Modeling the response of pyrophylli..."
...While several attempts to address this research need have been reported [48, 53 , 57, 62, 78, 81], the large range of estimated solid clay stiffness values emphasize the difficulty to assess the intrinsic elasticity of single clay crystals....
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References
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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
"Modeling the response of pyrophylli..." refers methods in this paper
...4 (Kale et al., 1999) and VMD (Humphrey et al., 1996), for interactive studies, were used....
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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
"Modeling the response of pyrophylli..." refers background or methods in this paper
...The energy in CHARMm (Brooks et al., 1983) force field is shown in equation 2, Epotential X bond k B rÿ r0 2 X angle k A yÿ y0 2 X dihedral V D 1 cos njÿ d X vanderWaals X i 6 j 4eij sij rij 8 >: 9 >; 12 ÿ sij rij 8 >: 9 >; 6 " # X electrostatic X i 6 j qiqj rij 2 where k B , r0, k A , y0, V D and…...
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...The energy in CHARMm (Brooks et al., 1983) force field is shown in equation 2,...
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Book•
17 Mar 1994
TL;DR: In this article, an introduction to modern soil chemistry describes chemical processes in soils in terms of established principles of inorganic, organic, and physical chemistry, providing an understanding of the structure of the solid mineral and organic materials from which soils are formed.
Abstract: This introduction to modern soil chemistry describes chemical processes in soils in terms of established principles of inorganic, organic, and physical chemistry. The text provides an understanding of the structure of the solid mineral and organic materials from which soils are formed, and explains such important processes as cation exchange, chemisorption and physical absorption of organic and inorganic ions and molecules, soil acidification and weathering, oxidation-reduction reactions, and development of soil alkalinity and swelling properties. Environmental rather than agricultural topics are emphasized, with individual chapters on such pollutants as heavy metals, trace elements, and inorganic chemicals.
6,735 citations
"Modeling the response of pyrophylli..." refers methods in this paper
...Likewise, another commonly used theory, the osmotic swelling model, fails to explain clay swelling quantitatively (McBride, 1994)....
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TL;DR: The NAMD2 program is presented, which uses spatial decomposition combined with force decomposition to enhance scalability and modularly organized, and implemented using Charm++, a parallel C++ dialect, so as to enhance its modifiability.
2,389 citations
"Modeling the response of pyrophylli..." refers background or methods in this paper
...4 (Kale et al., 1999), which was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at UrbanaChampaign....
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...4 (Kale et al., 1999) and VMD (Humphrey et al., 1996), for interactive studies, were used....
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TL;DR: It is shown that the techniques introduced here for exploring the quantum energy surface can be used to determine the extent of transferability and range of validity of the force field.
Abstract: A new method for deriving force fields for molecular simulations has been developed. It is based on the derivation and parameterization of analytic representations of the ab initio potential energy surfaces. The general method is presented here and used to derive a quantum mechanical force field (QMFF) for alkanes. It is based on sampling the energy surfaces of 16 representative alkane species. For hydrocarbons, this force field contains 66 force constants and reference values. These were fit to 128,376 quantum mechanical energies and energy derivatives describing the energy surface. The detailed form of the analytic force field expression and the values of all resulting parameters are given. A series of computations is then performed to test the ability of this force field to reproduce the features of the ab initio energy surface in terms of energies as well as the first and second derivatives of the energies with respect to molecular deformations. The fit is shown to be good, with rms energy deviations of less than 7% for all molecules. Also, although only two atom types are employed, the force field accounts for the properties of both highly strained species, such as cyclopropane and methylcyclopropanes, as well as unstrained systems. The information contained in the quantum energy surface indicates that it is significantly anharmonic and that important intramolecular coupling interactions exist between internals. The representation of the nature of these interactions, not present in diagonal, quadratic force fields (Class I force fields), is shown to be important in accounting accurately for molecular energy surfaces. The Class I1 force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each
730 citations
"Modeling the response of pyrophylli..." refers background or methods in this paper
...(1997) for the consistent force field, CFF (Maple et al., 1994)....
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...Parameters have been developed by Teppen et al. (1997) for the consistent force field, CFF (Maple et al., 1994)....
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