Strategies for multiscale modeling and simulation of organic materials: polymers and biopolymers (original) (raw)
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This thesis is concerned with new paradigms and methods far computer simulation of polymers in order to study the structure and dynamics of these materials beyond the limitations in the length and time scales of the existing techniques. Atomistic simulation, although of considerable technological
Molecular dynamics (MD) is a powerful technique for computing the equilibrium and dynamical properties of classical many-body systems. Over the last fifteen years, due to the rapid development of computers, polymeric systems have been the subject of intense study with MD simulations [1]. At the heart of this technique is the solution of the classical equations of motion, which are integrated numerically to give information for the positions and velocities of atoms in the system [2], [3], [4]
CHAPTER XX MOLECULAR DYNAMICS SIMULATIONS OF POLYMERS
2000
Molecular dynamics (MD) is a powerful technique for computing the equilibrium and dynamical properties of classical many-body systems. Over the last fifteen years, due to the rapid development of computers, polymeric systems have been the subject of intense study with MD simulations [1]. At the heart of this technique is the solution of the classical equations of motion, which are integrated numerically to give information for the positions and velocities of atoms in the system [2], [3], [4]
Molecular Dynamics Simulations of Polymers
Simulation Methods for Polymers, 2004
Molecular dynamics (MD) is a powerful technique for computing the equilibrium and dynamical properties of classical many-body systems. Over the last fifteen years, due to the rapid development of computers, polymeric systems have been the subject of intense study with MD simulations [1]. At the heart of this technique is the solution of the classical equations of motion, which are integrated numerically to give information for the positions and velocities of atoms in the system [2], [3], [4]
Dynamics of Small Molecules in Bulk Polymers
Atomistic Modeling of Physical Properties, 1994
The mechanisms operative in diffusion and solubility of light gases in amorphous, dense polymer systems are discussed. Two types of methods used, Molecular Dymanics simulation and an approach based on Transition State Theory, are described. The methods prove to be complementary and to yield identical results in the areas where both can be independently applied.
Multiscale modeling for polymer systems of industrial interest
Progress in Organic Coatings, 2007
Atomistic-based simulations such as molecular mechanics (MM), molecular dynamics (MD), and Monte Carlo-based methods (MC) have come into wide use for materials design. Using these atomistic simulation tools, one can analyze molecular structure on the scale of 0.1-10 nm. Although molecular structures can be studied easily and extensively by these atom-based simulations, it is less realistic to predict structures defined on the scale of 100-1000 nm with these methods. For the morphology on these scales, mesoscopic modeling techniques such as the dynamic mean field density functional theory (Mesodyn) and dissipative particle dynamics (DPD) are now available as effective simulation tools. Furthermore, it is possible to transfer the simulated mesoscopic structure to finite element modeling tools (FEM) for calculating macroscopic properties for a given system of interest. In this paper, we present a hierarchical procedure for bridging the gap between atomistic and macroscopic modeling passing through mesoscopic simulations. In particular, we will discuss the concept of multiscale modeling, and present examples of applications of multiscale procedures to polymer-organoclay nanocomposites. Examples of application of multiscale modeling to immiscible polymer blends and polymer-carbon nanotubes systems will also be presented.
Size and shape matter! A multiscale molecular simulation approach to polymer nanocomposites
Journal of Materials Chemistry, 2012
The proposed computational procedure of the multiscale simulation and modeling is based on the following ansatz: 1) fully atomistic molecular dynamics simulations are perform to retrieve fundamental structural and energetical information at the molecular level; 2) the data gathered at point 1) are mapped into the corresponding structural and energetical information necessary to run coarse-grained simulations at a mesoscopic level; 3) the main output of point 2), i.e., the system mesoscopic morphologies and density distributions finally constitute the input for finite element calculations and macroscopic properties predictions. The core step in the entire computational recipe is undoubtedly constituted by point 2), or the mesoscale level simulations. In mesoscale modeling, the familiar atomistic description of the molecules is coarse-grained, leading to beads of material (representing the collective degree of freedom of many atoms). These beads interact through pair-potentials which capture the underlying interactions of the constituent atoms. The primary output of mesoscale modeling are phase morphologies with size up to the micron level. These morphologies are of interest per se, although little prediction of the material properties is available with the mesoscale tools. Finite element modeling then comes into play, and the material properties of interest can be calculated accordingly by mapping the material structures formed at the nanometer scale onto the finite element grid and coupling this information with the properties of the pure components that comprise the complex system. Using standard solvers the finite element code can then calculate the properties of the realistic structured material. Atomistic molecular dynamics (MD) simulations As mentioned above, atomistic MD simulations constitute the first MsM step, necessary to gather basic structural and energetical information of each PNC system at the molecular level. In particular, the interaction energies among all system components are of paramount importance, as they will, after proper remapping, constitute the major input parameter for performing mesoscale (MS) simulations. Hence, the choice of a reliable force field for the description of inter-and intra-molecular interactions in atomistic MD simulations is
Molecular and Mesoscale Simulation Methods for Polymer Materials
Annual Review of Materials Research, 2002
▪ Polymers offer a wide spectrum of possibilities for materials applications, in part because of the chemical complexity and variability of the constituent molecules, and in part because they can be blended together with other organic as well as inorganic components. The majority of applications of polymeric materials is based on their excellent mechanical properties, which arise from the long-chain nature of the constituents. Microscopically, this means that polymeric materials are able to respond to external forces in a broad frequency range, i.e., with a broad range of relaxation processes. Computer simulation methods are ideally suited to help to understand these processes and the structural properties that lead to them and to further our ability to predict materials properties and behavior. However, the broad range of timescales and underlying structure prohibits any one single simulation method from capturing all of these processes.This manuscript provides an overview of som...
Multi-Scale Molecular Dynamics Simulations of a Membrane Protein Stabilizing Polymer
Biophysical Journal, 2011
A positional interpolation/extrapolation method for the mapping of coarse-grained (CG) to atomistic (AT) resolution is presented and tested for single-component micelles formed by lysophospholipids of different chain length. The target CG nanoaggregates were self-assembled from random mixtures of surfactants in explicit MARTINI water and equilibrated by molecular dynamics simulations, at the microsecond time scale. The ambiguity inherent in the definition of the CG particles was explored by mapping the same CG structures to AT resolution surfactants of different size. After the conversion, the obtained AT micelles were simulated for 250 ns and the resulting trajectories were analyzed in detail. The mean lifetime of the surfactant-solvent interactions as well as the lateral diffusion coefficients of the surfactant molecules within the micellar aggregates were obtained for the first time. The results suggest that the individual molecules within the micelle behave like lipids in a fluid membrane. The employed mapping back method is efficient and versatile, as it can be applied to diverse combinations of force fields and systems with a minimum of code development. In a general context, this work illustrates the power of multiscale molecular dynamics simulations for the generation and subsequent examination of self-assembled structures, including the fine characterization of structural and dynamic properties of the resulting aggregate.